[English] 日本語
Yorodumi
- PDB-2gu0: Crystal Structure of Human Rotavirus NSP2 (Group C / Bristol Strain) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gu0
TitleCrystal Structure of Human Rotavirus NSP2 (Group C / Bristol Strain)
ComponentsNonstructural protein 2
KeywordsVIRAL PROTEIN / NSP2 / rotavirus / HIT motif / Bristol
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides / viral genome replication / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / host cell cytoplasm / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Rotavirus NSP2 fragment, C-terminal domain / Rotavirus NSP2 fragment, N-terminal domain / Rotavirus NSP2 fragment, N-terminal domain / Rotavirus NSP2, N-terminal / Rotavirus NSP2, C-terminal / Rotavirus non-structural protein 35, C-terminal / Rotavirus non-structural protein 2 / HIT family, subunit A / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Non-structural protein 2
Similarity search - Component
Biological speciesHuman rotavirus C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJiang, X. / Prasad, B.V.V.
CitationJournal: J.Virol. / Year: 2006
Title: Structure-function analysis of rotavirus NSP2 octamer by using a novel complementation system
Authors: Taraporewala, Z.F. / Jiang, X. / Vasquez-Del Carpio, R. / Jayaram, H. / Prasad, B.V.V. / Patton, J.T.
History
DepositionApr 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nonstructural protein 2
B: Nonstructural protein 2


Theoretical massNumber of molelcules
Total (without water)71,9282
Polymers71,9282
Non-polymers00
Water0
1
A: Nonstructural protein 2
B: Nonstructural protein 2

A: Nonstructural protein 2
B: Nonstructural protein 2

A: Nonstructural protein 2
B: Nonstructural protein 2

A: Nonstructural protein 2
B: Nonstructural protein 2


Theoretical massNumber of molelcules
Total (without water)287,7138
Polymers287,7138
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Unit cell
Length a, b, c (Å)134.181, 134.181, 112.294
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
DetailsThe biological assembly is a octamer generated from the two monomers in the asymmetric unit by the operations: (-x, -y, z), (-y, x, z) and (y, -x, z).

-
Components

#1: Protein Nonstructural protein 2


Mass: 35964.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rotavirus C / Species: Rotavirus C / Strain: Bristol / Gene: NSP2, segment 9 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q9PY93

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 1.5-1.7M ammonium sulfate, 0.1M MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2004
RadiationMonochromator: high-resolution double-crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→500 Å / Num. all: 23492 / Num. obs: 23468 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 30.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 5.6 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
ADSCdata collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→500 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2310 9.4 %Random
Rwork0.231 ---
all0.238 23492 --
obs0.236 23468 95.5 %-
Solvent computationBsol: 19.957 Å2
Displacement parametersBiso mean: 45.124 Å2
Baniso -1Baniso -2Baniso -3
1-10.873 Å20 Å20 Å2
2--10.873 Å20 Å2
3----21.747 Å2
Refinement stepCycle: LAST / Resolution: 2.8→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4872 0 0 0 4872
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4191.5
X-RAY DIFFRACTIONc_scbond_it1.9452
X-RAY DIFFRACTIONc_mcangle_it2.4862
X-RAY DIFFRACTIONc_scangle_it3.0342.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:ion.param

+
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