[English] 日本語
Yorodumi
- EMDB-8737: RNA pol II elongation complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8737
TitleRNA pol II elongation complex
Map dataRNA pol II elongation complex
SampleBinary complex of RNA Pol II and transcription scaffold
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • (nucleic-acidNucleic acid) x 3
  • (ligand) x 2
Function / homologyArchaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA-binding domain, S1 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase RBP11 / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit ...Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA-binding domain, S1 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase RBP11 / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RPB6/omega subunit-like superfamily / RPB5-like RNA polymerase subunit / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPB10 / RNA polymerases, subunit N, zinc binding site / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase subunit, RPB6/omega / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / HRDC-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase subunit/transcription factor S / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases L / 13 to 16 Kd subunits signature. / Rpb4/RPC9 superfamily / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb3/Rpb11 dimerisation domain / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerases D / 30 to 40 Kd subunits signature. / Zinc finger TFIIS-type signature. / RNA polymerases M / 15 Kd subunits signature. / RNA polymerases H / 23 Kd subunits signature. / RNA polymerase Rpb2, domain 4 / RNA polymerase beta subunit / S1 RNA binding domain / RNA polymerases N / 8 kDa subunit / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb3/RpoA insert domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb6 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases M/15 Kd subunit / RNA polymerase Rpb2, domain 2 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb8 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb4 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 3 / RNA polymerases N / 8 Kd subunits signature. / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase II, heptapeptide repeat, eukaryotic / DNA-directed RNA polymerase, subunit N/Rpb10 / RNA polymerases beta chain signature. / Zinc finger TFIIS-type profile. / Formation of the Early Elongation Complex / RNA polymerase, beta subunit, protrusion / RNA Polymerase II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / TP53 Regulates Transcription of DNA Repair Genes / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA polymerase, alpha subunit / RNA polymerases K / 14 to 18 Kd subunits signature. / Zinc finger, TFIIS-type / RNA polymerase Rpb4/RPC9, core / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 7
Function and homology information
SourceSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / 6.4 Å resolution
AuthorsLahiri I / Leschziner AE
CitationJournal: Nature / Year: 2017
Title: Structural basis for the initiation of eukaryotic transcription-coupled DNA repair.
Authors: Jun Xu / Indrajit Lahiri / Wei Wang / Adam Wier / Michael A Cianfrocco / Jenny Chong / Alissa A Hare / Peter B Dervan / Frank DiMaio / Andres E Leschziner / Dong Wang
Validation ReportPDB-ID: 5vvs

SummaryFull reportAbout validation report
DateDeposition: May 20, 2017 / Header (metadata) release: Jul 26, 2017 / Map release: Nov 22, 2017 / Last update: Dec 13, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0256
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0256
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5vvs
  • Surface level: 0.0256
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_8737.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.2 Å/pix.
= 460.8 Å
384 pix
1.2 Å/pix.
= 460.8 Å
384 pix
1.2 Å/pix.
= 460.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density
Contour Level:0.0256 (by author), 0.0256 (movie #1):
Minimum - Maximum-0.010574434 - 0.06867047
Average (Standard dev.)0.0002605232 (0.002640295)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin000
Limit383383383
Spacing384384384
CellA=B=C: 1 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z460.800460.800460.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0110.0690.000

-
Supplemental data

-
Sample components

+
Entire Binary complex of RNA Pol II and transcription scaffold

EntireName: Binary complex of RNA Pol II and transcription scaffold
Number of components: 18

+
Component #1: protein, Binary complex of RNA Pol II and transcription scaffold

ProteinName: Binary complex of RNA Pol II and transcription scaffold
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

+
Component #2: protein, DNA-directed RNA polymerase II subunit RPB1

ProteinName: DNA-directed RNA polymerase II subunit RPB1Polymerase / Recombinant expression: No
MassTheoretical: 191.821578 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

+
Component #3: protein, DNA-directed RNA polymerase II subunit RPB2

ProteinName: DNA-directed RNA polymerase II subunit RPB2Polymerase / Recombinant expression: No
MassTheoretical: 138.937297 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

+
Component #4: protein, DNA-directed RNA polymerase II subunit RPB3

ProteinName: DNA-directed RNA polymerase II subunit RPB3Polymerase / Recombinant expression: No
MassTheoretical: 35.330457 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

+
Component #5: protein, DNA-directed RNA polymerase II subunit RPB4

ProteinName: DNA-directed RNA polymerase II subunit RPB4Polymerase / Recombinant expression: No
MassTheoretical: 25.451191 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

+
Component #6: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC1

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC1RNA polymerase
Recombinant expression: No
MassTheoretical: 25.117094 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

+
Component #7: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC2

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC2RNA polymerase
Recombinant expression: No
MassTheoretical: 17.931834 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

+
Component #8: protein, DNA-directed RNA polymerase II subunit RPB7

ProteinName: DNA-directed RNA polymerase II subunit RPB7Polymerase / Recombinant expression: No
MassTheoretical: 19.081053 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

+
Component #9: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
Recombinant expression: No
MassTheoretical: 16.525363 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

+
Component #10: protein, DNA-directed RNA polymerase II subunit RPB9

ProteinName: DNA-directed RNA polymerase II subunit RPB9Polymerase / Recombinant expression: No
MassTheoretical: 14.308161 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

+
Component #11: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC5

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
Recombinant expression: No
MassTheoretical: 8.290732 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

+
Component #12: protein, DNA-directed RNA polymerase II subunit RPB11

ProteinName: DNA-directed RNA polymerase II subunit RPB11Polymerase
Recombinant expression: No
MassTheoretical: 13.633493 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

+
Component #13: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC4

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC4RNA polymerase
Recombinant expression: No
MassTheoretical: 7.729969 kDa
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

+
Component #14: nucleic-acid, RNA

Nucleic-acidName: RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUCGAGAGGA
MassTheoretical: 3.264036 kDa

+
Component #15: nucleic-acid, DNA (NTS)

Nucleic-acidName: DNA (NTS) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DT)(DA)(DG)(DT)(DT)(DG)(DA)(DT)(DC) (DT)(DC)(DA)(DT)(DA)(DT)(DT)(DT)(DC)(DA) (DT)(DT)(DC)(DC)(DT)(DA)(DC)(DT)(DC)(DA) (DG)(DG)(DA)(DG)(DA)(DA)(DG)(DG)(DA)(DG) (DC)(DA)(DG)(DA)(DG)(DC)(DG)
MassTheoretical: 14.494314 kDa

+
Component #16: nucleic-acid, DNA (TS)

Nucleic-acidName: DNA (TS) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DG)(DC)(DT)(DC)(DT)(DG)(DC)(DT)(DC) (DC)(DT)(DT)(DC)(DT)(DC)(DC)(DC)(DA)(DT) (DC)(DC)(DT)(DC)(DT)(DC)(DG)(DA)(DT)(DG) (DG)(DC)(DT)(DA)(DT)(DG)(DA)(DG)(DA)(DT) (DC)(DA)(DA)(DC)(DT)(DA)(DG)
MassTheoretical: 14.269129 kDa

+
Component #17: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #18: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 90 %

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 7.7 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 19331
3D reconstructionSoftware: RELION / Resolution: 6.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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