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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: 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
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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