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- PDB-9i3w: Structure of anti-EV71 human monoclonal antibody 16-2-8C Fab -

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Basic information

Entry
Database: PDB / ID: 9i3w
TitleStructure of anti-EV71 human monoclonal antibody 16-2-8C Fab
Components
  • heavy chain
  • light chain
KeywordsANTIVIRAL PROTEIN / EV71 / antibody / 16-2-8C / Fab
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsZhou, D. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N00065X/1 United Kingdom
Wellcome Trust090532/Z/09/Z United Kingdom
CitationJournal: Sci Adv / Year: 2026
Title: Structural and functional mapping of protective human monoclonal antibodies against enterovirus A71.
Authors: Daming Zhou / Abhay Kotecha / James T Kelly / Peng-Nien Huang / Yi-Yin Chen / Thomas S Walter / Helen M E Duyvesteyn / Raymond J Owens / Shu-Yuan Ho / Tzou-Yien Lin / Elizabeth E Fry / ...Authors: Daming Zhou / Abhay Kotecha / James T Kelly / Peng-Nien Huang / Yi-Yin Chen / Thomas S Walter / Helen M E Duyvesteyn / Raymond J Owens / Shu-Yuan Ho / Tzou-Yien Lin / Elizabeth E Fry / Jingshan Ren / Kuan-Ying A Huang / David I Stuart /
Abstract: EV-A71 has been responsible for recent severe HFMD outbreaks. We report structures for 12 potently neutralizing human anti-EV-A71 monoclonal antibody Fabs, alone and complexed with virus. Most ...EV-A71 has been responsible for recent severe HFMD outbreaks. We report structures for 12 potently neutralizing human anti-EV-A71 monoclonal antibody Fabs, alone and complexed with virus. Most recognize the native antigenic state with epitopes that span interfaces, together covering 85% of the capsid surface. The majority (8 of 12) bind the canyon, while the others cluster around the icosahedral two- and threefold axes. Blocking SCARB2 receptor binding likely contributes to neutralization for all, and a subset induces empty particles. A predominant gene family (IGHV4-39) does not dictate a common binding pose. Long CDR-H3 loops are frequently key to binding, especially at the canyon, suggesting that antigenicity data based on antibodies with shorter CDR3s (e.g., murine) may be misleading. This dataset reveals neutralization mechanisms for recently circulating EV-A71 genotypes, which will inform immunotherapies. We demonstrate synergy in vitro between canyon binding and both two- and threefold binding antibodies to increase neutralization potency.
History
DepositionJan 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.title / _citation.year
Revision 1.2Jun 17, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,4985
Polymers49,1652
Non-polymers3333
Water10,178565
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-18 kcal/mol
Surface area21190 Å2
Unit cell
Length a, b, c (Å)47.013, 80.394, 57.572
Angle α, β, γ (deg.)90.000, 93.832, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein heavy chain


Mass: 26488.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody light chain


Mass: 22676.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 25% (w/v) PEG 3350, 0.1 M Bis-Tris, pH 6.5, protein concentration: 26.4mg/ml

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.14→46.908 Å / Num. obs: 153940 / % possible obs: 99.1 % / Redundancy: 6 % / CC1/2: 1 / Net I/σ(I): 11.5
Reflection shellResolution: 1.14→1.169 Å / Num. unique obs: 7168 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.14→46.908 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.045 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.038 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1938 7459 4.896 %
Rwork0.1661 144890 -
all0.168 --
obs-152349 98.102 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.136 Å2
Baniso -1Baniso -2Baniso -3
1--0.367 Å20 Å2-0.358 Å2
2---1.346 Å2-0 Å2
3---1.745 Å2
Refinement stepCycle: LAST / Resolution: 1.14→46.908 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3352 0 22 565 3939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0123630
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163314
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.7945027
X-RAY DIFFRACTIONr_angle_other_deg0.6121.7087770
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9355522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.53359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.89610563
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.32310118
X-RAY DIFFRACTIONr_chiral_restr0.0910.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024273
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02767
X-RAY DIFFRACTIONr_nbd_refined0.2160.2453
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.22699
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21663
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21688
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2329
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1760.215
X-RAY DIFFRACTIONr_nbd_other0.2010.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1770.237
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_mcbond_it5.9111.8141870
X-RAY DIFFRACTIONr_mcbond_other5.9091.8141870
X-RAY DIFFRACTIONr_mcangle_it8.5343.2922353
X-RAY DIFFRACTIONr_mcangle_other8.5333.2932354
X-RAY DIFFRACTIONr_scbond_it7.3542.0621760
X-RAY DIFFRACTIONr_scbond_other7.3522.0631761
X-RAY DIFFRACTIONr_scangle_it10.4443.6482636
X-RAY DIFFRACTIONr_scangle_other10.4423.6492637
X-RAY DIFFRACTIONr_lrange_it17.11924.9423878
X-RAY DIFFRACTIONr_lrange_other15.3721.2323701
X-RAY DIFFRACTIONr_rigid_bond_restr3.69736944
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.14-1.1690.3885130.38898210.388114700.8760.86390.09590.383
1.169-1.2010.3884880.362101330.363112160.8810.994.69510.352
1.201-1.2360.3645450.338100800.339108510.9030.91397.91720.326
1.236-1.2740.3374900.31498230.315105200.9130.93198.03230.295
1.274-1.3160.3154560.28995600.29101750.9230.94598.43730.265
1.316-1.3620.2734710.24893070.24998930.9470.95898.83760.22
1.362-1.4130.234810.21389570.21495560.9620.9798.76520.185
1.413-1.4710.2284340.19487020.19592280.9630.97599.0030.165
1.471-1.5360.2144320.16682530.16987650.9690.98299.08730.141
1.536-1.6110.1824740.13579220.13884430.9780.98999.44330.115
1.611-1.6980.1583840.11875930.1280210.9840.99199.45140.103
1.698-1.8010.1563330.11272300.11476010.9840.99299.50010.101
1.801-1.9250.1733250.11867550.1271110.9820.99299.56410.112
1.925-2.0790.1563240.11763000.11866430.9860.99299.7140.117
2.079-2.2770.1573340.12257850.12461300.9840.99199.82060.127
2.277-2.5450.1872720.1452570.14355410.9790.98899.78340.152
2.545-2.9370.1832710.15346490.15549220.980.98699.95940.172
2.937-3.5940.162110.15339480.15341660.9850.98699.8320.18
3.594-5.0680.1641490.14630660.14732150.9850.9881000.185
5.068-46.9080.182720.18117490.18118290.9760.9899.56260.228

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