[English] 日本語
Yorodumi
- PDB-2j7o: STRUCTURE OF THE RNAI POLYMERASE FROM NEUROSPORA CRASSA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2j7o
TitleSTRUCTURE OF THE RNAI POLYMERASE FROM NEUROSPORA CRASSA
ComponentsRNA DEPENDENT RNA POLYMERASERNA-dependent RNA polymerase
KeywordsHYDROLASE / RNA DEPENDENT RNA POLYMERASE / RNAI RESPONSE / HYPOTHETICAL PROTEIN / RNA-DIRECTED RNA POLYMERASE
Function / homology
Function and homology information


regulatory ncRNA-mediated gene silencing / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / RNA binding / identical protein binding / metal ion binding
Similarity search - Function
RNA-dependent RNA polymerase, slab domain, helical subdomain-like / RNA-dependent RNA polymerase, eukaryotic-type / RNA dependent RNA polymerase / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA-dependent RNA polymerase
Similarity search - Component
Biological speciesNEUROSPORA CRASSA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSalgado, P.S. / Koivunen, M.R.L. / Makeyev, E.V. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M.
CitationJournal: Plos Biol. / Year: 2006
Title: The Structure of an Rnai Polymerase Links RNA Silencing and Transcription.
Authors: Salgado, P.S. / Koivunen, M.R.L. / Makeyev, E.V. / Bamford, D.H. / Stuart, D.I. / Grimes, J.M.
History
DepositionOct 13, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA DEPENDENT RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,7332
Polymers116,7091
Non-polymers241
Water0
1
A: RNA DEPENDENT RNA POLYMERASE
hetero molecules

A: RNA DEPENDENT RNA POLYMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,4664
Polymers233,4182
Non-polymers492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)114.596, 125.015, 102.204
Angle α, β, γ (deg.)90.00, 108.75, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein RNA DEPENDENT RNA POLYMERASE / RNA-dependent RNA polymerase / HYPOTHETICAL PROTEIN NCU075341


Mass: 116708.938 Da / Num. of mol.: 1 / Fragment: RESIDUES 381-1402
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEUROSPORA CRASSA (fungus) / Plasmid: PEM69 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): INVSC1 / References: UniProt: Q9Y7G6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 59 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.975
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 3.45→20 Å / Num. obs: 22247 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 8.7
Reflection shellResolution: 3.45→3.6 Å / Mean I/σ(I) obs: 2.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: RESIDUAL
Details: DOMAINS OF MODEL TREATED AS RIGID BODIES IN REFINEMENT. INDIVIDUAL BFACTOR REFINEMENT OF RIGID BODY REFINED MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.3597 773 4.5 %RANDOM
Rwork0.3531 ---
obs0.3531 15720 91.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 80 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-28.231 Å20 Å2-4.865 Å2
2---54.06 Å20 Å2
3---25.829 Å2
Refinement stepCycle: LAST / Resolution: 3.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7520 0 1 0 7521
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.63
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.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