[English] 日本語
Yorodumi
- PDB-1qyp: THERMOCOCCUS CELER RPB9, NMR, 25 STRUCTURES -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qyp
TitleTHERMOCOCCUS CELER RPB9, NMR, 25 STRUCTURES
ComponentsRNA POLYMERASE II
KeywordsTRANSCRIPTION / RNA POLYMERASE II SUBUNIT / RPB9 / ZN RIBBON / HYPERTHERMOPHILIC / EXTREMOPHILE
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / DNA-directed RNA polymerase activity / DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / zinc ion binding
Similarity search - Function
Transcription factor S / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Zinc finger TFIIS-type signature. / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S ...Transcription factor S / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Zinc finger TFIIS-type signature. / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerase subunit 9 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase subunit/transcription factor S / Zinc finger, TFIIS-type / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / C2C2 Zinc finger / Single Sheet / Mainly Beta
Similarity search - Domain/homology
Transcription factor S
Similarity search - Component
Biological speciesThermococcus celer (archaea)
MethodSOLUTION NMR
AuthorsWang, B. / Jones, D.N.M. / Kaine, B.P. / Weiss, M.A.
Citation
Journal: Structure / Year: 1998
Title: High-resolution structure of an archaeal zinc ribbon defines a general architectural motif in eukaryotic RNA polymerases.
Authors: Wang, B. / Jones, D.N. / Kaine, B.P. / Weiss, M.A.
#1: Journal: Nature / Year: 1995
Title: Erratum. Structure of a New Nucleic-Acid-Binding Motif in Eukaryotic Transcriptional Elongation Factor Tfiis
Authors: Qian, X. / Jeon, C. / Yoon, H. / Agarwal, K. / Weiss, M.A.
#2: Journal: Nature / Year: 1993
Title: Structure of a New Nucleic-Acid-Binding Motif in Eukaryotic Transcriptional Elongation Factor Tfiis
Authors: Qian, X. / Jeon, C. / Yoon, H. / Agarwal, K. / Weiss, M.A.
History
DepositionAug 19, 1997Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Item: _pdbx_database_status.process_site
Revision 1.4May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA POLYMERASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7082
Polymers6,6421
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / -
Representative

-
Components

#1: Protein RNA POLYMERASE II


Mass: 6642.467 Da / Num. of mol.: 1 / Fragment: SUBUNIT RPB9, C-TERMINAL DOMAIN, RESIDUES 58 -110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus celer (archaea) / Cell line: BL21 / Plasmid: PET15-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) LYSS / References: UniProt: Q56254
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR

-
Sample preparation

Sample conditionspH: 6 / Temperature: 313 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
Processing

Software
NameClassification
VNMRmodel building
X-PLORmodel building
X-PLORrefinement
VNMRphasing
X-PLORphasing
NMR softwareName: X-PLOR / Developer: BRUNGER / Classification: refinement
NMR ensembleConformers submitted total number: 25

+
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