[English] 日本語
Yorodumi
- PDB-6kf4: Cryo-EM structure of Thermococcus kodakarensis RNA polymerase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6kf4
TitleCryo-EM structure of Thermococcus kodakarensis RNA polymerase
Components
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 8
  • (DNA-directed RNA polymerase, subunit ...Polymerase) x 2
  • DNA-directed RNA polymerase subunitPolymerase
  • Transcription factor E
KeywordsTRANSCRIPTION / apo-RNA polymerase
Function / homology
Function and homology information


transcription open complex formation at RNA polymerase II promoter / RNA polymerase complex / DNA-templated transcription, initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription, DNA-templated / protein dimerization activity / nucleotide binding / regulation of transcription, DNA-templated ...transcription open complex formation at RNA polymerase II promoter / RNA polymerase complex / DNA-templated transcription, initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / transcription, DNA-templated / protein dimerization activity / nucleotide binding / regulation of transcription, DNA-templated / DNA binding / zinc ion binding / metal ion binding
Similarity search - Function
Alpha-Beta Plaits - #3110 / Helix Hairpins - #10 / Transcription factor TFE, archaea / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo11 ...Alpha-Beta Plaits - #3110 / Helix Hairpins - #10 / Transcription factor TFE, archaea / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo1N / DNA-directed RNA polymerase subunit Rpo2 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo3 / DNA-directed RNA polymerase subunit Rpo11 / HRDC domain / DNA-directed RNA polymerase, subunit E/RPC8 / RNA polymerase Rpb7-like, N-terminal domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription initiation factor IIE / TFE/IIEalpha-type HTH domain profile. / TFIIE alpha subunit / Transcription factor TFE/TFIIEalpha HTH domain / Transcription factor E / Transcription initiation factor IIE subunit alpha, N-terminal / RNA polymerase ii, chain L / RPB5-like RNA polymerase subunit / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Rubrerythrin, domain 2 / S1 domain profile. / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerase subunit RPB10 / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases, subunit N, zinc binding site / RNA polymerases N / 8 kDa subunit / Helix Hairpins / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerase subunit CX / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb5, C-terminal domain / : / : / RNA polymerase, subunit H/Rpb5, conserved site / RPB5-like RNA polymerase subunit superfamily / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerases K / 14 to 18 Kd subunits signature. / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Gyrase A; domain 2 / Ribosomal protein S1-like RNA-binding domain / RNA-binding domain, S1 / S1 RNA binding domain / S1 domain / Homeodomain-like / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb6 / RPB6/omega subunit-like superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / Single Sheet / : / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 3 / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase, alpha subunit / RNA polymerase, N-terminal / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, beta subunit, protrusion / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb3/RpoA insert domain / DNA-directed RNA polymerase, insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type
Similarity search - Domain/homology
Transcription factor E / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase, subunit F / DNA-directed RNA polymerase, subunit E / DNA-directed RNA polymerase subunit Rpo10 ...Transcription factor E / DNA-directed RNA polymerase subunit Rpo12 / DNA-directed RNA polymerase subunit Rpo5 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerase subunit Rpo1C / DNA-directed RNA polymerase subunit Rpo11 / DNA-directed RNA polymerase, subunit F / DNA-directed RNA polymerase, subunit E / DNA-directed RNA polymerase subunit Rpo10 / DNA-directed RNA polymerase subunit Rpo6 / DNA-directed RNA polymerase subunit Rpo3
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsJun, S.-H. / Hyun, J. / Jeong, H. / Cha, J.S. / Kim, H. / Bartlett, M.S. / Cho, H.-S. / Murakami, K.S.
Funding support Korea, Republic Of, United States, 4items
OrganizationGrant numberCountry
Ministry of Education (Korea)2015R1D1A1A01059097 Korea, Republic Of
Ministry of Science, ICT and Future PlanningNRF-2017M3A9F6029755 Korea, Republic Of
National Institutes of Health/National Institute of General Medical SciencesR35 GM131860 United States
National Institutes of Health/National Institute of Environmental Health SciencesR15 GM083306 United States
CitationJournal: Nat Commun / Year: 2020
Title: Direct binding of TFEα opens DNA binding cleft of RNA polymerase.
Authors: Sung-Hoon Jun / Jaekyung Hyun / Jeong Seok Cha / Hoyoung Kim / Michael S Bartlett / Hyun-Soo Cho / Katsuhiko S Murakami /
Abstract: Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron ...Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron microscopy structures of the RNAP, RNAP-TFEα binary, and RNAP-TFEα-promoter DNA ternary complexes from archaea, Thermococcus kodakarensis (Tko). The structures reveal that TFEα bridges the RNAP clamp and stalk domains to open the DNA binding cleft. Positioning of promoter DNA into the cleft closes it while maintaining the TFEα interactions with the RNAP mobile modules. The structures and photo-crosslinking results also suggest that the conserved aromatic residue in the extended winged-helix domain of TFEα interacts with promoter DNA to stabilize the transcription bubble. This study provides a structural basis for the functions of TFEα and elucidates the mechanism by which the DNA binding cleft is opened during transcription initiation in the stalk-containing RNAPs, including archaeal and eukaryotic RNAPs.
History
DepositionJul 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: Database references / Category: database_2 / pdbx_database_related
Item: _database_2.database_code / _pdbx_database_related.db_id
Revision 1.2Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9961
  • Imaged by UCSF Chimera
  • Download
  • Superimposition on EM map
  • EMDB-9969
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase subunit A''
D: DNA-directed RNA polymerase subunit D
E: DNA-directed RNA polymerase, subunit E
F: DNA-directed RNA polymerase, subunit F
H: DNA-directed RNA polymerase subunit H
K: DNA-directed RNA polymerase subunit K
L: DNA-directed RNA polymerase subunit L
N: DNA-directed RNA polymerase subunit N
P: DNA-directed RNA polymerase subunit P
G: Transcription factor E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)402,56019
Polymers402,14312
Non-polymers4177
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area59970 Å2
ΔGint-436 kcal/mol
Surface area159180 Å2

-
Components

-
Protein , 2 types, 2 molecules AG

#1: Protein DNA-directed RNA polymerase subunit / Polymerase


Mass: 103038.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JE33, DNA-directed RNA polymerase
#12: Protein Transcription factor E / TFE / TFIIE subunit alpha homolog / Transcription initiation factor TFIIE


Mass: 22088.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: tfe, TK2024 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JDD5

-
DNA-directed RNA polymerase subunit ... , 8 types, 8 molecules BCDHKLNP

#2: Protein DNA-directed RNA polymerase subunit beta / Polymerase


Mass: 127468.039 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JE32, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit A'' / Polymerase


Mass: 43727.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JE34, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase subunit D / Polymerase


Mass: 29429.645 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JJF4, DNA-directed RNA polymerase
#7: Protein DNA-directed RNA polymerase subunit H / Polymerase


Mass: 9522.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JE31, DNA-directed RNA polymerase
#8: Protein DNA-directed RNA polymerase subunit K / Polymerase


Mass: 6286.519 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JJD0, DNA-directed RNA polymerase
#9: Protein DNA-directed RNA polymerase subunit L / Polymerase


Mass: 11013.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JE88, DNA-directed RNA polymerase
#10: Protein DNA-directed RNA polymerase subunit N / Polymerase


Mass: 7601.975 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JJC9, DNA-directed RNA polymerase
#11: Protein/peptide DNA-directed RNA polymerase subunit P / Polymerase


Mass: 5553.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / References: UniProt: Q5JDM8, DNA-directed RNA polymerase

-
DNA-directed RNA polymerase, subunit ... , 2 types, 2 molecules EF

#5: Protein DNA-directed RNA polymerase, subunit E / Polymerase


Mass: 21893.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK1699 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JIY4
#6: Protein DNA-directed RNA polymerase, subunit F / Polymerase


Mass: 14519.659 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (archaea)
Strain: ATCC BAA-918 / JCM 12380 / KOD1 / Gene: TK0901 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JI52

-
Non-polymers , 2 types, 7 molecules

#13: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#14: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Complex of RNA polymerase and TFE / Type: COMPLEX / Entity ID: #1-#12 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.40 MDa / Experimental value: NO
Source (natural)Organism: Thermococcus kodakarensis KOD1 (archaea)
Source (recombinant)Organism: Escherichia coli BL21 (bacteria) / Strain: BL21
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 35 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252508 / Symmetry type: POINT

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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