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Ghanim GE, Sekne Z, Balch S, van Roon AMM, Nguyen THD. 2.7 Å cryo-EM structure of human telomerase H/ACA ribonucleoprotein. Nat Commun 2024; 15:746. [PMID: 38272871 PMCID: PMC10811338 DOI: 10.1038/s41467-024-45002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
Telomerase is a ribonucleoprotein (RNP) enzyme that extends telomeric repeats at eukaryotic chromosome ends to counterbalance telomere loss caused by incomplete genome replication. Human telomerase is comprised of two distinct functional lobes tethered by telomerase RNA (hTR): a catalytic core, responsible for DNA extension; and a Hinge and ACA (H/ACA) box RNP, responsible for telomerase biogenesis. H/ACA RNPs also have a general role in pseudouridylation of spliceosomal and ribosomal RNAs, which is critical for the biogenesis of the spliceosome and ribosome. Much of our structural understanding of eukaryotic H/ACA RNPs comes from structures of the human telomerase H/ACA RNP. Here we report a 2.7 Å cryo-electron microscopy structure of the telomerase H/ACA RNP. The significant improvement in resolution over previous 3.3 Å to 8.2 Å structures allows us to uncover new molecular interactions within the H/ACA RNP. Many disease mutations are mapped to these interaction sites. The structure also reveals unprecedented insights into a region critical for pseudouridylation in canonical H/ACA RNPs. Together, our work advances understanding of telomerase-related disease mutations and the mechanism of pseudouridylation by eukaryotic H/ACA RNPs.
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Affiliation(s)
| | - Zala Sekne
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
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2
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Hu H, van Roon AMM, Ghanim GE, Ahsan B, Oluwole AO, Peak-Chew SY, Robinson CV, Nguyen THD. Structural basis of telomeric nucleosome recognition by shelterin factor TRF1. Sci Adv 2023; 9:eadi4148. [PMID: 37624885 PMCID: PMC10456876 DOI: 10.1126/sciadv.adi4148] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023]
Abstract
Shelterin and nucleosomes are the key players that organize mammalian chromosome ends into the protective telomere caps. However, how they interact with each other at telomeres remains unknown. We report cryo-electron microscopy structures of a human telomeric nucleosome both unbound and bound to the shelterin factor TRF1. Our structures reveal that TRF1 binds unwrapped nucleosomal DNA ends by engaging both the nucleosomal DNA and the histone octamer. Unexpectedly, TRF1 binding shifts the register of the nucleosomal DNA by 1 bp. We discovered that phosphorylation of the TRF1 C terminus and a noncanomical DNA binding surface on TRF1 are critical for its association with telomeric nucleosomes. These insights into shelterin-chromatin interactions have crucial implications for understanding telomeric chromatin organization and other roles of shelterin at telomeres including replication and transcription.
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Affiliation(s)
- Hongmiao Hu
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | | | | | - Bilal Ahsan
- MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Abraham O. Oluwole
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU UK
| | | | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford, OX1 3QZ UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, OX1 3QU UK
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Abstract
Telomerase maintains genome stability by extending the 3' telomeric repeats at eukaryotic chromosome ends, thereby counterbalancing progressive loss caused by incomplete genome replication. In mammals, telomerase recruitment to telomeres is mediated by TPP1, which assembles as a heterodimer with POT1. We report structures of DNA-bound telomerase in complex with TPP1 and with TPP1-POT1 at 3.2- and 3.9-angstrom resolution, respectively. Our structures define interactions between telomerase and TPP1-POT1 that are crucial for telomerase recruitment to telomeres. The presence of TPP1-POT1 stabilizes the DNA, revealing an unexpected path by which DNA exits the telomerase active site and a DNA anchor site on telomerase that is important for telomerase processivity. Our findings rationalize extensive prior genetic and biochemical findings and provide a framework for future mechanistic work on telomerase regulation.
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Affiliation(s)
- Zala Sekne
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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Leung AKW, Kondo Y, Krummel DAP, Li J, Price SR, van Roon AMM. Engineering Crystal Packing in RNA-Protein Complexes II: A Historical Perspective from the Structural Studies of the Spliceosome. Crystals (Basel) 2021; 11:948. [PMID: 35154816 PMCID: PMC7612351 DOI: 10.3390/cryst11080948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cryo-electron microscopy has greatly advanced our understanding of how the spliceosome cycles through different conformational states to conduct the chemical reactions that remove introns from pre-mRNA transcripts. The Cryo-EM structures were built upon decades of crystallographic studies of various spliceosomal RNA-protein complexes. In this review we give an overview of the crystal structures solved in the Nagai group, utilizing many of the strategies to design crystal packing as described in the accompanying paper.
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Affiliation(s)
- Adelaine Kwun-Wai Leung
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Yasushi Kondo
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Daniel A. Pomeranz Krummel
- Department of Neurology and Rehabilitation Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jade Li
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Stephen R. Price
- Research Department of Cell and Developmental Biology, UCL Division of Biosciences, London WC1E 6DE, UK
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Ghanim GE, Fountain AJ, van Roon AMM, Rangan R, Das R, Collins K, Nguyen THD. Structure of human telomerase holoenzyme with bound telomeric DNA. Nature 2021; 593:449-453. [PMID: 33883742 DOI: 10.1038/s41586-021-03415-4] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/03/2021] [Indexed: 12/15/2022]
Abstract
Telomerase adds telomeric repeats at chromosome ends to compensate for the telomere loss that is caused by incomplete genome end replication1. In humans, telomerase is upregulated during embryogenesis and in cancers, and mutations that compromise the function of telomerase result in disease2. A previous structure of human telomerase at a resolution of 8 Å revealed a vertebrate-specific composition and architecture3, comprising a catalytic core that is flexibly tethered to an H and ACA (hereafter, H/ACA) box ribonucleoprotein (RNP) lobe by telomerase RNA. High-resolution structural information is necessary to develop treatments that can effectively modulate telomerase activity as a therapeutic approach against cancers and disease. Here we used cryo-electron microscopy to determine the structure of human telomerase holoenzyme bound to telomeric DNA at sub-4 Å resolution, which reveals crucial DNA- and RNA-binding interfaces in the active site of telomerase as well as the locations of mutations that alter telomerase activity. We identified a histone H2A-H2B dimer within the holoenzyme that was bound to an essential telomerase RNA motif, which suggests a role for histones in the folding and function of telomerase RNA. Furthermore, this structure of a eukaryotic H/ACA RNP reveals the molecular recognition of conserved RNA and protein motifs, as well as interactions that are crucial for understanding the molecular pathology of many mutations that cause disease. Our findings provide the structural details of the assembly and active site of human telomerase, which paves the way for the development of therapeutic agents that target this enzyme.
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Affiliation(s)
- George E Ghanim
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Adam J Fountain
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | | | - Ramya Rangan
- Biophysics Program, Stanford University, Stanford, CA, USA
| | - Rhiju Das
- Biophysics Program, Stanford University, Stanford, CA, USA.,Department of Biochemistry, Stanford University, Stanford, CA, USA.,Department of Physics, Stanford University, Stanford, CA, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.,California Institute for Quantitative Biology (QB3), University of California, Berkeley, CA, USA
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van Roon AMM, Oubridge C, Obayashi E, Sposito B, Newman AJ, Séraphin B, Nagai K. Crystal structure of U2 snRNP SF3b components: Hsh49p in complex with Cus1p-binding domain. RNA 2017; 23:968-981. [PMID: 28348170 PMCID: PMC5435868 DOI: 10.1261/rna.059378.116] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 03/17/2017] [Indexed: 05/02/2023]
Abstract
Spliceosomal proteins Hsh49p and Cus1p are components of SF3b, which together with SF3a, Msl1p/Lea1p, Sm proteins, and U2 snRNA, form U2 snRNP, which plays a crucial role in pre-mRNA splicing. Hsh49p, comprising two RRMs, forms a heterodimer with Cus1p. We determined the crystal structures of Saccharomyces cerevisiae full-length Hsh49p as well as its RRM1 in complex with a minimal binding region of Cus1p (residues 290-368). The structures show that the Cus1 fragment binds to the α-helical surface of Hsh49p RRM1, opposite the four-stranded β-sheet, leaving the canonical RNA-binding surface available to bind RNA. Hsh49p binds the 5' end region of U2 snRNA via RRM1. Its affinity is increased in complex with Cus1(290-368)p, partly because an extended RNA-binding surface forms across the protein-protein interface. The Hsh49p RRM1-Cus1(290-368)p structure fits well into cryo-EM density of the Bact spliceosome, corroborating the biological relevance of our crystal structure.
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Affiliation(s)
| | - Chris Oubridge
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Eiji Obayashi
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Benedetta Sposito
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Andrew J Newman
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Bertrand Séraphin
- Equipe Labellisée La Ligue, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Centre National de la Recherche Scientifique (CNRS) UMR 7104/Institut National de la Santé et de la Recherche Médicale (INSERM), U964/Université de Strasbourg, 67404 Illkirch, France
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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van Roon AMM, Yang JC, Mathieu D, Bermel W, Nagai K, Neuhaus D. ¹¹³Cd NMR experiments reveal an unusual metal cluster in the solution structure of the yeast splicing protein Bud31p. Angew Chem Int Ed Engl 2015; 54:4861-4. [PMID: 25703931 PMCID: PMC4471582 DOI: 10.1002/anie.201412210] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Indexed: 11/09/2022]
Abstract
Establishing the binding topology of structural zinc ions in proteins is an essential part of their structure determination by NMR spectroscopy. Using (113)Cd NMR experiments with (113)Cd-substituted samples is a useful approach but has previously been limited mainly to very small protein domains. Here we used (113)Cd NMR spectroscopy during structure determination of Bud31p, a 157-residue yeast protein containing an unusual Zn3Cys9 cluster, demonstrating that recent hardware developments make this approach feasible for significantly larger systems.
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8
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van Roon AMM, Yang JC, Mathieu D, Bermel W, Nagai K, Neuhaus D. 113Cd NMR Experiments Reveal an Unusual Metal Cluster in the Solution Structure of the Yeast Splicing Protein Bud31p. ACTA ACUST UNITED AC 2015; 127:4943-4946. [PMID: 27478262 PMCID: PMC4954022 DOI: 10.1002/ange.201412210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Indexed: 01/29/2023]
Abstract
Establishing the binding topology of structural zinc ions in proteins is an essential part of their structure determination by NMR spectroscopy. Using 113Cd NMR experiments with 113Cd‐substituted samples is a useful approach but has previously been limited mainly to very small protein domains. Here we used 113Cd NMR spectroscopy during structure determination of Bud31p, a 157‐residue yeast protein containing an unusual Zn3Cys9 cluster, demonstrating that recent hardware developments make this approach feasible for significantly larger systems.
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Affiliation(s)
| | - Ji-Chun Yang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH (UK)
| | - Daniel Mathieu
- Bruker BioSpin GmbH, Silberstreifen, 76287 Rheinstetten (Germany)
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen, 76287 Rheinstetten (Germany)
| | - Kiyoshi Nagai
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH (UK)
| | - David Neuhaus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH (UK)
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9
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Kondo Y, Oubridge C, van Roon AMM, Nagai K. Crystal structure of human U1 snRNP, a small nuclear ribonucleoprotein particle, reveals the mechanism of 5' splice site recognition. eLife 2015; 4. [PMID: 25555158 PMCID: PMC4383343 DOI: 10.7554/elife.04986] [Citation(s) in RCA: 171] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/06/2014] [Indexed: 12/12/2022] Open
Abstract
U1 snRNP binds to the 5′ exon-intron junction of pre-mRNA and thus plays a
crucial role at an early stage of pre-mRNA splicing. We present two crystal
structures of engineered U1 sub-structures, which together reveal at atomic
resolution an almost complete network of protein–protein and RNA-protein
interactions within U1 snRNP, and show how the 5′ splice site of pre-mRNA is
recognised by U1 snRNP. The zinc-finger of U1-C interacts with the duplex between
pre-mRNA and the 5′-end of U1 snRNA. The binding of the RNA duplex is
stabilized by hydrogen bonds and electrostatic interactions between U1-C and the RNA
backbone around the splice junction but U1-C makes no base-specific contacts with
pre-mRNA. The structure, together with RNA binding assays, shows that the selection
of 5′-splice site nucleotides by U1 snRNP is achieved predominantly through
basepairing with U1 snRNA whilst U1-C fine-tunes relative affinities of mismatched
5′-splice sites. DOI:http://dx.doi.org/10.7554/eLife.04986.001 Genes are made up of long stretches of DNA. The regions of a gene that code for
proteins (known as exons) are interrupted by stretches of non-coding DNA called
introns. To produce proteins from a gene, the DNA is ‘transcribed’ to
form pre-mRNA molecules, from which the introns must be removed in a process called
splicing. The remaining exons are then joined together to form a mature mRNA molecule
that contains the instructions to build a protein. Errors in the splicing process can
lead to numerous diseases, such as cancer. A molecular machine known as a spliceosome is responsible for splicing the pre-mRNA
molecules. This consists of five different complexes called small nuclear
ribonucleoprotein particles (snRNPs), which are in turn made up from numerous
proteins and RNA molecules. The spliceosome assembles anew every time it splices, and
an early step in this assembly process involves the interaction of an snRNP called U1
with the start of an intron in the pre-mRNA. This interaction then stimulates the
assembly of the rest of the spliceosome. In 2009, researchers reported the structure
of the U1 snRNP, but the structure did not contain enough detail to reveal how the
snRNP recognizes the start of an intron. Kondo, Oubridge et al., including some of the researchers involved in the 2009 work,
now present the crystal structure of the human version of the U1 snRNP in more
detail. High-quality crystal structures of the complete U1 snRNP molecule could not
be obtained because the arrangement of the RNA molecules in the snRNP prevented a
regular crystal from forming. Kondo, Oubridge et al. instead engineered two
subcomponents of U1 snRNP that each crystallized well, and determined their
structures. This revealed that the interactions between the various parts of the U1
snRNP form a complex network. A protein present in the U1 snRNP, known as U1-C, had previously been reported to be
able to recognize introns on its own—without requiring the complete U1 snRNP.
Kondo, Oubridge et al. reveal that this is not the case and that U1-C does not read
the intron RNA sequence directly. Instead, U1 snRNP is able to find the start of the
intron because the U1 RNA can stably bind to this site. The U1-C protein can however
adjust the strength of this binding to ensure that the spliceosome can operate with a
variety of intron start sequences (or signals). DOI:http://dx.doi.org/10.7554/eLife.04986.002
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Affiliation(s)
- Yasushi Kondo
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Chris Oubridge
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Anne-Marie M van Roon
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - Kiyoshi Nagai
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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de Geus DC, van Roon AMM, Thomassen EAJ, Hokke CH, Deelder AM, Abrahams JP. Characterization of a diagnostic Fab fragment binding trimeric Lewis X. Proteins 2008; 76:439-47. [DOI: 10.1002/prot.22356] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Worrall JAR, van Roon AMM, Ubbink M, Canters GW. The effect of replacing the axial methionine ligand with a lysine residue in cytochrome c-550 from Paracoccus versutus assessed by X-ray crystallography and unfolding. FEBS J 2005; 272:2441-55. [PMID: 15885094 DOI: 10.1111/j.1742-4658.2005.04664.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The structure of cytochrome c-550 from the nonphotosynthetic bacteria Paraccocus versutus has been solved by X-ray crystallography to 1.90 A resolution, and reveals a high structural homology to other bacterial cytochromes c(2). The effect of replacing the axial heme-iron methionine ligand with a lysine residue on protein structure and unfolding has been assessed using the M100K variant. From X-ray structures at 1.95 and 1.55 A resolution it became clear that the amino group of the lysine side chain coordinates to the heme-iron. Structural differences compared to the wild-type protein are confined to the lysine ligand loop connecting helices four and five. In the heme cavity an additional water molecule is found which participates in an H-bonding interaction with the lysine ligand. Under cryo-conditions extra electron density in the lysine ligand loop is revealed, leading to residues K97 to T101 being modeled with a double main-chain conformation. Upon unfolding, dissociation of the lysine ligand from the heme-iron is shown to be pH dependent, with NMR data consistent with the occurrence of a ligand exchange mechanism similar to that seen for the wild-type protein.
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Affiliation(s)
- Jonathan A R Worrall
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, Leiden, the Netherlands
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van Roon AMM, Aguilera B, Cuenca F, van Remoortere A, van der Marel GA, Deelder AM, Overkleeft HS, Hokke CH. Synthesis and antibody-binding studies of a series of parasite fuco-oligosaccharides. Bioorg Med Chem 2005; 13:3553-64. [PMID: 15848768 DOI: 10.1016/j.bmc.2005.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2004] [Accepted: 02/08/2005] [Indexed: 10/25/2022]
Abstract
Complex multifucosylated oligosaccharides are structural elements of glycoprotein and glycolipid subsets of larval, egg, and adult stages of Schistosoma, the parasitic worms that cause schistosomiasis, a serious disease affecting more than 200 million people in the tropics. The fucosylated structures are thought to play an important role in the immunology of schistosomiasis. Defined schistosomal oligosaccharides that enable immunological studies are difficult to obtain from natural sources. Therefore, we have chemically synthesized spacer-linked GlcNAc, Fucalpha1-3GlcNAc, Fucalpha1-2Fucalpha1-3GlcNAc, and Fucalpha1-2Fucalpha1-2Fucalpha1-3GlcNAc. This series of linear oligosaccharides was used to screen a library of anti-schistosome monoclonal antibodies by surface plasmon resonance spectroscopy. Interestingly, the reactive antibodies could be grouped according to their specificity for the different oligosaccharides tested, showing that these oligosaccharides form different immunological entities based on the number and linkage of the fucose residues. Subsequently, the thus defined monoclonal antibodies were used to visualize the expression of the corresponding oligosaccharide epitopes by adult Schistosoma mansoni worms.
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Affiliation(s)
- Anne-Marie M van Roon
- Department of Parasitology, Center of Infectious Diseases, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
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van Roon AMM, Bink HHJ, Plaisier JR, Pleij CWA, Abrahams JP, Pannu NS. Crystal Structure of an Empty Capsid of Turnip Yellow Mosaic Virus. J Mol Biol 2004; 341:1205-14. [PMID: 15321716 DOI: 10.1016/j.jmb.2004.06.085] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2004] [Revised: 06/24/2004] [Accepted: 06/30/2004] [Indexed: 11/26/2022]
Abstract
Empty capsids (artificial top component) of turnip yellow mosaic virus were co-crystallized with an encapsidation initiator RNA hairpin. No clear density was observed for the RNA, but there were clear differences in the conformation of a loop of the coat protein at the opening of the pentameric capsomer (formed by five A-subunits) protruding from the capsid, compared to the corresponding loop in the intact virus. Further differences were found at the N terminus of the A-subunit. These differences have implications for the mechanism of decapsidation of the virus, required for infection.
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Affiliation(s)
- Anne-Marie M van Roon
- Biophysical Structural Chemistry, Leiden Institute of Chemistry, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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15
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van Roon AMM, Pannu NS, de Vrind JPM, van der Marel GA, van Boom JH, Hokke CH, Deelder AM, Abrahams JP. Structure of an Anti-Lewis X Fab Fragment in Complex with Its Lewis X Antigen. Structure 2004; 12:1227-36. [PMID: 15242599 DOI: 10.1016/j.str.2004.05.008] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2004] [Revised: 04/28/2004] [Accepted: 05/02/2004] [Indexed: 11/25/2022]
Abstract
The Lewis X trisaccharide is pivotal in mediating specific cell-cell interactions. Monoclonal antibody 291-2G3-A, which was generated from mice infected with schistosomes, has been shown to recognize the Lewis X trisaccharide. Here we describe the structure of the Fab fragment of 291-2G3-A, with Lewis X, to 1.8 A resolution. The crystallographic analysis revealed that the antigen binding site is a rather shallow binding pocket, and residues from all six complementary determining regions of the antibody contact all sugar residues. The high specificity of the binding pocket does not result in high affinity; the K(D) determined by isothermal calorimetry is 11 microM. However, this affinity is in the same range as for other sugar-antibody complexes. The detailed understanding of the antibody-Lewis X interaction revealed by the crystal structure may be helpful in the design of better diagnostic tools for schistosomiasis and for studying Lewis X-mediated cell-cell interactions by antibody interference.
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Affiliation(s)
- Anne-Marie M van Roon
- Department of Biophysical Structural Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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van Roon AMM, Pannu NS, Hokke CH, Deelder AM, Abrahams JP. Crystallization and preliminary X-ray analysis of an anti-LewisX Fab fragment with and without its LewisX antigen. Acta Crystallogr D Biol Crystallogr 2003; 59:1306-9. [PMID: 12832795 DOI: 10.1107/s0907444903010096] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2003] [Accepted: 05/07/2003] [Indexed: 11/10/2022]
Abstract
LewisX-containing glycoconjugates are abundantly expressed by schistosomes and are assumed to be of prime importance for the survival of the parasite within the human host. Monoclonal antibody 291-2G3-A, which was generated from mice infected with schistosomes, was found to interact with monomers, dimers and trimers of the LewisX trisaccharide. The Fab fragment of monoclonal antibody 291-2G3-A has been crystallized and soaked with its LewisX antigen. X-ray data sets were recorded for the different Fab crystals with and without LewisX. Crystals grown from 25% polyethylene glycol 3350, 0.17 M ammonium sulfate and 15% glycerol belong to the triclinic space group P1, with unit-cell parameters a = 67.4, b = 71.6, c = 104.8 A, alpha = 86.5, beta = 71.3, gamma = 83.3 degrees for the native crystals and with slightly different unit-cell parameters a = 67.3, b = 72.4, c = 104.8 A, alpha = 85.8, beta = 71.3, gamma = 83.3 degrees for the crystals containing bound LewisX. Crystals grown from 14% PEG 3350, 50 mM Tris pH 8 and soaked with LewisX also belong to the triclinic space group P1, but with different unit-cell parameters a = 45.1, b = 60.8, c = 91.6 A, alpha = 96.0, beta = 95.4, gamma = 101.8 degrees.
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Affiliation(s)
- Anne-Marie M van Roon
- Biophysical Structural Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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Verheijen JC, Roon AMMV, Laan ACVD, Marel GAVD, Boom JHV. Synthesis of DNA-(3′)-PNA Chimeras with Conformationally Restricted Linkers Based on 4-Hydroxyproline. ACTA ACUST UNITED AC 1999. [DOI: 10.1080/15257779908043093] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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