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- EMDB-22576: TFIIH/Rad4-23-33 Complex in NER focused on Rad4-33 -

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Basic information

Entry
Database: EMDB / ID: EMD-22576
TitleTFIIH/Rad4-23-33 Complex in NER focused on Rad4-33
Map dataCryo-EM map of TFIIH in complex with Rad4-Rad33 on AAF DNA with focused classification on Rad4-33-Ssl2 contacts. Composite map after multibody refinement.
Sample
  • Complex: Ternary complex of Saccharomyces cerevisiae TFIIH, DNA damage proteins Rad4-Rad23-Rad33 and N-acetoxy-acetominofluorinated DNA.
Function / homology
Function and homology information


nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / SUMOylation of DNA damage response and repair proteins / positive regulation of mitotic recombination / DNA translocase activity ...nucleotide-excision repair factor 2 complex / single-strand break-containing DNA binding / XPC complex / nucleotide-excision repair, DNA damage recognition / regulation of mitotic recombination / RNA polymerase II promoter clearance / phosphatidylinositol-5-phosphate binding / SUMOylation of DNA damage response and repair proteins / positive regulation of mitotic recombination / DNA translocase activity / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / transcription open complex formation at RNA polymerase II promoter / phosphatidylinositol-3-phosphate binding / 5'-3' DNA helicase activity / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / 3'-5' DNA helicase activity / transcription preinitiation complex / poly(A)+ mRNA export from nucleus / DNA duplex unwinding / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / 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 Polymerase II Pre-transcription Events / Dual incision in TC-NER / ATPase activator activity / Gap-filling DNA repair synthesis and ligation in TC-NER / DNA topological change / mismatch repair / transcription by RNA polymerase I / ATP-dependent activity, acting on DNA / DNA helicase activity / transcription initiation at RNA polymerase II promoter / nucleotide-excision repair / ubiquitin protein ligase activity / single-stranded DNA binding / 4 iron, 4 sulfur cluster binding / double-stranded DNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA helicase / transcription by RNA polymerase II / damaged DNA binding / DNA repair / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Rad33 / Rad33 / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 ...Rad33 / Rad33 / DNA repair protein Rad4 / DNA repair protein Rad4, subgroup / Rad4/PNGase transglutaminase-like fold / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4, beta-hairpin domain 3 superfamily / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 3 / Rad4 beta-hairpin domain 1 / Rad4 beta-hairpin domain 2 / Rad4 beta-hairpin domain 3 / Rad4 transglutaminase-like domain / Bacterial type XPD DNA helicase, FeS cluster domain / Transglutaminase-like superfamily / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / RAD3/XPD family / Helicase XPB/Ssl2 / Helical and beta-bridge domain / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helical and beta-bridge domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH subunit p52/Tfb2 / ATP-dependent helicase Rad3/Chl1-like / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / TFIIH subunit TTDA/Tfb5 / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / Helicase superfamily 1/2, DinG/Rad3-like / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / DEAD2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD_2 / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 / HELICc2 / Helicase/UvrB, N-terminal / Type III restriction enzyme, res subunit / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / C1-like domain superfamily / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-type / Papain-like cysteine peptidase superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
General transcription and DNA repair factor IIH helicase subunit XPD / DNA repair protein RAD4 / General transcription and DNA repair factor IIH subunit TFB1 / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription and DNA repair factor IIH subunit TFB2 / DNA repair protein RAD33 / General transcription and DNA repair factor IIH subunit SSL1 / General transcription and DNA repair factor IIH subunit TFB4 / General transcription and DNA repair factor IIH subunit TFB5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
Authorsvan Eeuwen T / Murakami K
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM123233 United States
CitationJournal: Nat Commun / Year: 2021
Title: Cryo-EM structure of TFIIH/Rad4-Rad23-Rad33 in damaged DNA opening in nucleotide excision repair.
Authors: Trevor van Eeuwen / Yoonjung Shim / Hee Jong Kim / Tingting Zhao / Shrabani Basu / Benjamin A Garcia / Craig D Kaplan / Jung-Hyun Min / Kenji Murakami /
Abstract: The versatile nucleotide excision repair (NER) pathway initiates as the XPC-RAD23B-CETN2 complex first recognizes DNA lesions from the genomic DNA and recruits the general transcription factor ...The versatile nucleotide excision repair (NER) pathway initiates as the XPC-RAD23B-CETN2 complex first recognizes DNA lesions from the genomic DNA and recruits the general transcription factor complex, TFIIH, for subsequent lesion verification. Here, we present a cryo-EM structure of an NER initiation complex containing Rad4-Rad23-Rad33 (yeast homologue of XPC-RAD23B-CETN2) and 7-subunit coreTFIIH assembled on a carcinogen-DNA adduct lesion at 3.9-9.2 Å resolution. A ~30-bp DNA duplex could be mapped as it straddles between Rad4 and the Ssl2 (XPB) subunit of TFIIH on the 3' and 5' side of the lesion, respectively. The simultaneous binding with Rad4 and TFIIH was permitted by an unwinding of DNA at the lesion. Translocation coupled with torque generation by Ssl2 and Rad4 would extend the DNA unwinding at the lesion and deliver the damaged strand to Rad3 (XPD) in an open form suitable for subsequent lesion scanning and verification.
History
DepositionSep 2, 2020-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateJul 28, 2021-
Current statusJul 28, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00239
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.00239
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7m2u
  • Surface level: 0.00239
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22576.png

Downloads & links

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Map

FileDownload / File: emd_22576.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of TFIIH in complex with Rad4-Rad33 on AAF DNA with focused classification on Rad4-33-Ssl2 contacts. Composite map after multibody refinement.
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.00239 / Movie #1: 0.00239
Minimum - Maximum-0.0019033871 - 0.0066725626
Average (Standard dev.)-1.4589203e-05 (±0.00044120074)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z324.000324.000324.000
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0020.007-0.000

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Supplemental data

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Additional map: Cryo-EM map of TFIIH in complex with Rad4-Rad33...

Fileemd_22576_additional_1.map
AnnotationCryo-EM map of TFIIH in complex with Rad4-Rad33 on AAF DNA with focused classification on Rad4-33-Ssl2 contacts. TFIIH body from multibody refinement used for composite map making.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Cryo-EM map of TFIIH in complex with Rad4-Rad33...

Fileemd_22576_additional_2.map
AnnotationCryo-EM map of TFIIH in complex with Rad4-Rad33 on AAF DNA with focused classification on Rad4-33-Ssl2 contacts. Map locally filtered to FSC=0.5 by blocre
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered Half Map 1

Fileemd_22576_half_map_1.map
AnnotationUnfiltered Half Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered Half Map 2

Fileemd_22576_half_map_2.map
AnnotationUnfiltered Half Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of Saccharomyces cerevisiae TFIIH, DNA damage pro...

EntireName: Ternary complex of Saccharomyces cerevisiae TFIIH, DNA damage proteins Rad4-Rad23-Rad33 and N-acetoxy-acetominofluorinated DNA.
Components
  • Complex: Ternary complex of Saccharomyces cerevisiae TFIIH, DNA damage proteins Rad4-Rad23-Rad33 and N-acetoxy-acetominofluorinated DNA.

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Supramolecule #1: Ternary complex of Saccharomyces cerevisiae TFIIH, DNA damage pro...

SupramoleculeName: Ternary complex of Saccharomyces cerevisiae TFIIH, DNA damage proteins Rad4-Rad23-Rad33 and N-acetoxy-acetominofluorinated DNA.
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightExperimental: 570 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
150.0 mMKoACPotassium Acetate
5.0 mMC4H10O2S2DTT
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC
Details: Manually blotted for 2-3 seconds prior to plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 595544 / Details: Particles autopicked by croySPARC blob picker
CTF correctionSoftware - Name: CTFFIND (ver. 4.13)
Startup modelType of model: OTHER / Details: Ab initio model derived from cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 32858
FSC plot (resolution estimation)

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