[English] 日本語
Yorodumi
- PDB-1kxa: SINDBIS VIRUS CAPSID, (WILD-TYPE) RESIDUES 106-264, TETRAGONAL CR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kxa
TitleSINDBIS VIRUS CAPSID, (WILD-TYPE) RESIDUES 106-264, TETRAGONAL CRYSTAL FORM
ComponentsSINDBIS VIRUS CAPSID PROTEIN
KeywordsVIRAL PROTEIN / SINDBIS VIRUS CAPSID PROTEIN / CHYMOTRYPSIN-LIKE SERINE PROTEINASE / WILD TYPE / COAT PROTEIN
Function / homology
Function and homology information


icosahedral viral capsid, spike / togavirin / T=4 icosahedral viral capsid / ubiquitin-like protein ligase binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / membrane fusion / viral translational frameshifting / serine-type endopeptidase activity ...icosahedral viral capsid, spike / togavirin / T=4 icosahedral viral capsid / ubiquitin-like protein ligase binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / host cell cytoplasm / membrane fusion / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane
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
Structural polyprotein
Similarity search - Component
Biological speciesSindbis virus
MethodX-RAY DIFFRACTION / Resolution: 3.1 Å
AuthorsChoi, H.-K. / Rossmann, M.G.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Structural analysis of Sindbis virus capsid mutants involving assembly and catalysis.
Authors: Choi, H.K. / Lee, S. / Zhang, Y.P. / McKinney, B.R. / Wengler, G. / Rossmann, M.G. / Kuhn, R.J.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Refined Structure of Sindbis Virus Core Protein and Comparison with Other Chymotrypsin-Like Serine Proteinase Structures
Authors: Tong, L. / Wengler, G. / Rossmann, M.G.
#2: Journal: Acta Crystallogr.,Sect.A / Year: 1992
Title: The Structure Determination of Sindbis Virus Core Protein Using Isomorphous Replacement and Molecular Replacement Averaging between Two Crystal Forms
Authors: Tong, L. / Choi, H.-K. / Minor, W. / Rossmann, M.G.
#3: Journal: Nature / Year: 1991
Title: Structure of Sindbis Virus Core Protein Reveals a Chymotrypsin-Like Serine Proteinase and the Organization of the Virion
Authors: Choi, H.K. / Tong, L. / Minor, W. / Dumas, P. / Boege, U. / Rossmann, M.G. / Wengler, G.
History
DepositionMay 5, 1996Processing site: BNL
Revision 1.0Nov 8, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SINDBIS VIRUS CAPSID PROTEIN


Theoretical massNumber of molelcules
Total (without water)17,4191
Polymers17,4191
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.000, 57.000, 109.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein SINDBIS VIRUS CAPSID PROTEIN


Mass: 17418.680 Da / Num. of mol.: 1 / Fragment: MET 106 - ALA 264 OF THE NATIVE SINDBIS CAPSID
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sindbis virus / Genus: Alphavirus / Description: T7 RNA POLYMERASE / Gene: SINDBIS VIRUS CAPSID PROTEIN / Plasmid: PET11A / Gene (production host): SINDBIS VIRUS CAPSID PROTEIN / Production host: Escherichia coli (E. coli)
References: UniProt: P03316, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 53 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 8.5 / PH range high: 7.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16-8 %(w/v)PEG80001reservoir
250-300 mMTris-HCl1reservoir
32.25-3.75 mg/mlprotein1drop
43-4 %(w/v)PEG80001drop
525-150 mMTris-HCl1drop

-
Data collection

Diffraction sourceSource: SEALED TUBE / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 3, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 2731 / % possible obs: 76.3 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Rmerge(I) obs: 0.076
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 9999 Å / Num. obs: 3596 / Num. measured all: 8276
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 3.2 Å / % possible obs: 27.1 % / Rmerge(I) obs: 0.237

-
Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementResolution: 3.1→6 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.174 -
obs0.174 2462
Displacement parametersBiso mean: 21.1 Å2
Refinement stepCycle: LAST / Resolution: 3.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 0 0 1216
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg27.6
X-RAY DIFFRACTIONx_improper_angle_deg1.4

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more