[English] 日本語
Yorodumi
- PDB-3sfg: crystal structure of murine norovirus RNA dependent RNA polymeras... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3sfg
Titlecrystal structure of murine norovirus RNA dependent RNA polymerase in complex with 2thiouridine(2TU)
ComponentsRNA polymerase
KeywordsTRANSFERASE / right hand conformation / POLYMERASE / RNA binding
Function / homology
Function and homology information


calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis ...calicivirin / ribonucleoside triphosphate phosphatase activity / nucleoside-triphosphate phosphatase / RNA helicase activity / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3230 / Viral polyprotein, Caliciviridae N-terminal / Viral polyprotein N-terminal / Norovirus 3C-like protease (NV 3CLpro) domain profile. / Norovirus peptidase C37 / Southampton virus-type processing peptidase / Mitochondrial Import Receptor Subunit Tom20; Chain A - #20 / Mitochondrial Import Receptor Subunit Tom20; Chain A / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Reverse transcriptase/Diguanylate cyclase domain / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Helix non-globular / Special / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-2TU / Genome polyprotein
Similarity search - Component
Biological speciesMurine norovirus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.209 Å
AuthorsKim, K.H. / Alam, I.
CitationJournal: Virology / Year: 2012
Title: Crystal structures of murine norovirus-1 RNA-dependent RNA polymerase in complex with 2-thiouridine or ribavirin.
Authors: Alam, I. / Lee, J.H. / Cho, K.J. / Han, K.R. / Yang, J.M. / Chung, M.S. / Kim, K.H.
History
DepositionJun 13, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 9, 2012Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA polymerase
B: RNA polymerase
C: RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,40462
Polymers175,5593
Non-polymers5,84659
Water9,782543
1
A: RNA polymerase
hetero molecules

A: RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,54848
Polymers117,0392
Non-polymers4,50946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
2
B: RNA polymerase
C: RNA polymerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,63138
Polymers117,0392
Non-polymers3,59236
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.794, 195.972, 109.335
Angle α, β, γ (deg.)90.00, 114.86, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein RNA polymerase


Mass: 58519.539 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine norovirus 1 / Gene: RdRp / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q80J95

-
Non-polymers , 5 types, 602 molecules

#2: Chemical ChemComp-2TU / 1-(beta-D-ribofuranosyl)-2-thioxo-2,3-dihydropyrimidin-4(1H)-one / 2-thiouridine


Mass: 260.267 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H12N2O5S
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO4
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 3.34 Å3/Da / Density % sol: 63.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0M ammonium sulphate, cacodylate pH 6.5, 0.2M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 113874 / % possible obs: 99.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 26.01 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.461 / Net I/σ(I): 12.5

-
Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.209→31.621 Å / FOM work R set: 0.8218 / SU ML: 0.68 / σ(F): 1.41 / Phase error: 25.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2526 1999 1.76 %
Rwork0.2026 --
obs0.2034 113865 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.789 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 137.6 Å2 / Biso min: 10.92 Å2
Baniso -1Baniso -2Baniso -3
1-2.6946 Å20 Å2-0.3541 Å2
2--1.1338 Å20 Å2
3----3.8284 Å2
Refinement stepCycle: LAST / Resolution: 2.209→31.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11454 0 344 543 12341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912052
X-RAY DIFFRACTIONf_angle_d1.22316306
X-RAY DIFFRACTIONf_dihedral_angle_d17.2184545
X-RAY DIFFRACTIONf_chiral_restr0.0811708
X-RAY DIFFRACTIONf_plane_restr0.0072085
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2087-2.26390.331330.28687418X-RAY DIFFRACTION92
2.2639-2.32510.33471410.26477946X-RAY DIFFRACTION99
2.3251-2.39350.30451440.25528009X-RAY DIFFRACTION99
2.3935-2.47080.29791420.24947965X-RAY DIFFRACTION99
2.4708-2.5590.32241430.25097977X-RAY DIFFRACTION99
2.559-2.66140.31911430.24278000X-RAY DIFFRACTION99
2.6614-2.78250.34041430.23927993X-RAY DIFFRACTION99
2.7825-2.92910.28321440.23078039X-RAY DIFFRACTION100
2.9291-3.11250.25541440.21148073X-RAY DIFFRACTION100
3.1125-3.35250.24451440.1928048X-RAY DIFFRACTION100
3.3525-3.68940.24231440.17628064X-RAY DIFFRACTION100
3.6894-4.22220.19471450.15368086X-RAY DIFFRACTION100
4.2222-5.31550.18861440.15358088X-RAY DIFFRACTION100
5.3155-31.62440.22611450.20048160X-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://pdbjlvh1.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