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- PDB-9hv1: Crystal structure of tri-specific FMDV mAb-17 Fab -

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Basic information

Entry
Database: PDB / ID: 9hv1
TitleCrystal structure of tri-specific FMDV mAb-17 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: 1.96 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 23, 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
H: heavy chain
L: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8406
Polymers46,4722
Non-polymers3684
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-29 kcal/mol
Surface area20090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.092, 136.092, 79.673
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Antibody heavy chain


Mass: 23698.453 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: 22773.049 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.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bicine pH 8.5, 15 % Polyethylene glycol (PEG) 1,500

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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: 1.96→68 Å / Num. obs: 60338 / % possible obs: 100 % / Redundancy: 21.1 % / Biso Wilson estimate: 52.72 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.031 / Net I/σ(I): 10.4
Reflection shellResolution: 1.96→1.99 Å / Num. unique obs: 3048 / CC1/2: 0.384

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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: 1.96→44.55 Å / SU ML: 0.3844 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 39.7961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2363 2748 5.3 %
Rwork0.212 49148 -
obs0.2133 51896 86.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 76.23 Å2
Refinement stepCycle: LAST / Resolution: 1.96→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 24 74 3344
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053336
X-RAY DIFFRACTIONf_angle_d0.79814545
X-RAY DIFFRACTIONf_chiral_restr0.0489532
X-RAY DIFFRACTIONf_plane_restr0.0059574
X-RAY DIFFRACTIONf_dihedral_angle_d12.13721178
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.992.009761.289690X-RAY DIFFRACTION3.16
2-2.030.8941130.8945285X-RAY DIFFRACTION10.2
2.03-2.070.5468580.50211418X-RAY DIFFRACTION49.38
2.07-2.110.48511000.45731847X-RAY DIFFRACTION65.56
2.11-2.160.4431630.4182856X-RAY DIFFRACTION99.18
2.16-2.210.39161490.39652802X-RAY DIFFRACTION99.39
2.21-2.260.39621640.39742827X-RAY DIFFRACTION99.83
2.26-2.320.33121680.34862827X-RAY DIFFRACTION99.7
2.33-2.390.36211590.33792820X-RAY DIFFRACTION99.43
2.39-2.470.34081430.32292838X-RAY DIFFRACTION99.27
2.47-2.560.3161920.30852806X-RAY DIFFRACTION99.57
2.56-2.660.30961460.30652834X-RAY DIFFRACTION99.33
2.66-2.780.30121650.29042817X-RAY DIFFRACTION99.27
2.78-2.930.26611530.2552849X-RAY DIFFRACTION99.54
2.93-3.110.26981650.2472822X-RAY DIFFRACTION99.6
3.11-3.350.26471650.22712875X-RAY DIFFRACTION99.84
3.35-3.690.24361750.21412833X-RAY DIFFRACTION99.9
3.69-4.220.21671590.17442862X-RAY DIFFRACTION99.9
4.22-5.320.15451330.13712907X-RAY DIFFRACTION99.93
5.32-44.550.1631720.14612933X-RAY DIFFRACTION99.78
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)
13.88164504267-2.30757827379-1.537353973623.78858461161-0.7800205001762.72118131585-0.2181485911010.5214426663480.600374029843-0.661301936767-0.1596645653080.316640102903-0.5779997183410.2903020665860.1945191785911.003603681240.15949101858-0.01864341246250.422967988493-0.03779528743430.403597106767-47.8719132787-21.3740858695-15.3499073101
23.25203517471-1.69759930123-0.01280401318274.172050562440.6238106755573.65878174146-0.236879224177-0.120349740309-0.324204414569-0.4355729585640.06690301377540.01476207610260.2258251883150.5448924312420.1513996527610.9926227736770.306534057840.1049551722480.553124092806-0.01006731618270.507230099903-44.9712834648-31.141920443-9.08024410584
31.93720676305-0.545950645610.6898004218051.68888557599-1.490545661793.208433684410.192252190644-0.1690623410510.0672568409775-0.1427116412980.04312123051690.170134883226-0.138363770286-0.00923670060482-0.2544327140481.01873823825-0.05718693636230.04111469676380.33437319215-0.02445286037070.412115966446-62.4911775982-3.27437624772-7.33998939279
45.927838186681.529243233332.015188607122.9316857521-1.075221226011.689640447030.371974773707-0.3828273486090.97914054204-0.122681294216-0.0217739982066-0.0304131661609-1.46908001442-0.783505167319-0.2754460704481.45601924814-0.02999061977450.09340184017770.3765542114710.001409783388230.548151273781-64.64831269899.15997902617-8.18519477479
53.936586793470.120806149282-1.122677646173.862083862781.090487516945.58159979348-0.525295071743-0.799751342209-0.09944833507130.7612626076280.401921328680.00570574022814-0.02239237886950.5577577930410.1268669968180.9031426167950.454207109331-0.01473292055290.867124311156-0.01779159038930.495330266791-45.0307854688-25.34742288212.3339428536
63.11107103805-0.7496327789170.2000805596587.735219057312.877185388186.76993084365-0.543296332324-0.5935722132070.002515367293730.2201456442690.2347097779330.1685031037610.06263955916240.2402982811870.3099660856170.9105030803070.3823133366020.06716975398390.74167086278-0.02753399947450.54329090058-48.1575792723-25.27064783857.36425520924
73.75128874912-0.198761470567-1.29047032843.318211521921.120940009220.940654322234-0.1652502953920.47880537810.5361537203810.1605652074190.217052423072-0.100804543815-0.06675920059130.37104553747-0.09056362527560.8994407831990.06067292134330.04383026231830.375212364055-0.02561838138810.385925886419-66.8434389865-2.223046304763.89366926909
83.97837498096-0.0313571539199-0.3520739879121.468705240270.1472411919096.854164468280.09888121885070.144521658941-0.09711234995790.06318950063810.1586516771570.06094267732290.430828532571-0.619336451904-0.2886038002420.987639898491-0.056930987526-0.004088661549110.3030654326340.03274971066810.444367219709-72.2180803551-5.681364080774.05960205409
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 17 )HA1 - 171 - 17
22chain 'H' and (resid 18 through 110 )HA18 - 11018 - 110
33chain 'H' and (resid 111 through 188 )HA111 - 188111 - 188
44chain 'H' and (resid 189 through 225 )HA189 - 225189 - 225
55chain 'L' and (resid 1 through 74 )LB1 - 741 - 74
66chain 'L' and (resid 75 through 101 )LB75 - 10175 - 101
77chain 'L' and (resid 102 through 129 )LB102 - 129102 - 129
88chain 'L' and (resid 130 through 212 )LB130 - 212130 - 212

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