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- PDB-9i4e: Structure of anti-EV71 human monoclonal antibody 34-1-6D Fab -

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Basic information

Entry
Database: PDB / ID: 9i4e
TitleStructure of anti-EV71 human monoclonal antibody 34-1-6D Fab
Components
  • heavy chain
  • light chain
KeywordsANTIVIRAL PROTEIN / EV71 / antibody / 34-1-6D / Fab
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsZhou, D. / Ren, J. / Stuart, D.I.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom) United Kingdom
Wellcome Trust 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
B: light chain
A: heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,32512
Polymers95,8294
Non-polymers4978
Water12,142674
1
L: light chain
H: heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1636
Polymers47,9142
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-19 kcal/mol
Surface area19120 Å2
MethodPISA
2
B: light chain
A: heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1636
Polymers47,9142
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-12 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.164, 55.981, 75.399
Angle α, β, γ (deg.)86.69, 86.39, 67.06
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody light chain


Mass: 23228.732 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: Protein heavy chain


Mass: 24685.678 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 674 / 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: 2.19 Å3/Da / Density % sol: 43.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 30% (w/v) PEG 3000, 0.1 M CHES, pH 9.6

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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: Jan 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.63→75.2 Å / Num. obs: 98557 / % possible obs: 97.1 % / Redundancy: 3.4 % / CC1/2: 1 / Net I/σ(I): 11.2
Reflection shellResolution: 1.63→1.672 Å / Num. unique obs: 4808 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.63→75.2 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.963 / SU B: 7.637 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20884 4593 4.7 %RANDOM
Rwork0.15837 ---
obs0.16077 93499 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.983 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20.64 Å2-0.12 Å2
2--1.51 Å20.83 Å2
3----0.8 Å2
Refinement stepCycle: 1 / Resolution: 1.63→75.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6518 0 32 674 7224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0126836
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166294
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.8029338
X-RAY DIFFRACTIONr_angle_other_deg0.4861.72614631
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9375918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.778519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.793101101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0690.21074
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028012
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021516
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it9.183.663510
X-RAY DIFFRACTIONr_mcbond_other9.1783.663510
X-RAY DIFFRACTIONr_mcangle_it12.8576.5844395
X-RAY DIFFRACTIONr_mcangle_other12.8576.5844396
X-RAY DIFFRACTIONr_scbond_it9.7833.9893326
X-RAY DIFFRACTIONr_scbond_other9.7823.9893327
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.0397.1684915
X-RAY DIFFRACTIONr_long_range_B_refined20.22241.447164
X-RAY DIFFRACTIONr_long_range_B_other19.606406984
X-RAY DIFFRACTIONr_rigid_bond_restr4.034313130
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 309 -
Rwork0.338 6737 -
obs--93.61 %

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