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- PDB-9i4d: Structure of anti-EV71 human monoclonal antibody 17-2-2B Fab -

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Basic information

Entry
Database: PDB / ID: 9i4d
TitleStructure of anti-EV71 human monoclonal antibody 17-2-2B Fab
Components
  • heavy chain
  • light chain
KeywordsANTIVIRAL PROTEIN / EV71 / antibody / Fab / 17-2-2B
Function / homologyACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 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)96,41414
Polymers95,7464
Non-polymers66810
Water1,928107
1
H: heavy chain
L: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0405
Polymers47,8732
Non-polymers1673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-57 kcal/mol
Surface area19830 Å2
MethodPISA
2
A: heavy chain
B: light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3749
Polymers47,8732
Non-polymers5017
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-73 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.480, 71.660, 93.060
Angle α, β, γ (deg.)90.00, 105.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 4 molecules HALB

#1: Antibody heavy chain


Mass: 25055.869 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: 22817.068 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) / Strain (production host): HEK2

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Non-polymers , 4 types, 117 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 30% (w/v) polyethylene glycol monomethyl ether 2000, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.56→49.98 Å / Num. obs: 29400 / % possible obs: 98.6 % / Redundancy: 11.9 % / CC1/2: 1 / Net I/σ(I): 9.7
Reflection shellResolution: 2.56→2.65 Å / Num. unique obs: 1109 / CC1/2: 0.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→49.98 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2431 1397 4.76 %
Rwork0.1942 --
obs0.1965 29372 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→49.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6502 0 35 107 6644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026707
X-RAY DIFFRACTIONf_angle_d0.5829166
X-RAY DIFFRACTIONf_dihedral_angle_d12.4992343
X-RAY DIFFRACTIONf_chiral_restr0.0441027
X-RAY DIFFRACTIONf_plane_restr0.0051158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.650.31861190.29592448X-RAY DIFFRACTION87
2.65-2.760.33381320.28542833X-RAY DIFFRACTION100
2.76-2.880.29821420.26982792X-RAY DIFFRACTION100
2.88-3.040.31381430.25272804X-RAY DIFFRACTION100
3.04-3.220.26491540.23322801X-RAY DIFFRACTION100
3.23-3.470.29031190.20952868X-RAY DIFFRACTION100
3.47-3.820.22511300.19072838X-RAY DIFFRACTION100
3.82-4.380.20051460.15522829X-RAY DIFFRACTION100
4.38-5.510.18341530.14362861X-RAY DIFFRACTION100
5.51-49.980.24461590.17192901X-RAY DIFFRACTION100
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)
11.14830.8435-0.82821.0137-0.04462.67050.0161-0.06540.14420.59370.07410.2136-0.6077-0.2167-0.01570.8250.17670.13220.4150.03810.5457-3.766117.675632.8289
21.71690.69890.98762.1830.32171.9256-0.13820.0891-0.2466-0.04190.11630.12980.02970.0037-0.05070.2188-0.00350.03840.24880.00350.4591-3.36826.57393.2958
31.4899-0.67140.2642.02070.30852.83280.1107-0.0917-0.17250.5530.0547-0.0754-0.0048-0.4085-0.03970.69980.0610.10660.38790.0440.456-1.0014-2.915238.6266
40.00190.1074-0.18982.0793-2.97916.63610.1521-0.13030.18930.0377-0.10220.16890.5067-0.0189-0.01230.3772-0.05630.00780.28320.06290.54580.9763-13.7139.1474
51.8795-0.37410.07343.2316-1.66583.5477-0.07840.15190.16240.14020.12970.0924-0.2131-0.0392-0.05840.265-0.01160.00820.2568-0.01560.41668.2921-2.79921.0262
62.6512-0.2601-1.42233.6661-1.45145.18880.01010.00030.0033-0.60050.1427-0.25530.81720.2206-0.01730.35830.0140.04490.3212-0.0230.31739.2457-11.1849-3.6574
71.92240.59280.7762.08820.87112.8206-0.0125-0.117-0.14440.58150.0748-0.34220.20620.2566-0.00130.55930.0245-0.01840.30740.00830.42531.2404-2.17732.5273
81.30570.2916-0.31680.7166-0.40181.91580.00570.11120.2044-0.01-0.00870.0483-0.0931-0.03020.02180.23680.02490.00250.208-0.0480.406535.33669.64045.5475
91.169-0.89340.11631.11160.26450.61680.11470.22370.0298-0.01090.0034-0.2736-0.00410.09760.00650.2774-0.0456-0.0810.2442-0.00520.574445.514115.53450.4087
103.36741.3855-1.20562.4593-0.53381.0292-0.0886-0.02630.0745-0.1308-0.1238-0.0726-0.1951-0.04920.12750.23070.0241-0.00610.19870.02950.400741.66823.46122.6922
111.39510.34420.16322.9160.56562.03950-0.0107-0.0710.43640.01380.0776-0.16530.1094-0.030.7206-0.0112-0.04550.3031-0.04430.377728.719618.388738.3334
121.5905-0.39040.10493.90161.19683.02250.02780.04190.02480.08890.02240.0540.1351-0.1414-0.05020.24590.0146-0.00480.2180.00880.425129.092822.1643-1.0234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 113 )
2X-RAY DIFFRACTION2chain 'H' and (resid 114 through 225 )
3X-RAY DIFFRACTION3chain 'L' and (resid 0 through 107 )
4X-RAY DIFFRACTION4chain 'L' and (resid 108 through 120 )
5X-RAY DIFFRACTION5chain 'L' and (resid 121 through 189 )
6X-RAY DIFFRACTION6chain 'L' and (resid 190 through 211 )
7X-RAY DIFFRACTION7chain 'A' and (resid 1 through 113 )
8X-RAY DIFFRACTION8chain 'A' and (resid 114 through 185 )
9X-RAY DIFFRACTION9chain 'A' and (resid 186 through 204 )
10X-RAY DIFFRACTION10chain 'A' and (resid 205 through 224 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 107 )
12X-RAY DIFFRACTION12chain 'B' and (resid 108 through 211 )

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