[English] 日本語
Yorodumi
- PDB-3bwq: Structure of free SV40 VP1 pentamer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bwq
TitleStructure of free SV40 VP1 pentamer
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / SV40 / polyomavirus / ganglioside / GM1 / viral receptor / virus attachment / Capsid protein / Late protein / Nucleus / Virion
Function / homology
Function and homology information


capsomere / symbiont-mediated perturbation of host cell endomembrane system / caveolin-mediated endocytosis of virus by host cell / viral capsid assembly / T=7 icosahedral viral capsid / host cell endoplasmic reticulum / molecular adaptor activity / virion attachment to host cell / host cell nucleus / structural molecule activity / identical protein binding
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus Vp1; Chain A / Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / Sandwich / Mainly Beta
Similarity search - Domain/homology
Major capsid protein VP1
Similarity search - Component
Biological speciesSimian virus 40
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNeu, U. / Stehle, T.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structural basis of GM1 ganglioside recognition by simian virus 40.
Authors: Neu, U. / Woellner, K. / Gauglitz, G. / Stehle, T.
History
DepositionJan 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 5, 2011Group: Other
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)148,6725
Polymers148,6725
Non-polymers00
Water12,178676
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.040, 93.660, 120.810
Angle α, β, γ (deg.)90.00, 105.54, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Capsid protein VP1


Mass: 29734.420 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian virus 40 / Genus: Polyomavirus / Gene: VP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03087
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 676 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.44 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop
Details: RESERVOIR: 0.1 M TRIS, PH 8.5, 24 % PEG3350. DROP: RESERVOIR MIXED 4:1 WITH 30 % ETHYLENE GLYCOL. THIS WAS MIXED 1:1 WITH VP1 (11 MG/ML), VAPOR DIFFUSION, HANGING DROP, temperature 273K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2006
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 73715 / Num. obs: 63985 / % possible obs: 86.8 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 6.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.4 / % possible all: 52.2

-
Processing

Software
NameVersionClassification
REFMAC5.4.0013refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SVA

1sva


Resolution: 2.3→39.78 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.912 / SU B: 8.224 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.453 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. some of the residues from Gly30 to Asp42 were disordered in several chains and were not modeled. The side chain of Asp42 of chain E was ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. some of the residues from Gly30 to Asp42 were disordered in several chains and were not modeled. The side chain of Asp42 of chain E was modeled as Ala due to missing density.
RfactorNum. reflection% reflectionSelection details
Rfree0.2542 6346 9.9 %RANDOM
Rwork0.20746 ---
obs0.21217 57548 86.81 %-
all-73715 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.406 Å2
Baniso -1Baniso -2Baniso -3
1--3.43 Å20 Å2-3.75 Å2
2--4.92 Å20 Å2
3----3.5 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10164 0 0 676 10840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02210392
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7481.95914143
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.36351312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26925.879461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83151716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1591530
X-RAY DIFFRACTIONr_chiral_restr0.0020.021600
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.027927
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.2576
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21352
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.25
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.391106572
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.7181510680
X-RAY DIFFRACTIONr_scbond_it2.906103818
X-RAY DIFFRACTIONr_scangle_it4.04153463
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 272 -
Rwork0.308 2440 -
obs--50.18 %

+
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