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- PDB-9i4b: Structure of anti-EV71 human monoclonal antibody 17-2-12A Fab -

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Basic information

Entry
Database: PDB / ID: 9i4b
TitleStructure of anti-EV71 human monoclonal antibody 17-2-12A Fab
Components
  • heavy chain
  • light chain
KeywordsANTIVIRAL PROTEIN / EV71 / antibody / 17-2-12A / Fab
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 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
H: heavy chain
L: light chain
A: heavy chain
B: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9306
Polymers96,7464
Non-polymers1842
Water2,000111
1
H: heavy chain
L: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4653
Polymers48,3732
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: heavy chain
B: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4653
Polymers48,3732
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.833, 72.626, 87.781
Angle α, β, γ (deg.)104.380, 93.150, 96.560
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 61 or resid 63...
d_2ens_1(chain "H" and (resid 2 through 61 or resid 63...
d_1ens_2(chain "B" and (resid 1 through 97 or resid 99...
d_2ens_2(chain "L" and (resid 1 through 97 or resid 99...

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_1VALVALTHRTHRAC2 - 612 - 61
d_12ens_1SERSERALAALAAC63 - 8863 - 88
d_13ens_1ASPASPALAALAAC90 - 10290 - 102
d_14ens_1ARGARGSERSERAC104 - 199104 - 199
d_15ens_1GLYGLYLYSLYSAC201 - 220201 - 220
d_16ens_1VALVALLYSLYSAC222 - 225222 - 225
d_21ens_1VALVALTHRTHRHA2 - 612 - 61
d_22ens_1SERSERALAALAHA63 - 8863 - 88
d_23ens_1ASPASPALAALAHA90 - 10290 - 102
d_24ens_1ARGARGSERSERHA104 - 199104 - 199
d_25ens_1GLYGLYLYSLYSHA201 - 220201 - 220
d_26ens_1VALVALLYSLYSHA222 - 225222 - 225
d_11ens_2GLNGLNSERSERBD1 - 971 - 97
d_12ens_2LEULEUPROPROBD99 - 11499 - 114
d_13ens_2ALAALAASNASNBD116 - 133116 - 133
d_14ens_2ALAALAPROPROBD135 - 187135 - 187
d_15ens_2GLNGLNHISHISBD189 - 193189 - 193
d_16ens_2SERSERPROPROBD195 - 213195 - 213
d_21ens_2GLNGLNSERSERLB1 - 971 - 97
d_22ens_2LEULEUPROPROLB99 - 11499 - 114
d_23ens_2ALAALAASNASNLB116 - 133116 - 133
d_24ens_2ALAALAPROPROLB135 - 187135 - 187
d_25ens_2GLNGLNHISHISLB189 - 193189 - 193
d_26ens_2SERSERPROPROLB195 - 213195 - 213

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.908845324551, -0.384506398765, -0.161725091904), (-0.397820840197, 0.682367835618, 0.613280291562), (-0.125454195414, 0.621714537568, -0.773131475643)2.38066896018, 15.3089850528, -39.1654211524
2given(-0.905519048691, -0.400220684484, -0.140920744282), (-0.39822032952, 0.686955564733, 0.60787549814), (-0.146478058476, 0.606560348023, -0.781427362326)4.0881313462, 15.2338581714, -39.1351031349

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Components

#1: Antibody heavy chain


Mass: 25209.197 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: 23163.746 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3350, 0.2 M di-ammonium hydrogen citrate or 25% (w/v) PEG 3350, 0.1 M citrate, pH 3.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.68→48.12 Å / Num. obs: 27165 / % possible obs: 99.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 46.39 Å2 / CC1/2: 1 / Net I/σ(I): 4.2
Reflection shellResolution: 2.68→2.78 Å / Num. unique obs: 1277 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.68→48.12 Å / SU ML: 0.4579 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.9098
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2526 1313 4.85 %
Rwork0.2078 25781 -
obs0.2099 27094 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.22 Å2
Refinement stepCycle: LAST / Resolution: 2.68→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6507 0 12 111 6630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00276683
X-RAY DIFFRACTIONf_angle_d0.60059124
X-RAY DIFFRACTIONf_chiral_restr0.0431040
X-RAY DIFFRACTIONf_plane_restr0.00451155
X-RAY DIFFRACTIONf_dihedral_angle_d14.0822338
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2ELX-RAY DIFFRACTIONTorsion NCS0.975183071112
ens_2d_2CAX-RAY DIFFRACTIONTorsion NCS0.903137451366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.68-2.83X-RAY DIFFRACTION
2.83-2.910.32231520.30122929X-RAY DIFFRACTION99.68
2.91-3.060.31911690.27262806X-RAY DIFFRACTION99.83
3.06-3.250.32941530.25362878X-RAY DIFFRACTION99.74
3.25-3.510.28311120.2262930X-RAY DIFFRACTION99.87
3.51-3.860.2611390.19282867X-RAY DIFFRACTION99.97
3.86-4.420.2131490.1722896X-RAY DIFFRACTION99.93
4.42-5.560.18621690.15432857X-RAY DIFFRACTION99.8
5.56-48.120.21851290.19022894X-RAY DIFFRACTION99.6
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)
12.349428906830.154712612437-0.6737681893761.545489199631.122918481941.87002795172-0.1465173242380.485754371061-0.0353110425926-0.242149165183-0.06109268697460.322360723755-0.0130406854786-0.730315017722-0.007612706812450.4429809540360.0782765282587-0.06040879818010.4911415663250.07265768824470.467633173734-25.292535116241.334275214-42.3605591431
22.477106853510.3057933634480.3399594472831.655971313180.4436253542863.5371832902-0.1136665782860.2277587873980.300256060454-0.1430788020350.06950021844070.125807841644-0.525889237930.0526897023520.07192974534940.5085299871550.0488418033651-0.1050823296420.436463070880.1496583430750.399631089474-15.52159863246.243058745-40.8129206717
34.93448338535-4.23786722493-2.716656923386.844663338974.079246926354.98374508927-0.5731083738670.271079243631-0.03371017567330.464905540220.01338883040730.3765985048130.18339145726-0.3192517573190.3356054240780.342670357190.0198962882259-0.06808317923480.493427426580.09412397493730.291994054162-18.046387941937.5427672061-39.6380750637
44.36770037095-1.0756096210.3767305144384.02870489944-0.641339155874.315414019960.2259764839910.52646360125-0.549196963056-0.220920673272-0.1799973494760.04624992055890.9509479730840.241473338118-0.04500170418260.5531668071990.0152630520779-0.01253469672510.426857074542-0.1283861281980.5021311822932.5715345601811.3967925776-42.0568473255
54.11487714232-0.5295583427150.3527477855493.63814059235-0.05328698712034.47971353417-0.05808543024890.484904031978-0.5794165986140.750408976276-0.2841795161530.3286510933390.257490417878-0.323299456275-0.04059932183110.41648206498-0.06436935255320.0182697878160.428550583844-0.08601830475920.372150911051-4.0339769321313.9562601493-43.3360634644
62.06817634073-0.157423429411-1.550556086564.254726292591.103655223371.366458193950.2932690362280.566610516888-0.791247734103-0.674974327123-0.1905637848240.4292254941011.59179827083-0.3822528290360.2478292252651.258583820730.175012837382-0.1697522284370.431499501636-0.2729020204270.6657859219813.391661495594.4263652241-46.9400327537
71.76321210215-0.0513351085025-0.7247228164682.747279348590.5205587809745.77868083327-0.143825827982-0.1089905407350.209640058465-0.08619118936730.3172207169160.0378940469415-0.710144185897-0.412353650067-0.1796463202240.6506689965430.0110411680386-0.1483598215840.3631268595770.04201418303040.3754833478410.5892988056536.15039424641.56804061364
81.45636907831-0.649598362753-0.2782144727882.267779672382.395156578852.91108793419-0.201204181256-0.3944230155650.659358593908-0.1400523789870.051316765955-0.410333852824-1.77808680083-0.463009751118-0.08154482495291.199093770670.150543803131-0.2083718989340.630360991841-0.01235144041090.501819721539-0.13276952370639.445160278511.1812726021
91.24183302566-1.329738436070.5117613049371.82536586167-0.8017099498211.63726883225-0.0625080368616-0.443680255591-0.2023713343080.1078334861380.2931086049910.410574131277-0.163715277578-0.473234133988-0.2093919934640.433735454552-0.00909426306163-0.05196657393460.5326143127260.1411363168610.413777659148-5.3168122112510.2943829156-0.984074104691
102.641995201330.00876336281358-0.577241474847.80838376564-1.636289026853.76710340087-0.0850112148853-0.4264302808670.1013245939780.274068939152-0.19654292643-0.753861050248-0.2957581587930.4406117639540.1320319618230.212218171817-0.0572770406992-0.04056383108470.591701409996-0.05894819725780.29394666620316.479895529727.56454518922.4604729035
111.88058903762-0.0245775027758-0.6406861980465.32447487843-0.5326856791114.10601017616-0.182777536881-0.5383187994520.2043814940550.2362439638170.2570704928780.200454440781-0.234896411968-0.345522286764-0.0839831683460.5212646279170.0712747364954-0.1404887306960.617275936317-0.03019502113860.3026510822535.4529591760728.261764054123.0341058348
122.5746396252.00037497827-1.485588997598.88322186915-3.468720841351.64123220183-0.347981391498-0.9002490109460.454308162028-0.315938766982-0.320854504552-1.37534466998-0.4229728858910.681489536037-0.07238524952680.898257252278-0.191161034723-0.1609746635450.34753808747-0.1317625249740.42239214987312.897080804338.460541134612.7114788196
130.7464247006351.463868158381.302506811672.599120325112.352459813682.50186631268-0.1994542671320.0342745849713-0.403690723518-0.02916661400530.580364245114-0.7990967802690.582651150655-0.104913784792-0.265257005960.6032128649250.0335828801549-0.1699180495420.5536818801880.08801858038950.4333034309248.70980855297.6738261335122.0409927705
142.160375312650.6497244575940.7463901347324.762522660221.299468319382.012679004310.0364340656995-0.111346605021-0.41490543915-0.7081896918870.7503420420190.280967708660.692344059012-0.8078477650040.09417228102110.589568427456-0.111039609605-0.09837970548340.4101416523240.03399020956220.49001668552-2.10260431105-4.77378243543-6.94728384905
152.10380062006-0.883941225478-0.5389246105984.324926514521.950471446037.246446729530.020351431427-0.268434099578-0.3373140305510.06713097243610.221438620279-0.02139682613740.1446398135170.433133372542-0.1442398018960.383667391412-0.0773437451062-0.09703673008540.3916937140830.1306857176630.447117506877.51935360987-0.6981916304764.91564195972
162.721507583590.301003398919-1.414384665696.720836998991.267385233935.60561312402-0.190750313565-0.0014095513271-0.657261631349-0.505088242030.130862124319-0.2362412026561.058610001130.791734574721-0.0714299391340.611173352912-0.00760692725941-0.1091764988120.3465021818190.04419968169650.543740373926.71336192476-11.4359699609-4.09562904202
173.96704837397-1.26193146209-1.932075654246.909373907830.1261593919968.752697165980.0973659889501-0.585992619922-0.901371214078-0.4565998932440.0714050269738-0.1130946632530.795005377461-0.42922682864-0.2179775576570.535052155143-0.0198736452686-0.1525750360030.3569828127750.1036353528270.4750928548654.80752434237-11.23693699086.15986815459
181.80958197479-0.1640205199750.311037525063.51627915812-0.3023545528412.87592032955-0.346121209517-0.1718304695060.125286863560.5102296243640.2292199047190.086292019934-0.588319561766-0.1562250018150.1237849753870.6614405779190.0391604542256-0.09068687899810.3671378529490.005534340714140.281137061629-11.580425881940.0099723158-18.5170441065
191.35787387425-0.544208450283-0.03559826823270.902495464951-0.0996918555941.46169396094-0.01503219277370.009192495844760.0882235799514-0.1350923109120.0289951616979-0.208640936422-0.1402662079330.1159271766230.001175509781110.388566443765-0.0430875157558-0.06492803599960.3325507926250.01073496414080.3442481846441.7677825281826.7895081517-30.2612575794
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 1 through 30 )BF1 - 301 - 30
22chain 'B' and (resid 31 through 91 )BF31 - 9131 - 91
33chain 'B' and (resid 92 through 118 )BF92 - 11892 - 118
44chain 'B' and (resid 119 through 155 )BF119 - 155119 - 155
55chain 'B' and (resid 156 through 185 )BF156 - 185156 - 185
66chain 'B' and (resid 186 through 213 )BF186 - 213186 - 213
77chain 'H' and (resid 1 through 91 )HA1 - 911 - 91
88chain 'H' and (resid 92 through 106 )HA92 - 10692 - 106
99chain 'H' and (resid 107 through 225 )HA107 - 225107 - 219
1010chain 'L' and (resid 1 through 30 )LB1 - 301 - 30
1111chain 'L' and (resid 31 through 91 )LB31 - 9131 - 91
1212chain 'L' and (resid 92 through 105 )LB92 - 10592 - 105
1313chain 'L' and (resid 106 through 118 )LB106 - 118106 - 118
1414chain 'L' and (resid 119 through 134 )LB119 - 134119 - 134
1515chain 'L' and (resid 135 through 185 )LB135 - 185135 - 185
1616chain 'L' and (resid 186 through 202 )LB186 - 202186 - 202
1717chain 'L' and (resid 203 through 214 )LB203 - 214203 - 214
1818chain 'A' and (resid 1 through 91 )AD1 - 911 - 91
1919chain 'A' and (resid 92 through 225 )AD92 - 22592 - 219

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