[English] 日本語
Yorodumi
- PDB-9hv9: Crystal structure of Fab34 complexed with a 7-mer peptide of FMDV VP1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hv9
TitleCrystal structure of Fab34 complexed with a 7-mer peptide of FMDV VP1
Components
  • Capsid protein VP1
  • heavy chain
  • light chain
KeywordsIMMUNE SYSTEM / foot-and-mouth disease virus / cattle antibody / cross-reactive / linear epitope / antibody structure
Function / homology
Function and homology information


L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...L-peptidase / symbiont-mediated perturbation of host chromatin organization / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / molecular adaptor activity / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Papain-like cysteine peptidase superfamily / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain ...Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Aphthovirus leader protease (L(pro)) domain profile. / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Papain-like cysteine peptidase superfamily / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
Foot-and-mouth disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRen, J. / Duyvesteyn, H.M.E. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/ 1 United Kingdom
Wellcome Trust060208/Z/00/Z United Kingdom
CitationJournal: NPJ Vaccines / Year: 2026
Title: Cattle antibodies identify a cross-serotype broadly neutralising foot-and-mouth disease virus epitope.
Authors: Marie Bonnet-Di Placido / Helen M E Duyvesteyn / Angela W Steyn / Abigail L Hay / Claudine Porta / Kristel Ramirez Valdez / Elena Lokhman / Sylvia Crossley / Kevan Hanson / William N Mwangi ...Authors: Marie Bonnet-Di Placido / Helen M E Duyvesteyn / Angela W Steyn / Abigail L Hay / Claudine Porta / Kristel Ramirez Valdez / Elena Lokhman / Sylvia Crossley / Kevan Hanson / William N Mwangi / Danish Munir / Eva Perez-Martin / Nick J Knowles / Alison Burman / Abdelaziz A Yassin / Amin Asfor / Cristina Faralla / Katherine J Lam / Róisín McComb / Carina Leifeld / Kimberly Pietersz / Donald P King / Erwin van den Born / Sherie K Duncan / Bryan Charleston / Elizabeth E Fry / Jingshan Ren / David I Stuart / John A Hammond /
Abstract: Foot-and-mouth disease virus (FMDV) causes a devastating disease that threatens global food security. Vaccination is hindered by antigenic diversity across serotypes. To identify cross-serotype ...Foot-and-mouth disease virus (FMDV) causes a devastating disease that threatens global food security. Vaccination is hindered by antigenic diversity across serotypes. To identify cross-serotype neutralising epitopes, we isolated 24 FMDV-specific antibodies from cattle sequentially vaccinated with antigens from four serotypes, of which three neutralised three vaccine strains. These three antibodies neutralised 21 and bound 59 additional topotypes across O, A, Asia 1, and C serotypes. Cryo-EM complexes of Fabs with FMD virus-like particles indicated all three recognise a common flexible epitope at the VP1 C-terminus, confirmed by binding competition. Crystallography and structural modelling revealed that a normally inaccessible surface of the hydrophobic VP1 C-terminal peptides inserts into a similar groove in all three antibodies. Comparison of neutralisation activity and integrin receptor blocking by whole antibodies, F(ab')s, and Fabs suggests neutralisation is mediated by Fc steric hindrance of receptor binding. This cryptic, linear, and cross-serotype neutralising epitope may inform improved FMD vaccines.
History
DepositionDec 24, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2026Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Apr 15, 2026Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jun 3, 2026Group: Database references / Category: citation / Item: _citation.journal_volume

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: heavy chain
L: light chain
A: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,89817
Polymers48,5393
Non-polymers1,35914
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-145 kcal/mol
Surface area19930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.258, 40.679, 71.704
Angle α, β, γ (deg.)90.000, 94.450, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11L-450-

HOH

-
Components

-
Protein/peptide , 1 types, 1 molecules A

#3: Protein/peptide Capsid protein VP1 / P1D / Virion protein 1


Mass: 755.987 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Foot-and-mouth disease virus / References: UniProt: P03305

-
Antibody , 2 types, 2 molecules HL

#1: Antibody heavy chain


Mass: 24988.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Homo sapiens (human)
#2: Antibody light chain


Mass: 22793.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Homo sapiens (human)

-
Non-polymers , 5 types, 180 molecules

#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium sulfate monohydrate, 0.1 M Sodium acetate trihydrate pH 4.5, 50 % v/v PEG 400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97627 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 7, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97627 Å / Relative weight: 1
ReflectionResolution: 1.8→87 Å / Num. obs: 44896 / % possible obs: 96 % / Redundancy: 6.7 % / Biso Wilson estimate: 37.82 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.036 / Net I/σ(I): 9.1
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 1575 / CC1/2: 0.294

-
Processing

Software
NameVersionClassification
GDA1.20.1_4487data collection
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→86.37 Å / SU ML: 0.2809 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.1295
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2285 2040 4.67 %
Rwork0.2008 41635 -
obs0.2021 43675 93.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.81 Å2
Refinement stepCycle: LAST / Resolution: 1.8→86.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3270 0 77 166 3513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033427
X-RAY DIFFRACTIONf_angle_d0.60094670
X-RAY DIFFRACTIONf_chiral_restr0.0461543
X-RAY DIFFRACTIONf_plane_restr0.005582
X-RAY DIFFRACTIONf_dihedral_angle_d10.59431207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.5783370.47521226X-RAY DIFFRACTION40.86
1.84-1.890.41581080.41742118X-RAY DIFFRACTION72.39
1.89-1.940.39731300.36152762X-RAY DIFFRACTION92.54
1.94-20.31781420.29992832X-RAY DIFFRACTION98.22
2-2.060.29171470.28322937X-RAY DIFFRACTION99.36
2.06-2.130.2621530.27382921X-RAY DIFFRACTION99.51
2.13-2.220.33111470.25712947X-RAY DIFFRACTION99.58
2.22-2.320.27851410.23612928X-RAY DIFFRACTION99.64
2.32-2.440.26911450.22032953X-RAY DIFFRACTION99.65
2.44-2.60.24551590.20682952X-RAY DIFFRACTION99.81
2.6-2.80.23031530.19932940X-RAY DIFFRACTION99.9
2.8-3.080.26821500.21342996X-RAY DIFFRACTION100
3.08-3.520.22041410.18512987X-RAY DIFFRACTION99.94
3.52-4.440.20991370.16483034X-RAY DIFFRACTION99.87
4.44-86.370.16351500.1693102X-RAY DIFFRACTION99.79
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.941926591350.6878989115970.3742186072072.618534167670.2515062802492.38174886933-0.0615127585574-0.124023759506-0.0167621620173-0.0366137422435-0.02788010781850.02406443418010.08042677776120.1065369443470.1034347080870.2842650900370.0234516097294-0.002179648505720.1772612362980.0372048191140.289660708714-35.10583859666.241457103134.6653900515
20.8149748458111.539433119171.432874317248.4994574626-1.322597959147.22747890007-0.04824866821280.0162692372204-0.2554560839310.2053892851220.005786230968331.1898139170.218373253271-1.245240267620.07812251159010.318882523765-0.04265012730240.006401213470020.3595228885310.0007850185097170.341284014868-45.36650320513.1603757874712.0052130962
38.86361532852-0.749533276972-4.423900840110.5788211691150.6996522602633.444254302730.1143938093280.181153677231-0.1113420733680.0548415443102-0.129129058368-0.08148094321890.01172787452870.08206232411390.0609417921760.312062990730.0114508566169-0.02519106494840.2289279914390.05364816739090.34799661706-28.42481455141.92994324418.07391281336
43.871482797450.03804772227-0.4388441647144.58706445999-0.7382443525044.45628862092-0.0927852588025-0.527290783666-0.2596766363730.3585732624910.0428581606718-0.1433591782830.361219118715-0.1027272168210.07081894117690.353387011876-0.005127862667280.02779330753040.5911819525480.03800036065980.347847973709-2.07734113138-9.1575098044611.9379864361
54.67900571448-0.5326892944741.608037458794.88550421123-1.541419544864.471540581270.115091347647-0.867463229072-0.0149882392890.408194643778-0.162140815377-0.00332470735779-0.0629906924565-0.178057718180.01164074544920.310006755639-0.02523771228030.03072947930270.5653332196190.01261842730520.259666134335-38.69987348920.87751199947928.1231080291
65.8248279229-0.396917614630.04130734976570.4236772636150.53034536511.378953951990.0261196893936-0.627525107445-0.3345922974060.22758229424-0.0839343246577-0.03812778840.103386099659-0.03529903315320.03893310421620.352857564963-0.0342963316344-0.009176089005710.374185411427-0.00201966845350.237659909634-30.8728368179-0.63288697598426.6518071848
74.053532185510.688835899019-1.611423736922.777977887-1.236320330754.152792825940.08506888707860.1810184393150.189422758992-0.0302134154790.3557128828270.0758851752234-0.0958493779033-0.30036828284-0.4809995543610.3411010090290.0840150972498-0.01482109447310.6262679194060.03004676304620.337414175992-4.919445690971.5520363629120.9434353374
89.201838247314.99994915156-3.598461567367.24116403771-3.915281397457.260799172840.398217647735-0.604502981140.1238806588320.692266516175-0.0978451048376-0.248307889308-0.5628075180930.696964533383-0.2132553677790.3624696652410.0266683342382-0.01896150855240.595635787562-0.06707237301850.2809076727150.4479506663653.7750856438928.5208704445
92.21662800217-2.46550041271.930810184628.79153290792-5.22208042713.242818242060.594553076838-0.6985615181020.2328479515330.1895711074820.6058759401520.376478462312-0.325561581034-1.01867334178-1.006363291690.3419176205890.05271377859430.07742673173730.511813207799-0.03079784430860.425174558568-50.990064498512.362903567618.9561503628
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'H' and (resid 1 through 90 )HA1 - 901 - 90
22chain 'H' and (resid 91 through 110 )HA91 - 11091 - 110
33chain 'H' and (resid 111 through 134 )HA111 - 134111 - 134
44chain 'H' and (resid 135 through 230 )HA135 - 230135 - 223
55chain 'L' and (resid 3 through 75 )LB3 - 751 - 73
66chain 'L' and (resid 76 through 115 )LB76 - 11574 - 113
77chain 'L' and (resid 116 through 188 )LB116 - 188114 - 186
88chain 'L' and (resid 189 through 213 )LB189 - 213187 - 211
99chain 'A' and (resid 204 through 210 )AC204 - 2101 - 7

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more