[English] 日本語
Yorodumi
- PDB-2r7p: Crystal Structure of H225A NSP2 and AMPPNP complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r7p
TitleCrystal Structure of H225A NSP2 and AMPPNP complex
ComponentsNon-structural RNA-binding protein 35
KeywordsRNA BINDING PROTEIN / Rotavirus / NDP Kinase / non structural protein / NTPase / RNA-binding
Function / homology
Function and homology information


nucleoside diphosphate kinase activity / viral genome replication / ribonucleoside triphosphate phosphatase activity / 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 35, N-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 NSP2, N-terminal / Rotavirus NSP2, C-terminal / : / : / Rotavirus non-structural protein 35, C-terminal / Rotavirus non-structural protein 35, N-terminal / Rotavirus non-structural protein 2 / HIT family, subunit A / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / PHOSPHATE ION / Non-structural protein 2
Similarity search - Component
Biological speciesSimian 11 rotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKumar, M. / Prasad, B.V.V.
Citation
Journal: J.Virol. / Year: 2007
Title: Crystallographic and Biochemical Analysis of Rotavirus NSP2 with Nucleotides Reveals a Nucleoside Diphosphate Kinase-Like Activity
Authors: Kumar, M. / Jayaram, H. / Vasquez-Del Carpio, R. / Jiang, X. / Taraporewala, Z.F. / Jacobson, R.H. / Patton, J.T. / Prasad, B.V.V.
#1: Journal: Nature / Year: 2002
Title: Rotavirus protein involved in genome replication and packaging exhibits a HIT-like fold
Authors: Jayaram, H. / Taraporewala, Z. / Patton, J.T. / Prasad, B.V.V.
History
DepositionSep 9, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-structural RNA-binding protein 35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1523
Polymers36,5511
Non-polymers6012
Water84747
1
A: Non-structural RNA-binding protein 35
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)297,21924
Polymers292,4108
Non-polymers4,80916
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation3_545-y,x-1,z1
crystal symmetry operation4_655y+1,-x,z1
crystal symmetry operation5_655-x+1,y,-z1
crystal symmetry operation6_545x,-y-1,-z1
crystal symmetry operation7_645y+1,x-1,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area25700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.430, 108.430, 154.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

-
Components

#1: Protein Non-structural RNA-binding protein 35 / NSP2 / NS35 / NCVP3


Mass: 36551.191 Da / Num. of mol.: 1 / Mutation: H225A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian 11 rotavirus (serotype 3 / strain SA11-Ramig)
Species: Rotavirus A / Strain: Ramig / Gene: S8, SEGMENT 8 / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: Q03243
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 6-8% PEG 10000, 20mM Tris-HCl pH 7.5, 10-15mM nucleotide, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9790903 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9790903 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 11704 / Num. obs: 11643 / % possible obs: 99.5 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 13.9 % / Biso Wilson estimate: 94 Å2 / Rmerge(I) obs: 0.115
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 14.3 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 5 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
CNS1.1refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1l9v

1l9v


Resolution: 2.8→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2633 838 -random
Rwork0.2225 ---
all-11704 --
obs-11643 99.5 %-
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 26 47 2579
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007455
X-RAY DIFFRACTIONc_angle_deg1.2505

+
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