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- PDB-9i4d: Structure of anti-EV71 human monoclonal antibody 17-2-2B Fab -

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Basic information

Entry
Database: PDB / ID: 9i4d
TitleStructure of anti-EV71 human monoclonal antibody 17-2-2B Fab
Components
  • heavy chain
  • light chain
KeywordsANTIVIRAL PROTEIN / EV71 / antibody / Fab / 17-2-2B
Function / homologyACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,41414
Polymers95,7464
Non-polymers66810
Water1,928107
1
H: heavy chain
L: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0405
Polymers47,8732
Non-polymers1673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-57 kcal/mol
Surface area19830 Å2
MethodPISA
2
A: heavy chain
B: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3749
Polymers47,8732
Non-polymers5017
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-73 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.480, 71.660, 93.060
Angle α, β, γ (deg.)90.00, 105.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules HALB

#1: Antibody heavy chain


Mass: 25055.869 Da / Num. of mol.: 2
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: 22817.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / Strain (production host): HEK2

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Non-polymers , 4 types, 117 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) polyethylene glycol monomethyl ether 2000, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.56→49.98 Å / Num. obs: 29400 / % possible obs: 98.6 % / Redundancy: 11.9 % / CC1/2: 1 / Net I/σ(I): 9.7
Reflection shellResolution: 2.56→2.65 Å / Num. unique obs: 1109 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→49.98 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 1397 4.76 %
Rwork0.1942 --
obs0.1965 29372 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→49.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6502 0 35 107 6644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026707
X-RAY DIFFRACTIONf_angle_d0.5829166
X-RAY DIFFRACTIONf_dihedral_angle_d12.4992343
X-RAY DIFFRACTIONf_chiral_restr0.0441027
X-RAY DIFFRACTIONf_plane_restr0.0051158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.650.31861190.29592448X-RAY DIFFRACTION87
2.65-2.760.33381320.28542833X-RAY DIFFRACTION100
2.76-2.880.29821420.26982792X-RAY DIFFRACTION100
2.88-3.040.31381430.25272804X-RAY DIFFRACTION100
3.04-3.220.26491540.23322801X-RAY DIFFRACTION100
3.23-3.470.29031190.20952868X-RAY DIFFRACTION100
3.47-3.820.22511300.19072838X-RAY DIFFRACTION100
3.82-4.380.20051460.15522829X-RAY DIFFRACTION100
4.38-5.510.18341530.14362861X-RAY DIFFRACTION100
5.51-49.980.24461590.17192901X-RAY DIFFRACTION100
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)
11.14830.8435-0.82821.0137-0.04462.67050.0161-0.06540.14420.59370.07410.2136-0.6077-0.2167-0.01570.8250.17670.13220.4150.03810.5457-3.766117.675632.8289
21.71690.69890.98762.1830.32171.9256-0.13820.0891-0.2466-0.04190.11630.12980.02970.0037-0.05070.2188-0.00350.03840.24880.00350.4591-3.36826.57393.2958
31.4899-0.67140.2642.02070.30852.83280.1107-0.0917-0.17250.5530.0547-0.0754-0.0048-0.4085-0.03970.69980.0610.10660.38790.0440.456-1.0014-2.915238.6266
40.00190.1074-0.18982.0793-2.97916.63610.1521-0.13030.18930.0377-0.10220.16890.5067-0.0189-0.01230.3772-0.05630.00780.28320.06290.54580.9763-13.7139.1474
51.8795-0.37410.07343.2316-1.66583.5477-0.07840.15190.16240.14020.12970.0924-0.2131-0.0392-0.05840.265-0.01160.00820.2568-0.01560.41668.2921-2.79921.0262
62.6512-0.2601-1.42233.6661-1.45145.18880.01010.00030.0033-0.60050.1427-0.25530.81720.2206-0.01730.35830.0140.04490.3212-0.0230.31739.2457-11.1849-3.6574
71.92240.59280.7762.08820.87112.8206-0.0125-0.117-0.14440.58150.0748-0.34220.20620.2566-0.00130.55930.0245-0.01840.30740.00830.42531.2404-2.17732.5273
81.30570.2916-0.31680.7166-0.40181.91580.00570.11120.2044-0.01-0.00870.0483-0.0931-0.03020.02180.23680.02490.00250.208-0.0480.406535.33669.64045.5475
91.169-0.89340.11631.11160.26450.61680.11470.22370.0298-0.01090.0034-0.2736-0.00410.09760.00650.2774-0.0456-0.0810.2442-0.00520.574445.514115.53450.4087
103.36741.3855-1.20562.4593-0.53381.0292-0.0886-0.02630.0745-0.1308-0.1238-0.0726-0.1951-0.04920.12750.23070.0241-0.00610.19870.02950.400741.66823.46122.6922
111.39510.34420.16322.9160.56562.03950-0.0107-0.0710.43640.01380.0776-0.16530.1094-0.030.7206-0.0112-0.04550.3031-0.04430.377728.719618.388738.3334
121.5905-0.39040.10493.90161.19683.02250.02780.04190.02480.08890.02240.0540.1351-0.1414-0.05020.24590.0146-0.00480.2180.00880.425129.092822.1643-1.0234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 113 )
2X-RAY DIFFRACTION2chain 'H' and (resid 114 through 225 )
3X-RAY DIFFRACTION3chain 'L' and (resid 0 through 107 )
4X-RAY DIFFRACTION4chain 'L' and (resid 108 through 120 )
5X-RAY DIFFRACTION5chain 'L' and (resid 121 through 189 )
6X-RAY DIFFRACTION6chain 'L' and (resid 190 through 211 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1 through 113 )
8X-RAY DIFFRACTION8chain 'A' and (resid 114 through 185 )
9X-RAY DIFFRACTION9chain 'A' and (resid 186 through 204 )
10X-RAY DIFFRACTION10chain 'A' and (resid 205 through 224 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 107 )
12X-RAY DIFFRACTION12chain 'B' and (resid 108 through 211 )

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