[English] 日本語
Yorodumi
- EMDB-3594: RNA polymerase I initially transcribing complex with visible tand... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3594
TitleRNA polymerase I initially transcribing complex with visible tandem Winged Helix domain
Map data
SampleRNA polymerase I initially transcribing complex:
RNA polymerase I / Initiation factor Rrn3 / Core Factor / Initial transcription DNA/RNA scaffold
Function / homologyRNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, insert domain superfamily / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Pol I subunit A12, C-terminal zinc ribbon / RPB5-like RNA polymerase subunit / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 ...RNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, insert domain superfamily / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Pol I subunit A12, C-terminal zinc ribbon / RPB5-like RNA polymerase subunit / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RNA polymerase Rpb7-like, N-terminal domain superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb1, domain 2 / RNA polymerase I transcription initiation factor TAF1B/Rrn7 / DNA-directed RNA polymerase, subunit RPB6 / Transcription factor S-II (TFIIS) / RNA polymerase I-specific transcription initiation factor Rrn6 / RNA polymerase I, subunit Rpa14, fungi / DNA-directed RNA polymerase I, subunit RPA34.5 / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerase Rpb2, OB-fold / DNA-directed RNA pol I, largest subunit / DNA-directed RNA polymerase, subunit 2 / Transcription initiation factor Rrn11, budding yeast / RNA polymerase subunit RPB10 / RNA polymerase I-specific transcription initiation factor RRN6-like / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Formation of TC-NER Pre-Incision Complex / Transcription initiation factor Rrn7, Zinc-finger / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb5, C-terminal domain / RNA polymerase subunit, RPB6/omega / Zinc finger TFIIS-type signature. / Yeast RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I-specific transcription-initiation factor / Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / 30 to 40 Kd subunits signature. / RNA polymerases M / 15 Kd subunits signature. / A49-like RNA polymerase I associated factor / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases beta chain signature. / Zinc finger TFIIS-type profile. / RNA polymerase I, Rpa2 specific domain / RNA polymerase I specific transcription initiation factor RRN3 / RNA polymerase Rpb6 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases N / 8 kDa subunit / RNA polymerases M/15 Kd subunit / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb8 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase I specific initiation factor / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase subunit/transcription factor S / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / Zinc finger, TFIIS-type / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit N/Rpb10 / Dual incision in TC-NER / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase II transcribes snRNA genes / RNA polymerase, Rpb5, N-terminal / 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, Rpb8 / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase Rpb7, N-terminal / Transcription initiation factor Rrn11 / DNA-directed RNA polymerase, insert domain
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 6.9 Å resolution
AuthorsEngel C / Gubbey T / Neyer S / Sainsbury S / Oberthuer C / Baejen C / Bernecky C / Cramer P
CitationJournal: Cell / Year: 2017
Title: Structural Basis of RNA Polymerase I Transcription Initiation.
Authors: Christoph Engel / Tobias Gubbey / Simon Neyer / Sarah Sainsbury / Christiane Oberthuer / Carlo Baejen / Carrie Bernecky / Patrick Cramer
Abstract: Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron ...Transcription initiation at the ribosomal RNA promoter requires RNA polymerase (Pol) I and the initiation factors Rrn3 and core factor (CF). Here, we combine X-ray crystallography and cryo-electron microscopy (cryo-EM) to obtain a molecular model for basal Pol I initiation. The three-subunit CF binds upstream promoter DNA, docks to the Pol I-Rrn3 complex, and loads DNA into the expanded active center cleft of the polymerase. DNA unwinding between the Pol I protrusion and clamp domains enables cleft contraction, resulting in an active Pol I conformation and RNA synthesis. Comparison with the Pol II system suggests that promoter specificity relies on a distinct "bendability" and "meltability" of the promoter sequence that enables contacts between initiation factors, DNA, and polymerase.
Validation ReportPDB-ID: 5n61

SummaryFull reportAbout validation report
DateDeposition: Feb 14, 2017 / Header (metadata) release: Mar 22, 2017 / Map release: Apr 12, 2017 / Last update: Sep 13, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5n61
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_3594.map.gz (map file in CCP4 format, 143749 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
330 pix
1.13 Å/pix.
= 372.9 Å
330 pix
1.13 Å/pix.
= 372.9 Å
330 pix
1.13 Å/pix.
= 372.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13 Å
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.050090574 - 0.13193528
Average (Standard dev.)0.0006353547 (0.008975409)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions330330330
Origin000
Limit329329329
Spacing330330330
CellA=B=C: 372.9 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.131.131.13
M x/y/z330330330
origin x/y/z0.0000.0000.000
length x/y/z372.900372.900372.900
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS330330330
D min/max/mean-0.0500.1320.001

-
Supplemental data

-
Sample components

+
Entire RNA polymerase I initially transcribing complex

EntireName: RNA polymerase I initially transcribing complex / Number of components: 5

+
Component #1: protein, RNA polymerase I initially transcribing complex

ProteinName: RNA polymerase I initially transcribing complex / Recombinant expression: No

+
Component #2: protein, RNA polymerase I

ProteinName: RNA polymerase I / Recombinant expression: No
MassTheoretical: 590 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

+
Component #3: protein, Initiation factor Rrn3

ProteinName: Initiation factor Rrn3 / Recombinant expression: No
MassTheoretical: 70 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #4: protein, Core Factor

ProteinName: Core Factor / Recombinant expression: No
MassTheoretical: 220 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #5: protein, Initial transcription DNA/RNA scaffold

ProteinName: Initial transcription DNA/RNA scaffold / Recombinant expression: No
MassTheoretical: 60 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: synthetic construct (others)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.8
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 345000
3D reconstructionResolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF

-
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