[English] 日本語
Yorodumi
- PDB-6auk: Crystal structure of rotavirus Non Structural protein 2 (NSP2) mu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6auk
TitleCrystal structure of rotavirus Non Structural protein 2 (NSP2) mutant S313D
ComponentsNon-structural protein 2
KeywordsVIRAL PROTEIN / Virus factory / phosphorylation / rotavirus / NSP2
Function / homology
Function and homology information


nucleoside diphosphate kinase activity / ribonucleoside triphosphate phosphatase activity / 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 non-structural protein 35, N-terminal / Rotavirus NSP2, N-terminal / Rotavirus NSP2, C-terminal / Rotavirus non-structural protein 35, C-terminal / Rotavirus non-structural protein 2 ...Rotavirus NSP2 fragment, C-terminal domain / Rotavirus NSP2 fragment, N-terminal domain / Rotavirus NSP2 fragment, N-terminal domain / : / : / Rotavirus non-structural protein 35, N-terminal / 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 / Non-structural protein 2
Similarity search - Component
Biological speciesRotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.603 Å
AuthorsHu, L. / Prasad, B.V.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI 36040 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI080656 United States
Welch FoundationQ1279 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Phosphorylation cascade regulates the formation and maturation of rotaviral replication factories.
Authors: Criglar, J.M. / Anish, R. / Hu, L. / Crawford, S.E. / Sankaran, B. / Prasad, B.V.V. / Estes, M.K.
History
DepositionSep 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-structural protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7783
Polymers36,6461
Non-polymers1322
Water1,63991
1
A: Non-structural protein 2
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)294,22224
Polymers293,1708
Non-polymers1,05216
Water1448
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
crystal symmetry operation5_557-x,y,-z+21
crystal symmetry operation6_557x,-y,-z+21
crystal symmetry operation7_557y,x,-z+21
crystal symmetry operation8_557-y,-x,-z+21
Buried area22680 Å2
ΔGint-290 kcal/mol
Surface area115370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.926, 107.926, 152.487
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-504-

HOH

-
Components

#1: Protein Non-structural protein 2


Mass: 36646.266 Da / Num. of mol.: 1 / Mutation: S313D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Gene: NSP2 / Production host: Escherichia coli (E. coli)
References: UniProt: A2T3N6, UniProt: A2T3P0*PLUS, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM lithium sulfate, 100 mM sodium citrate, pH5.5, 20% PEG 1000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 26, 2015
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 14160 / % possible obs: 100 % / Redundancy: 16.9 % / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.038 / Net I/σ(I): 23.6
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 17.8 % / Rmerge(I) obs: 1.333 / Num. unique obs: 702 / CC1/2: 0.662 / Rpim(I) all: 0.326 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-2000v715data scaling
SCALEPACK7.0.043data reduction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L9V

1l9v


Resolution: 2.603→46.016 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.73
RfactorNum. reflection% reflection
Rfree0.2458 769 5.43 %
Rwork0.2059 --
obs0.2082 14160 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.603→46.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 6 91 2645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072606
X-RAY DIFFRACTIONf_angle_d0.8743520
X-RAY DIFFRACTIONf_dihedral_angle_d7.0441581
X-RAY DIFFRACTIONf_chiral_restr0.048392
X-RAY DIFFRACTIONf_plane_restr0.007446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6026-2.80360.37641240.29052613X-RAY DIFFRACTION98
2.8036-3.08570.33141330.26392665X-RAY DIFFRACTION100
3.0857-3.5320.26521580.22022644X-RAY DIFFRACTION100
3.532-4.44940.2221630.18212680X-RAY DIFFRACTION100
4.4494-46.0230.20551910.17392789X-RAY DIFFRACTION100

+
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