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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: To Be Published
Title: Fine antigenic mapping of human enterovirus 71 from structures of cognate complexes for a panel of 12 patient derived monoclonal antibodies
Authors: Zhou, D. / Ren, J. / Stuart, D.I.
History
DepositionJan 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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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
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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)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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