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- PDB-9hv2: Crystal structure of tri-specific FMDV mAb-34 Fab -

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Basic information

Entry
Database: PDB / ID: 9hv2
TitleCrystal structure of tri-specific FMDV mAb-34 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: 1.77 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: heavy chain
B: light chain
H: heavy chain
L: light chain


Theoretical massNumber of molelcules
Total (without water)95,5664
Polymers95,5664
Non-polymers00
Water9,188510
1
A: heavy chain
B: light chain


Theoretical massNumber of molelcules
Total (without water)47,7832
Polymers47,7832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: heavy chain
L: light chain


Theoretical massNumber of molelcules
Total (without water)47,7832
Polymers47,7832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.411, 81.468, 74.472
Angle α, β, γ (deg.)90.000, 116.030, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 2 through 101 or resid 107 through 227))
d_2ens_1(chain "H" and (resid 2 through 52 or resid 55 through 227))
d_1ens_2(chain "B" and resid 3 through 212)
d_2ens_2chain "L"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1VALVALTHRTHRAA2 - 1012 - 101
d_12ens_1GLYGLYASPASPAA107 - 227107 - 227
d_21ens_1VALVALCYSCYSHC2 - 522 - 52
d_22ens_1GLYGLYASPASPHC55 - 22755 - 227
d_11ens_2TYRTYRGLUGLUBB3 - 2122 - 211
d_21ens_2TYRTYRGLUGLULD3 - 2122 - 211

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.984739250681, -0.111913987138, 0.133281160153), (-0.089663096955, 0.982608060772, 0.162609741252), (-0.149161446807, 0.148177793168, -0.977647280157)12.7367301093, 19.2825560292, 33.0017517623
2given(-0.965917377385, -0.193301215616, 0.17215766061), (-0.177218466733, 0.978609411174, 0.104485575131), (-0.188672295565, 0.0704149160554, -0.979512380975)13.4217991625, 19.8062735419, 29.4435921196

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Components

#1: Antibody heavy chain


Mass: 24988.916 Da / Num. of mol.: 2
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: 22793.988 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M CHES pH 9.5 30 % w/v PEG 3K

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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 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.77→64 Å / Num. obs: 72419 / % possible obs: 97.3 % / Redundancy: 6.5 % / Biso Wilson estimate: 31.93 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.037 / Net I/σ(I): 11.5
Reflection shellResolution: 1.77→1.8 Å / Num. unique obs: 2781 / CC1/2: 0.307

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Processing

Software
NameVersionClassification
GDA1.20.1_4487data collection
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→40.73 Å / SU ML: 0.2909 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.2598
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.235 3614 5.07 %
Rwork0.2082 67692 -
obs0.2095 71306 95.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.8 Å2
Refinement stepCycle: LAST / Resolution: 1.77→40.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6312 0 0 510 6822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00356443
X-RAY DIFFRACTIONf_angle_d0.73198787
X-RAY DIFFRACTIONf_chiral_restr0.0491041
X-RAY DIFFRACTIONf_plane_restr0.00521110
X-RAY DIFFRACTIONf_dihedral_angle_d13.10312265
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS3.74733808317
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS3.16515627242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.80.3813610.43591460X-RAY DIFFRACTION53.97
1.8-1.820.43971130.41391919X-RAY DIFFRACTION71.07
1.82-1.850.40731290.39162195X-RAY DIFFRACTION80.86
1.85-1.870.38041300.35442432X-RAY DIFFRACTION89.86
1.87-1.90.34951450.33732586X-RAY DIFFRACTION95.82
1.9-1.930.30781600.29832706X-RAY DIFFRACTION99.51
1.93-1.970.28771420.29252662X-RAY DIFFRACTION99.93
1.97-20.341170.28642751X-RAY DIFFRACTION99.86
2-2.040.3041280.27382708X-RAY DIFFRACTION99.89
2.04-2.080.29121540.24912730X-RAY DIFFRACTION99.9
2.08-2.130.26741610.24532654X-RAY DIFFRACTION99.93
2.13-2.180.28921600.23982687X-RAY DIFFRACTION100
2.18-2.230.27161600.22982682X-RAY DIFFRACTION100
2.23-2.290.25211620.23012699X-RAY DIFFRACTION99.9
2.29-2.360.30021220.23742740X-RAY DIFFRACTION99.97
2.36-2.440.28161170.23672741X-RAY DIFFRACTION99.93
2.44-2.520.26621560.24382692X-RAY DIFFRACTION100
2.52-2.620.27571530.24312724X-RAY DIFFRACTION100
2.62-2.740.261630.23922714X-RAY DIFFRACTION100
2.74-2.890.25421390.21612725X-RAY DIFFRACTION99.97
2.89-3.070.21641390.22372724X-RAY DIFFRACTION100
3.07-3.310.25011500.20962704X-RAY DIFFRACTION99.83
3.31-3.640.21851580.18532730X-RAY DIFFRACTION99.76
3.64-4.170.1921450.17732747X-RAY DIFFRACTION100
4.17-5.250.15011270.13922760X-RAY DIFFRACTION100
5.25-40.730.18531230.16252820X-RAY DIFFRACTION99.59
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)
13.62915330636-0.2240159202150.6537643876185.62847876-1.94577377918.57105437640.0596162256931-0.727129416334-0.689251241527-0.08434393635380.2431703335380.1930813356730.257095663852-1.05645171021-0.1953935219770.378436519152-0.00450253265908-0.03996621698030.1779740760770.01259926502280.348390295567-7.51926237692-34.079038965411.746455862
23.42446484066-1.185702121070.6146331636073.66779702042-2.214435407994.572002334190.07072668653060.253153557337-0.191793238736-0.409181045627-0.0852310690348-0.1447630979150.3201451461510.2125752861180.02063548424120.3137956136540.00344518233762-0.03697727061510.258449973685-0.03226603879890.285588362891-4.33785413557-30.91824681970.838831294899
32.63993760683-1.26378808423-1.026349484863.890303735321.121678105973.48716910228-0.165816568203-0.0731215366704-0.05098776737590.3343667166930.05106631846180.661857720068-0.0795033254103-0.3795086981070.09896144535060.3242554183820.00793493091824-0.0187913588720.202234117978-0.006733957695470.408644622406-17.6373568455-23.251945608732.980595706
44.47749201751-0.828274639855-0.07339151274194.312153314942.56273223716.92087442436-0.1296638482570.03637523237190.427079233272-0.161812713255-0.0262208278230.00278868622432-0.4754182762080.06609522754560.09424832352230.240494977039-0.0410796501693-0.07275090847370.21042599110.02804398935070.289331404766-5.91011938247-11.0795315964-1.31110225996
51.92894512891-0.794756596951-0.1832913882432.31457137267-0.3543663524696.53818411902-0.0929371774680.0210127989125-0.1426618594610.5134616349980.02979383884980.372178446357-0.554575847106-0.270416146181-0.09075865054190.2545695956050.0139238387282-0.04343784591670.206017848586-0.07708458476920.315165368584-13.4948542687-10.199535636130.921705366
64.74662627413-2.034833594241.903321104086.92350695551-1.675263616885.37324625604-0.21080480605-0.002186529035260.21851801460.01579514433690.09104481451230.0298242053229-0.2847962802950.0528051118870.0836175351380.3393317632690.0292265781105-0.02062837237560.169850499721-0.02775281465360.283507501519-8.85227505475-8.514945936735.1175093573
73.649713305020.5585037291140.5782034971444.807162570181.10527951316.033769726240.149133785902-0.205033579611-0.3555998320840.3147859075550.127640066684-0.5454128921410.40474233688-0.0176933795647-0.2183278863210.326360839164-0.023121479223-0.09037080815830.1539713849460.0217629898910.35173524698522.3355400137-10.603001971524.102181137
82.269900253570.7615571728020.5644694381584.596229261810.9564657483923.621676238150.286779420094-0.247137188968-0.5547814789370.437801849361-0.00527000890314-0.478735195090.602979806479-0.0354254288395-0.1945300779930.382337944087-0.0214788654177-0.09322547875070.2347874983060.07064172268670.37976298436622.1252223816-10.475627074626.1697818131
93.637590723111.01907646386-2.989295767372.57267487415-0.6023886038263.07349015616-0.07271985461760.402358174454-0.537338645973-0.0829777391630.0261908237053-0.1358270525460.379840675347-0.2894220859380.330488277860.335585026034-0.0211464132349-0.008614751557750.312455340785-0.1005728108690.33711397179622.8978131441-8.298511180054.47195734396
106.03843604768-1.7304846666-0.9971765638597.127296485831.424293266054.522110660470.04222784510420.1609510802520.185311170231-0.141019492475-0.0765257094091-0.39751686338-0.1652345707570.2298359840910.05923048063240.29349337670.0410792663471-0.02533862729140.1839450325-0.01944475097110.23101091095837.38085413713.694920119171.50455385708
112.88127886511.392100105180.70662444346.48980585883-1.007756132474.281457361260.00915521215844-0.1388905998250.1794263121250.3783439187330.02361393739130.171253109712-0.281700627791-0.409245103949-0.04234824885920.2984859425020.0431196655347-0.005881736148850.215805884722-0.0436569169410.19199014292521.994525711310.599872964432.0436486442
121.250481395110.314812791684-1.098118162171.48935924853-1.348002421894.35032783337-0.01426545705020.0473805476753-0.0630926121051-0.196693302509-0.09232530454940.02928367237740.0923403815871-0.04686311624670.188081526360.2025812971790.0383378283304-0.06059172822690.174624057931-0.0302686190880.26418668442327.093779627210.29921291410.378518609
132.57817714476-0.1254159839070.4207581635724.92007580869-0.05631564411245.575767686150.05255930507430.3984112931890.00933026601527-0.847971594842-0.08683943550260.1717241645070.0771628161644-0.02728313812650.03897756795780.348161494420.0296100736068-0.01574959079930.189162158418-0.01830298804870.27740569156129.926339174917.5641805842-5.16554818096
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 17 )AA1 - 171 - 17
22chain 'A' and (resid 18 through 121 )AA18 - 12118 - 119
33chain 'A' and (resid 122 through 231 )AA122 - 231120 - 219
44chain 'B' and (resid 3 through 102 )BB3 - 1021 - 100
55chain 'B' and (resid 103 through 130 )BB103 - 130101 - 128
66chain 'B' and (resid 131 through 213 )BB131 - 213129 - 211
77chain 'H' and (resid 2 through 63 )HC2 - 631 - 62
88chain 'H' and (resid 64 through 121 )HC64 - 12163 - 115
99chain 'H' and (resid 122 through 134 )HC122 - 134116 - 128
1010chain 'H' and (resid 135 through 227 )HC135 - 227129 - 211
1111chain 'L' and (resid 3 through 91 )LD3 - 911 - 89
1212chain 'L' and (resid 92 through 130 )LD92 - 13090 - 128
1313chain 'L' and (resid 131 through 212 )LD131 - 212129 - 210

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