[English] 日本語
Yorodumi
- PDB-7m2u: Nucleotide Excision Repair complex TFIIH Rad4-33 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7m2u
TitleNucleotide Excision Repair complex TFIIH Rad4-33
Components
  • (DNA repair helicase ...) x 2
  • (DNA repair protein ...) x 2
  • (General transcription and DNA repair factor IIH subunit ...) x 5
  • Damaged DNA strand
  • Undamaged DNA strand
KeywordsNUCLEAR PROTEIN/DNA / NER / nucleotide excision repair / TFIIH / Rad4 / XPC / NUCLEAR PROTEIN / NUCLEAR PROTEIN-DNA complex
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
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / 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 ...IRON/SULFUR CLUSTER / DNA / DNA (> 10) / 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)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 Å
Authorsvan Eeuwen, T. / Murakami, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)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
DepositionMar 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-22576
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
7: DNA repair helicase RAD25
Y: Undamaged DNA strand
W: Damaged DNA strand
5: General transcription and DNA repair factor IIH subunit TFB5
0: DNA repair helicase RAD3
1: General transcription and DNA repair factor IIH subunit TFB1
4: General transcription and DNA repair factor IIH subunit TFB4
6: General transcription and DNA repair factor IIH subunit SSL1
A: DNA repair protein RAD4
E: DNA repair protein RAD33
2: General transcription and DNA repair factor IIH subunit TFB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)529,98319
Polymers529,22411
Non-polymers7598
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
DNA repair helicase ... , 2 types, 2 molecules 70

#1: Protein DNA repair helicase RAD25 / General transcription and DNA repair factor IIH subunit RAD25 / TFIIH subunit RAD25 / Suppressor of ...General transcription and DNA repair factor IIH subunit RAD25 / TFIIH subunit RAD25 / Suppressor of stem-loop mutation 2


Mass: 95461.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SSL2, LOM3, RAD25, UVS112, YIL143C / Production host: Escherichia coli (E. coli) / References: UniProt: Q00578, DNA helicase
#5: Protein DNA repair helicase RAD3 / General transcription and DNA repair factor IIH subunit RAD3 / TFIIH subunit RAD3


Mass: 89899.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P06839, DNA helicase

-
DNA chain , 2 types, 2 molecules YW

#2: DNA chain Undamaged DNA strand


Mass: 3003.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Damaged DNA strand


Mass: 4297.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
General transcription and DNA repair factor IIH subunit ... , 5 types, 5 molecules 51462

#4: Protein General transcription and DNA repair factor IIH subunit TFB5 / TFIIH subunit TFB5 / RNA polymerase II transcription factor B subunit 5


Mass: 7482.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q3E7C1
#6: Protein General transcription and DNA repair factor IIH subunit TFB1 / TFIIH subunit TFB1 / RNA polymerase II transcription factor B 73 kDa subunit / RNA polymerase II ...TFIIH subunit TFB1 / RNA polymerase II transcription factor B 73 kDa subunit / RNA polymerase II transcription factor B p73 subunit / RNA polymerase II transcription factor B subunit 1


Mass: 72993.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32776
#7: Protein General transcription and DNA repair factor IIH subunit TFB4 / TFIIH subunit TFB4 / RNA polymerase II transcription factor B 34 kDa subunit / RNA polymerase II ...TFIIH subunit TFB4 / RNA polymerase II transcription factor B 34 kDa subunit / RNA polymerase II transcription factor B p34 subunit / RNA polymerase II transcription factor B subunit 4


Mass: 37506.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q12004
#8: Protein General transcription and DNA repair factor IIH subunit SSL1 / TFIIH subunit SSL1 / RNA polymerase II transcription factor B subunit SSL1 / TFB subunit SSL1 / ...TFIIH subunit SSL1 / RNA polymerase II transcription factor B subunit SSL1 / TFB subunit SSL1 / Suppressor of stem-loop protein 1


Mass: 52370.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q04673
#11: Protein General transcription and DNA repair factor IIH subunit TFB2 / TFIIH subunit TFB2 / RNA polymerase II transcription factor B 52 kDa subunit / RNA polymerase II ...TFIIH subunit TFB2 / RNA polymerase II transcription factor B 52 kDa subunit / RNA polymerase II transcription factor B p52 subunit / RNA polymerase II transcription factor B subunit 2


Mass: 58602.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q02939

-
DNA repair protein ... , 2 types, 2 molecules AE

#9: Protein DNA repair protein RAD4 /


Mass: 87315.445 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RAD4, YER162C / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P14736
#10: Protein DNA repair protein RAD33 /


Mass: 20291.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RAD33, YML011C, YM9571.07C / Production host: Escherichia coli (E. coli) / References: UniProt: Q04231

-
Non-polymers , 3 types, 8 molecules

#12: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#13: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#14: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Ternary Complex of TFIIH/Rad4-Rad33 on damaged DNA focused on Ssl2/DNA interaction
Type: COMPLEX / Entity ID: #1-#11 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer-ID
120 mMHEPES1
280 mMpotassium acetate1
32 mMDTT1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
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: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 34000 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00523273
ELECTRON MICROSCOPYf_angle_d0.92531474
ELECTRON MICROSCOPYf_dihedral_angle_d16.9728363
ELECTRON MICROSCOPYf_chiral_restr0.0513491
ELECTRON MICROSCOPYf_plane_restr0.0064062

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
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

-
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