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- EMDB-8736: Structural Basis forEukaryotic Transcription-Coupled Repair Initiation -

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Basic information

Entry
Database: EMDB / ID: 8736
TitleStructural Basis forEukaryotic Transcription-Coupled Repair Initiation
Map dataTernary complex of RNA Pol II, transcription scaffold and Rad26
SampleTernary complex of RNA Pol II, transcription scaffold and Rad26:
Function / homologyArchaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerase subunit RPB10 / Rpb4/RPC9 superfamily / 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 ...Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerase subunit RPB10 / Rpb4/RPC9 superfamily / 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 superfamily / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, subunit RPB6 / RNA-binding domain, S1 / RNA polymerase Rpb2, domain 6 / Nucleic acid-binding, OB-fold / 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 / RNA polymerase subunit, RPB6/omega / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerases, subunit N, zinc binding site / 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 beta chain signature. / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase Rpb1, domain 7 superfamily / S1 RNA binding domain / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb1 C-terminal repeat / 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, domain 4 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb2, domain 4 / 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 polymerases K / 14 to 18 Kd subunits signature. / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb1, domain 2 / RNA polymerases M/15 Kd subunit / 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 N / 8 kDa subunit / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase beta 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 2 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerase Rpb2, domain 4 / RNA polymerases L / 13 to 16 Kd subunits signature. / TP53 Regulates Transcription of DNA Repair Genes / RNA polymerase, alpha subunit / RNA polymerase II, heptapeptide repeat, eukaryotic / DNA-directed RNA polymerase, subunit N/Rpb10 / Zinc finger TFIIS-type profile. / Formation of the Early Elongation Complex / RNA polymerase Rpb2, domain 3 / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase II transcribes snRNA genes / Zinc finger, TFIIS-type / 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, subunit H/Rpb5 C-terminal / RNA Polymerase II Pre-transcription Events / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerase Rpb4/RPC9, core / RNA polymerase, beta subunit, protrusion / 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 / 4.5 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
DateDeposition: May 19, 2017 / Header (metadata) release: Jul 26, 2017 / Map release: Dec 6, 2017 / Last update: Dec 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0376
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0376
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8736.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:0.0376 (by author), 0.0376 (movie #1):
Minimum - Maximum-0.041569784 - 0.10906077
Average (Standard dev.)0.00030721095 (0.0032241244)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin000
Limit383383383
Spacing384384384
CellA=B=C: 460.80002 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-0.0420.1090.000

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Supplemental data

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Sample components

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Entire Ternary complex of RNA Pol II, transcription scaffold and Rad26

EntireName: Ternary complex of RNA Pol II, transcription scaffold and Rad26
Number of components: 1

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Component #1: protein, Ternary complex of RNA Pol II, transcription scaffold an...

ProteinName: Ternary complex of RNA Pol II, transcription scaffold and Rad26
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Experimental details

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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 %

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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)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 19331
3D reconstructionSoftware: RELION / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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