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- PDB-9i3x: Structure of anti-EV71 human monoclonal antibody 16-2-11B Fab -

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Basic information

Entry
Database: PDB / ID: 9i3x
TitleStructure of anti-EV71 human monoclonal antibody 16-2-11B Fab
Components
  • heavy chain
  • light chain
KeywordsANTIVIRAL PROTEIN / EV71 / antibody / 16-2-11B / Fab
Function / homologyFORMIC ACID / IMIDAZOLE
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 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
A: light chain
B: heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,04917
Polymers96,3314
Non-polymers71813
Water1,56787
1
L: light chain
H: heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,71312
Polymers48,1662
Non-polymers54710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: light chain
B: heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3365
Polymers48,1662
Non-polymers1703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.319, 83.945, 84.955
Angle α, β, γ (deg.)90.000, 103.500, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 2 through 24 or resid 26...
d_2ens_1(chain "L" and (resid 2 through 24 or resid 26...
d_1ens_2(chain "B" and (resid 2 or resid 4 through 12...
d_2ens_2(chain "H" and (resid 2 or resid 4 through 12...

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_1SERSERGLYGLYAC2 - 242 - 24
d_12ens_1SERSERVALVALAC26 - 5326 - 53
d_13ens_1ASNASNSERSERAC55 - 6155 - 61
d_14ens_1ARGARGTHRTHRAC63 - 10563 - 105
d_15ens_1LEULEUVALVALAC107 - 109107 - 109
d_16ens_1PROPROTRPTRPAC113 - 152113 - 152
d_17ens_1ALAALAALAALAAC154154
d_18ens_1SERSERVALVALAC156 - 163156 - 163
d_19ens_1THRTHRHISHISAC165 - 192165 - 192
d_110ens_1TYRTYRVALVALAC195 - 206195 - 206
d_111ens_1LYSLYSCYSCYSAC208 - 215208 - 215
d_21ens_1SERSERGLYGLYLA2 - 242 - 24
d_22ens_1SERSERVALVALLA26 - 5326 - 53
d_23ens_1ASNASNSERSERLA55 - 6155 - 61
d_24ens_1ARGARGTHRTHRLA63 - 10563 - 105
d_25ens_1LEULEUVALVALLA107 - 109107 - 109
d_26ens_1PROPROTRPTRPLA113 - 152113 - 152
d_27ens_1ALAALAALAALALA154154
d_28ens_1SERSERVALVALLA156 - 163156 - 163
d_29ens_1THRTHRHISHISLA165 - 192165 - 192
d_210ens_1TYRTYRVALVALLA195 - 206195 - 206
d_211ens_1LYSLYSCYSCYSLA208 - 215208 - 215
d_11ens_2VALVALVALVALBD22
d_12ens_2LEULEULYSLYSBD4 - 124 - 12
d_13ens_2PROPROLYSLYSBD14 - 2314 - 23
d_14ens_2SERSERGLYGLYBD25 - 4225 - 42
d_15ens_2GLYGLYGLNGLNBD44 - 6244 - 62
d_16ens_2PHEPHEPHEPHEBD6464
d_17ens_2GLYGLYTHRTHRBD66 - 7466 - 74
d_18ens_2SERSERSERSERBD7777
d_19ens_2VALVALGLYGLYBD79 - 10279 - 102
d_110ens_2CYSCYSSERSERBD104 - 139104 - 139
d_111ens_2GLYGLYVALVALBD144 - 161144 - 161
d_112ens_2VALVALTHRTHRBD163 - 171163 - 171
d_113ens_2GLYGLYSERSERBD173 - 198173 - 198
d_114ens_2LEULEUTHRTHRBD200 - 202200 - 202
d_115ens_2THRTHRTHRTHRBD204 - 216204 - 216
d_116ens_2VALVALSERSERBD218 - 226218 - 226
d_21ens_2VALVALVALVALHB22
d_22ens_2LEULEULYSLYSHB4 - 124 - 12
d_23ens_2PROPROLYSLYSHB14 - 2314 - 23
d_24ens_2SERSERGLYGLYHB25 - 4225 - 42
d_25ens_2GLYGLYGLNGLNHB44 - 6244 - 62
d_26ens_2PHEPHEPHEPHEHB6464
d_27ens_2GLYGLYTHRTHRHB66 - 7466 - 74
d_28ens_2SERSERSERSERHB7777
d_29ens_2VALVALGLYGLYHB79 - 10279 - 102
d_210ens_2CYSCYSSERSERHB104 - 139104 - 139
d_211ens_2GLYGLYVALVALHB144 - 161144 - 161
d_212ens_2VALVALTHRTHRHB163 - 171163 - 171
d_213ens_2GLYGLYSERSERHB173 - 198173 - 198
d_214ens_2LEULEUTHRTHRHB200 - 202200 - 202
d_215ens_2THRTHRTHRTHRHB204 - 216204 - 216
d_216ens_2VALVALSERSERHB218 - 226218 - 226

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(-0.772094237023, 0.58117985935, 0.25710009771), (0.53119919298, 0.368119826656, 0.76309580696), (0.348852270357, 0.725753239269, -0.592945468958)-44.410359915, -38.3901441154, 106.971325966
2given(-0.760904579887, 0.572264613552, 0.305838899396), (0.50921687405, 0.234524513356, 0.828067888411), (0.402147231111, 0.785818977062, -0.469857573951)-48.4343484542, -45.0644443873, 99.5002109972

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Components

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Antibody , 2 types, 4 molecules LAHB

#1: Antibody light chain


Mass: 22870.238 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: 25295.326 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)

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Non-polymers , 4 types, 100 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3350, 0.2 M sodium formate

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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: May 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.57→82.61 Å / Num. obs: 32644 / % possible obs: 99 % / Redundancy: 6.7 % / Biso Wilson estimate: 65.46 Å2 / CC1/2: 1 / Net I/σ(I): 14.4
Reflection shellResolution: 2.57→2.65 Å / Num. unique obs: 1595 / CC1/2: 0.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→82.61 Å / SU ML: 0.4469 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.2937
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2553 1588 4.89 %
Rwork0.2087 30858 -
obs0.211 32446 98.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.83 Å2
Refinement stepCycle: LAST / Resolution: 2.57→82.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6603 0 47 87 6737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00376819
X-RAY DIFFRACTIONf_angle_d0.68699279
X-RAY DIFFRACTIONf_chiral_restr0.04741054
X-RAY DIFFRACTIONf_plane_restr0.00691186
X-RAY DIFFRACTIONf_dihedral_angle_d13.56592414
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CAX-RAY DIFFRACTIONTorsion NCS1.95266668447
ens_2d_2DBX-RAY DIFFRACTIONTorsion NCS2.41482657559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.57-2.650.44491510.43462724X-RAY DIFFRACTION96.19
2.65-2.750.40381430.36952722X-RAY DIFFRACTION97.15
2.75-2.860.41331330.33222784X-RAY DIFFRACTION97.85
2.86-2.990.32491420.30232780X-RAY DIFFRACTION97.79
2.99-3.140.32511340.28552828X-RAY DIFFRACTION98.47
3.14-3.340.32981360.28472789X-RAY DIFFRACTION98.68
3.34-3.60.28111600.24072825X-RAY DIFFRACTION99.04
3.6-3.960.27331560.21132810X-RAY DIFFRACTION99.06
3.96-4.530.2141590.16942809X-RAY DIFFRACTION99.26
4.54-5.710.18561350.14452869X-RAY DIFFRACTION99.34
5.71-82.610.2041390.15742918X-RAY DIFFRACTION99.32
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)
12.82720847673-1.05869125832-0.8806690058031.41633410066-0.798818701392.242419117010.3150016605680.8146712595670.133992195751-0.690503226038-0.1986396498080.7637624331560.179278252515-1.049209649750.1304780772810.785645190268-0.0712949556838-0.007267857788221.31450012353-0.3739732278720.951521801659-55.7652243462-0.69249866998372.4719068187
24.517292657190.0480353242886-1.691122088083.304354078-0.8627927987952.4765636830.304455691420.9725999098080.784499304688-0.495780847023-0.1693426093570.0263837340547-0.292507938112-0.764152314731-0.07665804103310.7212972209720.02665941247470.104372129141.13679088333-0.1777318900520.819210720664-52.87382261625.8697288220278.4140774776
32.885005278520.0323270770917-1.959940250330.8963788333330.3939002233281.956222844060.347602354459-0.3872122586990.4591667531340.172954133092-0.29066041460.1600509264720.0125196285419-0.319187209926-0.07923084654030.616222056715-0.2032452941310.008766903115260.932984734494-0.3065459648770.473291178015-36.3963888233-7.691236335176.1021967542
42.50957618623-1.148533426440.5639431709864.31509098538-0.5204205033392.196043676480.0752926558201-0.417233319205-0.00875115525650.1839105300590.3201008136620.07630736456020.121124074869-0.148821402229-0.4031848728130.522574151129-0.1092100926310.01153384645230.691863836507-0.04293539511280.424753169643-23.0590567341-15.76814121366.8782096207
54.063198254380.637653618508-0.232018442724.679158772450.6133061278233.224197151080.3691698025230.3593170974720.2292654344-0.3069103305860.0636056651099-0.2371795256330.09776379287030.0396888282796-0.5801063343810.6806164934980.154280259568-0.04705112580790.402099666633-0.008112202666960.5295839500899.6375665727910.044819044426.8052613489
65.73112535685-2.81269482461.333698076321.94623048871-1.639946054143.146733239140.4465714200650.577323372797-0.111903489809-0.491166335069-0.251601374707-0.1874350653010.240729119341-0.0977518622782-0.2264910347630.59109374950.024481414027-0.02055882888220.381099606639-0.09205226527430.43845961673716.20263372343.3162017550626.5509631076
73.526469391530.930932213659-1.398449795391.15719429746-1.34904402152.502861499540.302589860188-0.07979296745630.7053248699730.195921308257-0.007994472304030.217488410507-0.3390023746060.231341075557-0.348440124840.522521246031-0.0988201421735-0.009943412927740.428092929169-0.05884721545310.623898080556-14.65781667019.5227072668443.9089254376
83.53183680799-0.867943237619-1.249397712883.175759245372.463249443977.316094848320.2932438602750.3938676086030.894105742201-0.0355239754358-0.2829914997650.51325764256-0.950615727585-0.755743007215-0.1191539802660.842182982554-0.0517278001992-0.01396926007740.5281147876840.02692115124410.980135008876-19.057741525917.844668483942.7554394555
95.74238434391-0.1710489175010.09384948690721.49518720283-0.4745415820814.494507958070.0436614374306-0.280533962409-0.4378567775210.01711409534990.02366927693520.08953106614660.28065485863-0.175111310427-0.05086068323550.444300560618-0.0481763517136-0.0508019898440.297483905640.007418909699920.46442626489619.3957351224-8.2227502113244.8342846505
104.362018563761.08385502520.1739333305191.669862723340.1348467718314.380239423350.1103164632880.581725974506-0.616714240818-0.2874092782430.109477303768-0.07925400070560.3740878392820.1874496927430.0121078434120.5527618273730.0491506281532-0.06870407616140.432828835018-0.1294608046650.53906420481521.7273646534-5.9578488144535.15717109
113.607388354770.65008676743-1.127512092222.32335162963-0.9339471784162.91633348009-0.165313379533-0.6674722367650.148964233186-0.0399809230110.333588361154-0.0529800616472-0.189608594376-0.408607039624-0.1382918550980.545863372242-0.04181116119650.09714291489730.42247364298-0.06100639653120.509827543717-20.60857274611.0412062248.9777723642
123.99841135921-0.664132285189-0.5779625665581.68318847822-1.804904250022.620087508180.258457012911-0.06096284199970.18148291024-0.239143183018-0.233325807148-0.03657006464160.2376964474190.249480971504-0.07649335888240.4184087996670.02112864658850.0365257865390.317833019198-0.08280028125280.412121090609-19.8567107268-5.0220982751645.4743724498
135.56839375572.31816126536-0.1221119921571.5347464407-1.824444199456.345299201660.318401323969-0.3104701898530.4645739472480.359977260117-0.02812298027531.06762988526-0.250464697319-0.999820263858-0.2754288582950.563952926388-0.002856794259770.07402129385510.572760208674-0.03788606596660.756151181345-28.6111819719-2.8507720303451.6327060598
144.551490016021.09369242795-0.5313306870333.113947501930.6557086784875.11126465695-0.16291665016-1.18323241042-0.849035291460.150828901769-0.267938239082-1.072750484590.7070019626330.8404134785640.4322185230990.8471408895-0.07907383047780.0588472548921.238282812350.1026918496431.01950144108-45.1629691986-9.81564072927100.427258849
153.853031966160.655876848444-0.2712582701562.48945716658-1.937510367094.90740407188-0.164476018244-0.627948278526-0.394078949802-0.128812382094-0.05644020331840.3072201229020.368097261359-0.3528014722640.2337627309860.679180049649-0.1767985426510.1456685364361.03254641912-0.1499715845290.737387189534-54.204630893-7.4164351615595.120067435
161.98425439379-1.77364498382-0.6394300747132.374298470681.287593808320.889060151126-0.388308246509-0.640589611695-0.2750266836670.1890663843030.3210892089870.1173960137130.1493426226870.3736418396760.04182374242780.56466340047-0.0469868989666-0.1165619711930.977290701704-0.1207785892180.631881540704-21.4849737456-13.841202067481.5582223146
171.90339304948-2.21119520715-1.040041807983.64249875956-0.5839956017464.78249549608-0.384722393255-1.102134951920.5931011886331.0400521240.5361281106320.315466774518-0.464800760752-0.0451704223147-0.04445537874310.8535623222680.1402817120530.04785777568051.28848564778-0.1689538001310.587200732378-22.0604217476-11.192884709484.9462473078
183.14647109058-0.314794144665-1.079449712924.23201122223-1.965566234522.63245635315-0.141375556472-0.833740850196-0.1316281647251.065448894990.11049606008-0.889230340912-0.5329718321550.5009989236330.1040578555590.946673795264-0.0267509902207-0.1769130500971.33369220342-0.2958996391150.754047415247-12.0764914508-9.6121509040482.9117362592
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 33 )BD1 - 331 - 33
22chain 'B' and (resid 34 through 98 )BD34 - 9834 - 98
33chain 'B' and (resid 99 through 156 )BD99 - 15699 - 156
44chain 'B' and (resid 157 through 227 )BD157 - 227157 - 227
55chain 'L' and (resid 1 through 23 )LA1 - 231 - 23
66chain 'L' and (resid 24 through 110 )LA24 - 11024 - 110
77chain 'L' and (resid 111 through 191 )LA111 - 191111 - 191
88chain 'L' and (resid 192 through 215 )LA192 - 215192 - 215
99chain 'H' and (resid 1 through 98 )HB1 - 981 - 98
1010chain 'H' and (resid 99 through 122 )HB99 - 12299 - 122
1111chain 'H' and (resid 123 through 156 )HB123 - 156123 - 156
1212chain 'H' and (resid 157 through 214 )HB157 - 214157 - 214
1313chain 'H' and (resid 215 through 228 )HB215 - 228215 - 228
1414chain 'A' and (resid 2 through 23 )AC2 - 231 - 22
1515chain 'A' and (resid 24 through 104 )AC24 - 10423 - 103
1616chain 'A' and (resid 105 through 133 )AC105 - 133104 - 132
1717chain 'A' and (resid 134 through 175 )AC134 - 175133 - 174
1818chain 'A' and (resid 176 through 216 )AC176 - 216175 - 215

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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