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- PDB-9i40: Structure of anti-EV71 human monoclonal antibody 16-3-4D Fab -

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Basic information

Entry
Database: PDB / ID: 9i40
TitleStructure of anti-EV71 human monoclonal antibody 16-3-4D Fab
Components
  • heavy chain
  • light chain
KeywordsANTIVIRAL PROTEIN / EV71 / antibody / 16-3-4D / Fab
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 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
L: light chain
H: heavy chain
B: heavy chain
A: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,00128
Polymers96,7004
Non-polymers2,30224
Water25214
1
L: light chain
H: heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,50314
Polymers48,3502
Non-polymers1,15312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: heavy chain
A: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,49914
Polymers48,3502
Non-polymers1,14912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.415, 121.415, 361.684
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 3 through 24 or resid 26...
d_2ens_1(chain "L" and (resid 3 through 24 or resid 26...
d_1ens_2(chain "B" and (resid 2 through 30 or resid 32...
d_2ens_2(chain "H" and (resid 2 through 30 or resid 32...

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_1VALVALGLYGLYAD3 - 243 - 24
d_12ens_1ARGARGGLYGLYAD26 - 3026 - 30
d_13ens_1LYSLYSGLNGLNAD32 - 3832 - 38
d_14ens_1LEULEUPROPROAD40 - 4540 - 45
d_15ens_1LEULEUTHRTHRAD47 - 5347 - 53
d_16ens_1ARGARGGLYGLYAD55 - 6955 - 69
d_17ens_1SERSERLEULEUAD71 - 7971 - 79
d_18ens_1ASPASPPHEPHEAD83 - 10183 - 101
d_19ens_1GLYGLYTHRTHRAD103 - 105103 - 105
d_110ens_1LEULEUVALVALAD107 - 159107 - 159
d_111ens_1ALAALAPROPROAD161 - 186161 - 186
d_112ens_1GLNGLNHISHISAD188 - 192188 - 192
d_113ens_1SERSERCYSCYSAD194 - 215194 - 215
d_21ens_1VALVALGLYGLYLA3 - 243 - 24
d_22ens_1ARGARGGLYGLYLA26 - 3026 - 30
d_23ens_1LYSLYSGLNGLNLA32 - 3832 - 38
d_24ens_1LEULEUPROPROLA40 - 4540 - 45
d_25ens_1LEULEUTHRTHRLA47 - 5347 - 53
d_26ens_1ARGARGGLYGLYLA55 - 6955 - 69
d_27ens_1SERSERLEULEULA71 - 7971 - 79
d_28ens_1ASPASPPHEPHELA83 - 10183 - 101
d_29ens_1GLYGLYTHRTHRLA103 - 105103 - 105
d_210ens_1LEULEUVALVALLA107 - 159107 - 159
d_211ens_1ALAALAPROPROLA161 - 186161 - 186
d_212ens_1GLNGLNHISHISLA188 - 192188 - 192
d_213ens_1SERSERCYSCYSLA194 - 215194 - 215
d_11ens_2LEULEUSERSERBC2 - 302 - 30
d_12ens_2SERSERSERSERBC3232
d_13ens_2TYRTYRLEULEUBC35 - 6535 - 65
d_14ens_2SERSERPROPROBC67 - 10267 - 102
d_15ens_2ALAALAGLYGLYBC104 - 105104 - 105
d_16ens_2GLYGLYASPASPBC107 - 114107 - 114
d_17ens_2TRPTRPSERSERBC116 - 141116 - 141
d_18ens_2GLYGLYLEULEUBC147 - 172147 - 172
d_19ens_2SERSERTHRTHRBC174 - 196174 - 196
d_110ens_2PROPROLEULEUBC198 - 202198 - 202
d_111ens_2TYRTYRHISHISBC207 - 213207 - 213
d_112ens_2PROPROLYSLYSBC215 - 222215 - 222
d_113ens_2VALVALVALVALBC224224
d_114ens_2PROPROASPASPBC226 - 230226 - 230
d_21ens_2LEULEUSERSERHB2 - 302 - 30
d_22ens_2SERSERSERSERHB3232
d_23ens_2TYRTYRLEULEUHB35 - 6535 - 65
d_24ens_2SERSERPROPROHB67 - 10267 - 102
d_25ens_2ALAALAGLYGLYHB104 - 105104 - 105
d_26ens_2GLYGLYASPASPHB107 - 114107 - 114
d_27ens_2TRPTRPSERSERHB116 - 141116 - 141
d_28ens_2GLYGLYLEULEUHB147 - 172147 - 172
d_29ens_2SERSERTHRTHRHB174 - 196174 - 196
d_210ens_2PROPROLEULEUHB198 - 202198 - 202
d_211ens_2TYRTYRHISHISHB207 - 213207 - 213
d_212ens_2PROPROLYSLYSHB215 - 222215 - 222
d_213ens_2VALVALVALVALHB224224
d_214ens_2PROPROASPASPHB226 - 230226 - 230

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.649233790645, -0.137067720298, -0.748136301175), (-0.226960746956, -0.903901087288, 0.362562606649), (-0.725936846031, 0.4051854692, 0.555734137087)-63.2715609087, 70.3654580135, -45.4490621744
2given(-0.706451024247, -0.190738258841, -0.681576017004), (-0.238101363106, -0.842824038923, 0.482654514431), (-0.666509333189, 0.503255954786, 0.549998866131)-57.8858261649, 72.1012676415, -49.5484442736

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Components

#1: Antibody light chain


Mass: 23097.504 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 heavy chain


Mass: 25252.293 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)
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.98 Å3/Da / Density % sol: 69.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 2% (v/v) PEG 400, 2 M ammonium sulphate,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: 2.78→90.9 Å / Num. obs: 40825 / % possible obs: 100 % / Redundancy: 18.9 % / CC1/2: 1 / Net I/σ(I): 15.5
Reflection shellResolution: 2.78→2.85 Å / Num. unique obs: 1957 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.78→90.9 Å / SU ML: 0.5899 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.5611
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2769 1957 4.98 %
Rwork0.2407 37303 -
obs0.2425 39260 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.36 Å2
Refinement stepCycle: LAST / Resolution: 2.78→90.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6656 0 121 14 6791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00226927
X-RAY DIFFRACTIONf_angle_d0.56989479
X-RAY DIFFRACTIONf_chiral_restr0.04441062
X-RAY DIFFRACTIONf_plane_restr0.0051186
X-RAY DIFFRACTIONf_dihedral_angle_d12.34152420
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DAX-RAY DIFFRACTIONTorsion NCS1.93774712205
ens_2d_2CBX-RAY DIFFRACTIONTorsion NCS2.34637036119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.850.49281090.41052420X-RAY DIFFRACTION88.77
2.85-2.930.4251470.39782590X-RAY DIFFRACTION96.07
2.93-3.010.51841340.46962620X-RAY DIFFRACTION97.11
3.01-3.110.52631610.41192638X-RAY DIFFRACTION97.9
3.11-3.220.43561380.38712651X-RAY DIFFRACTION97.65
3.22-3.350.40541360.32092670X-RAY DIFFRACTION97.8
3.35-3.50.33081460.30472644X-RAY DIFFRACTION97.04
3.5-3.690.33211440.30782647X-RAY DIFFRACTION96.71
3.69-3.920.35261450.28752620X-RAY DIFFRACTION95.51
3.92-4.220.19961230.20572641X-RAY DIFFRACTION95.61
4.22-4.640.23161320.17042668X-RAY DIFFRACTION95.69
4.64-5.320.19391520.17082693X-RAY DIFFRACTION96.11
5.32-6.70.23031400.21192789X-RAY DIFFRACTION97.41
6.7-90.90.21581500.19123012X-RAY DIFFRACTION98.11
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)
19.293324066252.440665181336.54800303115.433172386961.219338627277.084440344920.4403385857620.1035184067020.1903947872810.24132346826-0.370064713208-0.395764471520.649035320390.621453818752-0.1339949230710.7851636983280.220642416957-0.09937861636240.6608923557420.1187362173780.469865494029-13.834745340736.7339317351-36.0404069935
23.717249211962.22335581317-1.364042878117.668733887941.202210817181.310464763960.1977083221730.8512484174160.841647164717-0.546162012543-0.9414272533910.999538197130.2396685120740.639778727058-0.1573475392580.8604146354410.4031359648270.06893130239811.441207711280.401622390690.499854258913-34.819896975574.2991224945-55.0749571332
36.72990891482-0.6482761134272.336577487595.44458723011-0.5716703910134.950586907720.8164268519910.838138857575-0.619400868459-0.336720447891-0.3750297203420.8259447187450.5328257808860.277357727272-0.4527129818780.8314344526920.3272766303070.01419264260180.7469399205590.1453305566890.733996069296-44.664204199569.467982113-51.8650588864
43.50773071518-5.034524194190.0582679756386.74848581301-0.5345382666461.762461719660.1485690750160.4557691910290.464184093585-0.302463655374-0.32533335102-0.7411829842410.05365268879670.04196256354340.2209962439410.7161656699060.162177841888-0.02489565627120.8060605688380.2268793360520.676696155564-12.777549469753.6610379266-49.0017443585
55.12188778757-2.49878605728-1.177170953077.240693343831.915040111864.79974560010.2049454796330.9260234944340.785230271008-1.34903275915-0.511425196572-1.03759380979-0.1228789019530.7693636492170.3034848291421.085669223150.2097519716940.06792618135440.9293058482620.3862615906140.900485102902-6.7980128242949.7617844338-52.2243767999
66.570069207821.999518462381.360768087565.521914564881.778791848132.343809888920.0532143211953-0.25886752817-0.5014726844480.895166431936-0.121269527932-0.7476762379530.3414842319620.2129008386970.09112621989330.7364394078590.094850965945-0.1202704430130.504189722860.1600894023280.7218898355-5.85140422273-2.57915773971-15.14139797
71.72919462159-1.38808818211.415699532973.87929138171-3.152670901435.304024726570.04457162740740.369426551061-0.192963161499-0.344647898969-0.03199292762160.501386764555-0.0828238440864-0.2553585232520.04869873108630.5726340116930.142929825378-0.1789585108910.617253642655-0.1811782493860.616394496039-25.29280985417.57411177137-45.2246880297
82.885769382982.13428300383-1.206629264725.15973370343-2.592781245068.998895694330.009579583183530.242391187609-0.882994790097-0.7156724420021.464741014731.921979734150.062303414217-1.64102820417-1.446523567590.8503509501620.22036503104-0.4580903371141.01242668464-0.08712357516211.18511738702-34.7713288456.92785257401-50.5561951185
92.65936299641-0.977579248608-2.592554136822.755102400681.900726952832.966833221330.144325203615-0.05611599547120.04855913605760.0978316608832-0.190237103748-0.2964953282580.100996468419-0.07536535815580.1645676125070.7831747189380.04799772306-0.3328040194640.5795148166330.07797133407930.725290293076-2.6954369509622.7358862481-18.3268046403
103.75838249706-1.04425217903-1.00319149726.50706196807-1.369525442274.77722981291-0.248378350802-0.387494370103-0.0434259572857-0.24981342188-0.00614526292594-0.2179589075490.1036821788450.5737066762550.2116542444140.5993038695620.0789672467555-0.1893259316190.5744844451360.1306681621350.7161875526183.6279355582913.9924550513-17.5030421694
112.53022233402-0.4733190226580.450481171291.85130437327-0.1393385927024.01078243346-0.0586233297564-0.2264198068620.06392982950870.16168448057-0.25139268597-0.442005976798-0.262251778960.4892066280220.304415516310.613111382870.039192385475-0.2423263380670.5591871345130.06148832649170.7234253530080.50776040039317.7124303172-20.3486343686
120.751749831855-1.65871668997-0.7938570699718.53112025023-0.6902631099877.95668872712-0.1161020483730.1097791946810.5670557855170.02984857158370.4339553859971.760888729070.925825353826-1.2582647541-0.1954237386470.8134002298540.0972225858462-0.1617046669250.829763802707-0.08666762622440.627659658831-37.020495475818.9620137863-42.7962978768
139.148277814080.9476884844560.9226160369396.078534361420.8484532623112.479912256820.1853728839650.0755072029981-0.01555150543310.543812471767-0.2913483028920.6623189436410.0143486226634-0.1399892481820.1211693964830.7745227179570.171422415618-0.08214364401470.497960997132-0.02711243324890.41591038408-26.68085759821.3206405387-36.6647259347
141.94739101967-0.1575272097530.1236873850755.561625251761.389161154395.623283053170.4922022622550.4201856521770.0687228231689-0.180824423345-0.3740199741712.023545340310.181575840852-0.908202899428-0.09228031229570.9433429658990.26709725913-0.1751139671440.855789855482-0.02430199045671.79411945663-51.693637530650.6982656568-49.5015185221
157.31110621231-3.365882256140.341103143135.710719373450.1349922887361.676927685180.3396134448710.2975009665350.3148764601970.0116679417945-0.2569555050980.00260912756599-0.05546716459960.281598158626-0.05980917556740.8104460703310.1081096852880.0801401726130.5341822993960.07403237106570.335729094143-24.305462390745.1431401918-43.8593994063
166.289147086051.449423374542.904022753464.663633169540.2727534406974.61292024134-0.1510609551080.2571583937330.524489804804-0.137570583583-0.3454987320630.263735472661-0.4222001395880.1974856739980.5383861931990.8423553965130.208145431843-0.1417965036550.4790311387920.009432774389150.538660907417-17.47498514844.3615504934-38.9287377984
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 214 through 231 )BC214 - 231214 - 231
22chain 'A' and (resid 2 through 23 )AE2 - 231 - 22
33chain 'A' and (resid 24 through 101 )AE24 - 10123 - 100
44chain 'A' and (resid 102 through 154 )AE102 - 154101 - 153
55chain 'A' and (resid 155 through 215 )AE155 - 215154 - 214
66chain 'L' and (resid 3 through 101 )LA3 - 1011 - 99
77chain 'L' and (resid 102 through 201 )LA102 - 201100 - 199
88chain 'L' and (resid 202 through 216 )LA202 - 216200 - 214
99chain 'H' and (resid 1 through 35 )HB1 - 351 - 35
1010chain 'H' and (resid 36 through 62 )HB36 - 6236 - 62
1111chain 'H' and (resid 63 through 132 )HB63 - 13263 - 132
1212chain 'H' and (resid 133 through 147 )HB133 - 147133 - 147
1313chain 'H' and (resid 148 through 231 )HB148 - 231148 - 231
1414chain 'B' and (resid 1 through 112 )BC1 - 1121 - 112
1515chain 'B' and (resid 113 through 147 )BC113 - 147113 - 147
1616chain 'B' and (resid 148 through 213 )BC148 - 213148 - 213

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