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- PDB-3rkd: Hepatitis E Virus E2s domain (Genotype I) in complex with a neutr... -

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Basic information

Entry
Database: PDB / ID: 3rkd
TitleHepatitis E Virus E2s domain (Genotype I) in complex with a neutralizing antibody
Components
  • Capsid protein
  • Monoclonal Antibody, Heavy Chain
  • Monoclonal Antibody, Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Hepatitis E virus capsid protein / neutralizing antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endoplasmic reticulum / T=1 icosahedral viral capsid / host cell surface / host cell Golgi apparatus / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding / extracellular region / identical protein binding
Similarity search - Function
Hepatitis E virus structural protein 2 / Structural protein 2 nucleoplasmin-like domain / : / Structural protein 2 second domain / : / Structural protein 2 C-terminal domain / Viral coat protein subunit / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pro-secreted protein ORF2 / Pro-secreted protein ORF2
Similarity search - Component
Biological speciesHepatitis E virus
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTang, X.H. / Sivaraman, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis for the neutralization and genotype specificity of hepatitis E virus
Authors: Tang, X.H. / Yang, C.Y. / Gu, Y. / Song, C.L. / Zhang, X. / Wang, Y.B. / Zhang, J. / Hew, C.L. / Li, S.W. / Xia, N.S. / Sivaraman, J.
History
DepositionApr 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 3, 2013Group: Database references
Revision 1.3Oct 25, 2017Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Revision 1.4Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
L: Monoclonal Antibody, Light Chain
H: Monoclonal Antibody, Heavy Chain
C: Monoclonal Antibody, Light Chain
D: Monoclonal Antibody, Heavy Chain


Theoretical massNumber of molelcules
Total (without water)127,2706
Polymers127,2706
Non-polymers00
Water13,709761
1
A: Capsid protein
L: Monoclonal Antibody, Light Chain
H: Monoclonal Antibody, Heavy Chain


Theoretical massNumber of molelcules
Total (without water)63,6353
Polymers63,6353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-30 kcal/mol
Surface area24990 Å2
MethodPISA
2
B: Capsid protein
C: Monoclonal Antibody, Light Chain
D: Monoclonal Antibody, Heavy Chain


Theoretical massNumber of molelcules
Total (without water)63,6353
Polymers63,6353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-30 kcal/mol
Surface area24590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.479, 95.198, 108.305
Angle α, β, γ (deg.)90.00, 107.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsid protein / Protein ORF2 / pORF2


Mass: 15510.313 Da / Num. of mol.: 2 / Fragment: UNP residues 459-603 / Mutation: Y532H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis E virus / Gene: ORF2 / Plasmid: pTO-T7 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: B0VX51, UniProt: P33426*PLUS
#2: Antibody Monoclonal Antibody, Light Chain


Mass: 23648.018 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Myeloma Cell Line / Strain: Sp2/0 Ag15
#3: Antibody Monoclonal Antibody, Heavy Chain


Mass: 24476.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Myeloma Cell Line / Strain: Sp2/0 Ag15
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 761 / Source method: isolated from a natural source / Formula: H2O
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: 2.88 Å3/Da / Density % sol: 57.29 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M HEPEPS, 0.4M KSCN, 0.4M NH4Cl, 18% PEG 3350, 5% w/v n-Dodecyl-beta-D-maltoside, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 112759 / Redundancy: 6.4 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GGQ and 1QBL

3ggq

1qbl


Resolution: 1.9→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 9963 -RANDOM
Rwork0.1885 ---
obs-99759 87.9 %-
Solvent computationBsol: 45.6126 Å2
Displacement parametersBiso mean: 26.0299 Å2
Baniso -1Baniso -2Baniso -3
1--0.016 Å20 Å20.947 Å2
2---1.124 Å20 Å2
3---1.14 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8772 0 0 761 9533
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1.384

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