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- PDB-5h23: Crystal structure of Chikungunya virus capsid protein -

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Basic information

Entry
Database: PDB / ID: 5h23
TitleCrystal structure of Chikungunya virus capsid protein
ComponentsCapsid ProteinCapsid
KeywordsVIRAL PROTEIN / Chikungunya virus / capsid protein
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / host cell cytoplasm / membrane => GO:0016020 / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane ...togavirin / T=4 icosahedral viral capsid / host cell cytoplasm / membrane => GO:0016020 / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane / cytoplasm
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Togavirin / Frameshifted structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSharma, R. / Kesari, P. / Tomar, S. / Kumar, P.
CitationJournal: Virology / Year: 2018
Title: Structure-function insights into chikungunya virus capsid protein: Small molecules targeting capsid hydrophobic pocket.
Authors: Sharma, R. / Kesari, P. / Kumar, P. / Tomar, S.
History
DepositionOct 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid Protein
B: Capsid Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,19211
Polymers34,0692
Non-polymers1,1239
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint11 kcal/mol
Surface area14810 Å2
2
A: Capsid Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5875
Polymers17,0341
Non-polymers5534
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7920 Å2
MethodPISA
3
B: Capsid Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6056
Polymers17,0341
Non-polymers5715
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-1 kcal/mol
Surface area7830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.307, 39.096, 59.261
Angle α, β, γ (deg.)92.36, 91.18, 103.00
Int Tables number1
Space group name H-MP1

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Capsid Protein / Capsid


Mass: 17034.400 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chikungunya virus / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: A0A1D8H158, UniProt: P0DOK1*PLUS
#5: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 4 types, 92 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS ADZ47899 FOR THIS SEQUENCE.

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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: 2.2 Å3/Da / Density % sol: 44.19 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 25% PEG 3,350, 50mM Bis-Tris, 2% Glycerol, 100mM BOG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 25, 2015 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 16535 / % possible obs: 91.12 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 14.48
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.221

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VCP

1vcp


Resolution: 2.2→32.713 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 32.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2607 650 4.84 %
Rwork0.1759 --
obs0.1801 13437 91.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→32.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2312 0 63 85 2460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072481
X-RAY DIFFRACTIONf_angle_d1.0893350
X-RAY DIFFRACTIONf_dihedral_angle_d14.304894
X-RAY DIFFRACTIONf_chiral_restr0.077355
X-RAY DIFFRACTIONf_plane_restr0.004427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.370.3295950.23852227X-RAY DIFFRACTION78
2.37-2.60840.35561510.24312515X-RAY DIFFRACTION91
2.6084-2.98570.29961270.22312684X-RAY DIFFRACTION95
2.9857-3.76080.27361480.16292643X-RAY DIFFRACTION95
3.7608-32.7170.19491290.14092718X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 2.8566 Å / Origin y: -7.9268 Å / Origin z: -14.605 Å
111213212223313233
T0.1658 Å2-0.0321 Å20.0149 Å2-0.2979 Å20.0041 Å2--0.2673 Å2
L0.5587 °2-0.2846 °2-0.4799 °2-1.9752 °22.3502 °2--4.7391 °2
S0.0282 Å °0.0296 Å °-0.0108 Å °-0.1082 Å °-0.0749 Å °0.0341 Å °-0.1307 Å °-0.1367 Å °0.0388 Å °
Refinement TLS groupSelection details: all

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