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- PDB-9i45: Structure of anti-EV71 human monoclonal antibody 16-3-10B Fab -

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Basic information

Entry
Database: PDB / ID: 9i45
TitleStructure of anti-EV71 human monoclonal antibody 16-3-10B Fab
Components
  • heavy chain
  • light chain
KeywordsANTIVIRAL PROTEIN / EV71 / antibody / Fab / 16-3-10B
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8107
Polymers47,4322
Non-polymers3785
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-44 kcal/mol
Surface area21170 Å2
Unit cell
Length a, b, c (Å)67.803, 50.059, 74.471
Angle α, β, γ (deg.)90.00, 116.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody light chain


Mass: 22941.486 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: Protein heavy chain


Mass: 24490.398 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)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 30% (w/v) PEG 6000, 0.1 M HEPES, pH 7.0

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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: 2.12→60.67 Å / Num. obs: 25701 / % possible obs: 99.7 % / Redundancy: 6.3 % / CC1/2: 1 / Net I/σ(I): 9
Reflection shellResolution: 2.12→2.2 Å / Num. unique obs: 1197 / 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: 2.12→60.67 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 1229 5.02 %
Rwork0.2039 --
obs0.2055 24497 95.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→60.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 0 22 177 3442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023343
X-RAY DIFFRACTIONf_angle_d0.4944560
X-RAY DIFFRACTIONf_dihedral_angle_d10.1531170
X-RAY DIFFRACTIONf_chiral_restr0.044518
X-RAY DIFFRACTIONf_plane_restr0.005575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.20.39521010.34481956X-RAY DIFFRACTION72
2.2-2.30.33551360.33562408X-RAY DIFFRACTION90
2.3-2.420.33681430.30512642X-RAY DIFFRACTION97
2.42-2.580.36651410.2912652X-RAY DIFFRACTION98
2.58-2.770.26891410.26552667X-RAY DIFFRACTION99
2.77-3.050.26631290.23342684X-RAY DIFFRACTION100
3.05-3.50.25331420.20492723X-RAY DIFFRACTION100
3.5-4.40.18541540.15752724X-RAY DIFFRACTION100
4.4-60.670.171420.14482812X-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)
14.0782-0.64640.15525.44290.63882.90180.12350.0192-0.12760.0057-0.0302-0.3979-0.2206-0.0520.07420.30830.03330.05090.17490.01910.405331.5917-13.3854-0.6284
23.8106-1.3454-0.75936.00170.06013.771-0.1172-0.7925-0.48360.270.0773-0.47440.09590.20970.02560.24930.0550.01090.25570.09380.389529.799-14.34959.5812
34.3858-0.6678-0.45616.93551.20234.7313-0.205-0.35350.18320.29240.403-0.8897-0.45710.4319-0.06410.29560.0707-0.0480.199-0.00090.482930.0323-6.6856.8134
44.3385-0.41441.58784.4244-0.96585.0601-0.03481.05270.0898-0.08460.0929-0.1645-0.25590.6358-0.07260.2882-0.0499-0.0030.5761-0.02160.289912.8313-1.8496-22.0643
52.5876-1.94010.67552.0081.11354.5323-0.05340.36980.27940.10550.0944-0.175-0.15930.8506-0.18620.2890.0108-0.10680.5530.00460.403416.6524-2.0995-17.5435
63.3785-0.18130.91023.94410.16754.9236-0.15841.61460.4375-0.85320.0723-0.8107-0.42691.22450.04840.4299-0.1390.04140.99170.15430.43816.58232.9096-26.836
74.42741.0240.40285.9423-0.9064.215-0.0305-0.6685-0.10920.06050.18331.06120.3031-0.2633-0.0360.2430.05860.07850.34330.00640.252110.97944.590113.2315
84.4166-2.16341.03726.80790.123.1809-0.3253-1.03290.14150.84310.4227-0.41170.07960.0843-0.08210.33640.1062-0.01710.4804-0.03660.223220.92832.601917.7606
93.9788-0.31451.72612.9287-2.6322.4309-0.45660.51710.1838-0.52950.04470.3183-0.55430.09460.46550.2756-0.00180.03140.27470.01120.26694.44044.2085-16.0208
104.74230.56441.60394.40360.82594.3307-0.24030.33030.1360.03050.12470.1974-0.2216-0.07620.12270.31310.02370.01740.2570.07470.2859-0.63140.2987-16.6012
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 23 )
2X-RAY DIFFRACTION2chain 'L' and (resid 24 through 93 )
3X-RAY DIFFRACTION3chain 'L' and (resid 94 through 110 )
4X-RAY DIFFRACTION4chain 'L' and (resid 111 through 154 )
5X-RAY DIFFRACTION5chain 'L' and (resid 155 through 175 )
6X-RAY DIFFRACTION6chain 'L' and (resid 176 through 214 )
7X-RAY DIFFRACTION7chain 'H' and (resid 1 through 17 )
8X-RAY DIFFRACTION8chain 'H' and (resid 18 through 111 )
9X-RAY DIFFRACTION9chain 'H' and (resid 112 through 139 )
10X-RAY DIFFRACTION10chain 'H' and (resid 140 through 220 )

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