[English] 日本語
Yorodumi
- PDB-9hv8: Crystal structure of tri-specific FMDV mAb-49 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hv8
TitleCrystal structure of tri-specific FMDV mAb-49 Fab
Components
  • heavy chain
  • light chain
KeywordsIMMUNE SYSTEM / foot-and-mouth disease virus / cattle antibody / cross-reactive / linear epitope / antibody structure
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: heavy chain
L: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5198
Polymers47,9662
Non-polymers5536
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-25 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.009, 78.552, 100.378
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

#1: Antibody heavy chain


Mass: 25113.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody light chain


Mass: 22853.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 9.1 M imidazole pH 7.0, 20 % w/v PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.72→62 Å / Num. obs: 56341 / % possible obs: 92.1 % / Redundancy: 12.7 % / Biso Wilson estimate: 33.73 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.019 / Net I/σ(I): 17.4
Reflection shellResolution: 1.72→1.75 Å / Num. unique obs: 1673 / CC1/2: 0.359

-
Processing

Software
NameVersionClassification
GDA1.20.1_4487data collection
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→42.29 Å / SU ML: 0.2387 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.3923
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2113 2570 4.64 %
Rwork0.1831 52783 -
obs0.1844 55353 90.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.57 Å2
Refinement stepCycle: LAST / Resolution: 1.72→42.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3277 0 36 367 3680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643377
X-RAY DIFFRACTIONf_angle_d0.79084597
X-RAY DIFFRACTIONf_chiral_restr0.0545536
X-RAY DIFFRACTIONf_plane_restr0.0053580
X-RAY DIFFRACTIONf_dihedral_angle_d12.39571198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.750.4746640.53071258X-RAY DIFFRACTION39.63
1.75-1.790.4222810.41771852X-RAY DIFFRACTION57.65
1.79-1.830.42911020.36392122X-RAY DIFFRACTION66.21
1.83-1.870.32551290.31262483X-RAY DIFFRACTION77.71
1.87-1.920.28811390.25562927X-RAY DIFFRACTION92.04
1.92-1.970.25981500.22753117X-RAY DIFFRACTION97.15
1.97-2.030.25511590.21553198X-RAY DIFFRACTION99.5
2.03-2.090.2081430.21873219X-RAY DIFFRACTION99.29
2.09-2.170.24191610.21583179X-RAY DIFFRACTION99.73
2.17-2.250.26111670.21483198X-RAY DIFFRACTION99.53
2.25-2.360.23841450.21063203X-RAY DIFFRACTION99.7
2.36-2.480.27811720.19623239X-RAY DIFFRACTION99.77
2.48-2.640.23471720.20043198X-RAY DIFFRACTION99.85
2.64-2.840.23881620.20273247X-RAY DIFFRACTION99.88
2.84-3.120.20281500.18053282X-RAY DIFFRACTION99.97
3.12-3.580.19981420.16413287X-RAY DIFFRACTION99.88
3.58-4.50.1741430.14683331X-RAY DIFFRACTION100
4.51-42.290.16721890.15553443X-RAY DIFFRACTION99.94
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)
13.50268978283-0.48137951246-0.5725441155824.69124313882-1.368373700233.10716130339-0.001238055922890.15054925266-0.0339244832982-0.0435798472210.03543844892470.205510568302-0.141836780893-0.279681294139-0.03239552253490.2699785064340.05439269227260.09208401417470.2765710421190.07256231163220.2406933212621.91789749515-11.018944626822.427801661
26.65283970188-2.300519230860.8198174643397.8611261891-1.321463985975.978351175390.13069509775-0.114211413546-0.7310825712450.396140317331-0.280587761927-0.5510955448660.7349046962090.2984121171510.1206135773550.3726095636280.01383052612350.09021072319740.3404686508710.1066770448640.44835395952913.2421962244-18.871896659622.4539960539
30.929335190521-1.492806864650.4875506647633.4193339674-2.365592457392.37892667524-0.0481742991418-0.0128907052359-0.03715126708830.328814316030.1997631838380.239165310484-0.184456475510.0580393511401-0.1776659305640.207978711011-0.003126449277880.03437562018790.295754179508-0.02261850211830.2619010478084.7277448022313.45726281921.05767038556
47.28502467167-0.0850551728235-1.232802492994.69306063742-1.548539435864.91469200424-0.04994181409630.7582327877730.281535936815-0.2432574146590.1323121566620.107737666615-0.4922824787210.145896828202-0.05500067264270.312329486289-0.0273357494839-0.002693488289620.313770430783-0.02297932656870.2223433543783.5369608596720.8529704775-7.48419003745
53.411171976680.940807904082-1.233404799024.86227495121-1.627186761995.17651840917-5.38377632243E-6-0.192896929164-0.1305426275450.173511534831-0.202843406223-0.4961400199010.08118552487150.3843557381960.1763431586360.1869228202820.04391429675970.01474240986930.2550976962840.07950138078510.25515275849926.3604684929-9.6293082414617.7807864155
62.087473539541.11788207799-0.8899734529984.3561977747-4.038551052844.345188962020.0492410487036-0.134943105501-0.1062716412350.263906705265-0.0644677999052-0.12229397238-0.09856275352320.01828771240030.04087755817520.2264302572760.03458886910620.003543110825730.2409834693890.03596592895260.2125792599423.1474391772-4.6480231533912.7757065712
74.6645273182-2.85434910841-0.184185824424.42943969774-0.3463869487762.40186865563-0.23661554852-0.2317963404090.1393243507390.4534164653060.1266425856860.0342721306245-0.250357630773-0.007358873776310.08350638679030.2163001812630.006920335989390.01648847564710.1940500647190.01812647912720.13989538746315.126062190918.9392450717.60009915366
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 117 )HA91 - 11791 - 117
33chain 'H' and (resid 118 through 191 )HA118 - 191118 - 191
44chain 'H' and (resid 192 through 231 )HA192 - 231192 - 231
55chain 'L' and (resid 2 through 74 )LB2 - 741 - 73
66chain 'L' and (resid 75 through 114 )LB75 - 11474 - 113
77chain 'L' and (resid 115 through 212 )LB115 - 212114 - 211

+
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