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- PDB-9i4c: Structure of anti-EV71 human monoclonal antibody 17-1-12A Fab -

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Basic information

Entry
Database: PDB / ID: 9i4c
TitleStructure of anti-EV71 human monoclonal antibody 17-1-12A Fab
Components
  • heavy chain
  • light chain
KeywordsANTIVIRAL PROTEIN / EV71 / antibody / Fab / 17-1-12A
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,14419
Polymers49,5832
Non-polymers1,56117
Water34219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-150 kcal/mol
Surface area21740 Å2
Unit cell
Length a, b, c (Å)152.750, 152.750, 120.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z
#9: y,x,-z
#10: -y,-x,-z
#11: -x+y,y,-z
#12: x,x-y,-z

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody heavy chain


Mass: 25706.764 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: 23876.639 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)

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Non-polymers , 4 types, 36 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 4.09 Å3/Da / Density % sol: 69.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1.5 M lithium sulphate mon, 0.1 M HEPES-Na, pH 7.5

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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: Apr 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.83→76.37 Å / Num. obs: 20091 / % possible obs: 98.7 % / Redundancy: 9.8 % / Biso Wilson estimate: 52.71 Å2 / CC1/2: 0.98 / Net I/σ(I): 7.6
Reflection shellResolution: 2.83→2.98 Å / Num. unique obs: 994 / CC1/2: 0.56

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→76.37 Å / SU ML: 0.4338 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.9761
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2669 1026 5.11 %
Rwork0.2226 19057 -
obs0.2248 20083 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.74 Å2
Refinement stepCycle: LAST / Resolution: 2.83→76.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 84 19 3503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293543
X-RAY DIFFRACTIONf_angle_d0.57494813
X-RAY DIFFRACTIONf_chiral_restr0.0419527
X-RAY DIFFRACTIONf_plane_restr0.0074606
X-RAY DIFFRACTIONf_dihedral_angle_d10.40211269
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.980.39071390.35332665X-RAY DIFFRACTION99.05
2.98-3.170.3841520.31572668X-RAY DIFFRACTION99.09
3.17-3.410.34611780.27882650X-RAY DIFFRACTION99.09
3.41-3.750.29441330.23512708X-RAY DIFFRACTION99.2
3.75-4.30.21411340.19662724X-RAY DIFFRACTION98.72
4.3-5.410.19581330.16012769X-RAY DIFFRACTION98.88
5.41-76.370.23481570.20312873X-RAY DIFFRACTION97.12
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)
11.96252237850.4208818672251.261841863834.032327212651.3227227413.786671136410.0329826336452-0.1047399399550.02889683587640.0309707524249-0.059515166603-0.157021208332-0.00257300903885-0.01053992683380.0353029342420.243561982133-0.02453382783990.03318065214530.2602122566130.02009649283490.51078814627-17.260256158252.350526914355.1453442569
20.5710766951020.199962756597-0.7218432520022.927847946210.4247173195883.95630341613-0.0359157938064-0.04035668931980.32432692628-0.1705456473880.1171236366120.294402841301-0.190131606375-0.166614039123-0.1083806900870.2563735468050.04915040363270.03282735913580.3210730132580.03222763122180.734267950194-17.101296711757.948988436953.8584708905
30.545995389714-0.618855215395-0.9573829620623.73677229251.971690825622.776959733610.0973193763222-0.0309156294719-0.157566348391-0.349184361317-0.0328741897982-0.8912095560720.14244167621-0.013543177758-0.0034703251540.4238946599170.02668713591090.02553447140770.3038502119080.09890285392750.608223585326-15.433344825146.647568105344.9188134883
46.251655542481.54958871015-3.004758746236.70211368121-0.1117453925247.73235953238-0.09552443010520.4842689147070.194792177278-0.7738658374-0.0315480081922-1.43756305891-0.3026275217030.2468178333310.1147244651610.4573526132870.07428437318680.01368572297070.3335792121240.08449945359990.8713595132122.3369605027834.238937750518.4679495285
53.140010080650.899796909747-1.253896477771.248784886170.742975058881.66579172630.322289605803-0.06556000790920.134969952580.2055552026250.107325204377-0.2074785462850.0396526083990.245701400638-0.392548911940.4875622131140.0219620371766-0.06577917624520.323795002125-0.05644205820120.733209547408-6.5817730358437.167341242231.1139630982
63.241459191420.365886453607-0.6741023108243.043086899190.5369449123153.55809917883-0.153747553076-0.09165367099630.1046863054830.20329742890.372898260433-0.7431037841950.270237520810.620812012797-0.2123337982540.4196098765580.0332674231578-0.04459538705520.347187879967-0.1101931374140.550295375667-3.0735759651536.1563709128.8608408884
77.420326776351.03907289495-5.895654489425.328474191641.251003367929.329262301580.636975734530.3687088361571.64137449736-1.053127132910.3061075683730.671988271657-1.19155468346-0.503113811489-0.9126562026730.7952835396860.119534440248-0.09346247471420.412017166440.04151699635530.83348808226-18.373723017870.190637370631.8123108162
82.21026898660.698256781875-0.74452721833.414045015091.082769371555.15397950856-0.0753396959526-0.009177552738350.641863436381-0.6161227711420.250431558342-0.28685603051-0.7426791527750.0707792549363-0.2257936578670.551985888243-0.01396743714970.06864110824060.299974969867-0.003504058703080.742510594282-13.123665562571.531794040542.633790919
90.499389609181-0.7430824143911.15160971045.920282701342.783379254746.776717410050.3943993700290.4089493886260.0781546032659-0.750007104760.43815560024-1.23963103402-0.7834658108050.667076854299-0.8281680645590.568751512803-0.0135165798040.05488129248380.390625002482-0.104257542820.717548415971-10.075847029266.099196463134.121610278
100.34148080107-0.318423513046-0.7195550615171.179733211081.593718934782.463039497640.21084705084-0.06633652981970.257472808232-0.5124481289930.119533743768-0.50541550029-0.4329778490090.0803607777637-0.3704667883610.5121507682550.009947531229320.04057717435950.325184822436-0.05311006892990.62743459347-12.381799061349.678155663626.8626934507
112.982262210082.694502241420.8474265065768.83057529112.895010928933.47713247038-0.2829990952340.1742896066410.852522931706-0.4865640724840.157810552980.0159376228729-0.88687582798-0.03471389649390.1717287678740.4500703825320.04233647004840.04092347880620.3643174145690.02581296694730.794048148503-12.016897998644.00179466314.6343599655
120.3273192254660.9671628954531.538133174393.020150261495.166134583219.102009575340.08545465817670.2001662755510.452571200414-0.288594039605-0.0518917001127-0.122648099353-0.408602795748-0.772323506161-0.03844559989510.3856544235140.0578251502070.0049974944920.62774655337-0.01027484323810.897634093498-18.937902010837.750087512313.0719748654
132.252434785211.840845826843.710387846968.569173945932.468284788126.421157235260.23005461149-0.226561654867-0.268257140668-0.1356220459490.271288360518-0.0585630432658-0.6456465234580.293510535933-0.5079061285210.743025368011-0.04968580166660.1549169297870.356892872315-0.02014790836970.849671900438-5.6572760157254.955874796423.8676185731
142.080590049540.955704030824-0.08649633804767.61490207590.03051715484783.469021480510.0865833031431-0.0168761267009-0.247316178224-0.842721600968-0.005078846349310.262622997610.0890792495728-0.011996036646-0.1499901709370.407600294063-0.003768712247890.0009411405063890.430896942716-0.03935329223220.549978373703-11.895684661535.070468254510.0019298532
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 83 )HA1 - 831 - 83
22chain 'H' and (resid 84 through 109 )HA84 - 10984 - 109
33chain 'H' and (resid 110 through 131 )HA110 - 131110 - 131
44chain 'H' and (resid 132 through 146 )HA132 - 146132 - 146
55chain 'H' and (resid 147 through 169 )HA147 - 169147 - 169
66chain 'H' and (resid 170 through 228 )HA170 - 228170 - 228
77chain 'L' and (resid 1 through 25 )LB1 - 251 - 25
88chain 'L' and (resid 26 through 80 )LB26 - 8026 - 80
99chain 'L' and (resid 81 through 95 )LB81 - 9581 - 95
1010chain 'L' and (resid 96 through 133 )LB96 - 13396 - 133
1111chain 'L' and (resid 134 through 155 )LB134 - 155134 - 155
1212chain 'L' and (resid 156 through 168 )LB156 - 168156 - 168
1313chain 'L' and (resid 169 through 179 )LB169 - 179169 - 179
1414chain 'L' and (resid 180 through 218 )LB180 - 218180 - 218

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