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- PDB-3ggq: Dimerization of Hepatitis E Virus Capsid Protein E2s Domain is Es... -

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Basic information

Entry
Database: PDB / ID: 3ggq
TitleDimerization of Hepatitis E Virus Capsid Protein E2s Domain is Essential for Virus-Host Interaction
ComponentsCapsid proteinCapsid
KeywordsVIRAL PROTEIN / BETA BARREL / Capsid protein / RNA-binding
Function / homology
Function and homology information


T=1 icosahedral viral capsid / host cell endoplasmic reticulum / host cell Golgi apparatus / host cell surface / 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
: / : / Structural protein 2 second domain / Structural protein 2 C-terminal domain / Hepatitis E virus structural protein 2 / Structural protein 2 nucleoplasmin-like domain / Viral coat protein subunit
Similarity search - Domain/homology
BROMIDE ION / Pro-secreted protein ORF2
Similarity search - Component
Biological speciesHepatitis E virus genotype 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsLi, S.W. / Tang, X.H. / Seetharaman, J. / Yang, C.Y. / Gu, Y. / Zhang, J. / Du, H.L. / Shih, J.W.K. / Hew, C.L. / Sivaraman, J. / Xia, N.S.
CitationJournal: Plos Pathog. / Year: 2009
Title: Dimerization of hepatitis E virus capsid protein E2s domain is essential for virus-host interaction
Authors: Li, S. / Tang, X. / Seetharaman, J. / Yang, C. / Gu, Y. / Zhang, J. / Du, H. / Shih, J.W. / Hew, C.L. / Sivaraman, J. / Xia, N.
History
DepositionMar 2, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0394
Polymers15,8001
Non-polymers2403
Water4,396244
1
A: Capsid protein
hetero molecules

A: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0798
Polymers31,5992
Non-polymers4796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
Buried area3100 Å2
ΔGint-16 kcal/mol
Surface area11920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.448, 111.448, 84.333
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Capsid protein / Capsid / Protein ORF2 / pORF2 / Capsid Protein E2s Domain


Mass: 15799.662 Da / Num. of mol.: 1 / Fragment: UNP residues 455-602 / Mutation: Y532H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hepatitis E virus genotype 1 / Gene: ORF2 / Plasmid: pTO-T7 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: P33426
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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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: 3.19 Å3/Da / Density % sol: 61.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, pH7.5, 12% PEG3350, 5mM cobalt chloride hexahydrate, 5mM nickel (II) chloride hexahydrate, 5mM cadmium chloride dehydrate, 5mM magnesium chloride hexahydrate, VAPOR DIFFUSION, ...Details: 0.1M HEPES, pH7.5, 12% PEG3350, 5mM cobalt chloride hexahydrate, 5mM nickel (II) chloride hexahydrate, 5mM cadmium chloride dehydrate, 5mM magnesium chloride hexahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9206,0.9208
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 27, 2007
RadiationMonochromator: Si(111), beam focused by a toroidal mirror / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.92061
20.92081
ReflectionResolution: 2→50 Å / Num. all: 24473 / Num. obs: 24473 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.054 / Rsym value: 0.088
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.8 % / Num. unique all: 1790 / Rsym value: 0.269 / % possible all: 68.2

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Processing

Software
NameClassification
CBASSdata collection
SnBphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2401 1006 -RANDOM
Rwork0.1975 ---
all0.235 26392 --
obs0.215 21159 80.2 %-
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1082 0 3 244 1329
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.0056

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