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- PDB-6ro4: Structure of the core TFIIH-XPA-DNA complex -

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Entry
Database: PDB / ID: 6ro4
TitleStructure of the core TFIIH-XPA-DNA complex
Components
  • (General transcription factor IIH subunit ...) x 4
  • DNA repair protein complementing XP-A cells
  • DNA1
  • DNA2
  • General transcription and DNA repair factor IIH helicase subunit XPB
  • TFIIH basal transcription factor complex helicase XPD subunit
KeywordsTRANSLOCASE / Complex / Helicase / DNA repair
Function / homology
Function and homology information


nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / response to auditory stimulus / positive regulation of DNA helicase activity / central nervous system myelin formation / CAK-ERCC2 complex / hair follicle maturation / Cytosolic iron-sulfur cluster assembly ...nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair factor 1 complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / response to auditory stimulus / positive regulation of DNA helicase activity / central nervous system myelin formation / CAK-ERCC2 complex / hair follicle maturation / Cytosolic iron-sulfur cluster assembly / positive regulation of mitotic recombination / hair cell differentiation / nucleotide-excision repair factor 3 complex / embryonic cleavage / transcription factor TFIIH core complex / UV protection / transcription factor TFIIH holo complex / UV-damage excision repair / transcription elongation from RNA polymerase I promoter / G protein-coupled receptor internalization / phosphorylation of RNA polymerase II C-terminal domain / RNA Polymerase I Transcription Termination / 5'-3' DNA helicase activity / RNA Pol II CTD phosphorylation and interaction with CE / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / Formation of the HIV-1 Early Elongation Complex / Formation of the Early Elongation Complex / mRNA Capping / intercellular bridge / 3'-5' DNA helicase activity / bone mineralization / transcription initiation from RNA polymerase I promoter / HIV Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II HIV Promoter Escape / RNA Polymerase II Transcription Initiation / RNA Polymerase II Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Transcription Initiation And Promoter Clearance / termination of RNA polymerase I transcription / nucleotide-excision repair, preincision complex stabilization / ATPase activator activity / RNA polymerase II general transcription initiation factor activity / nucleotide-excision repair, DNA incision, 3'-to lesion / RNA Polymerase I Transcription Initiation / transcription factor TFIID complex / spinal cord development / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / erythrocyte maturation / hematopoietic stem cell differentiation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / protein localization to nucleus / DNA topological change / RNA Polymerase II Pre-transcription Events / transcription preinitiation complex / regulation of mitotic cell cycle phase transition / embryonic organ development / 7-methylguanosine mRNA capping / response to UV / transcription elongation from RNA polymerase II promoter / post-embryonic development / RNA Polymerase I Promoter Escape / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / nucleotide-excision repair, DNA damage recognition / NoRC negatively regulates rRNA expression / nucleotide-excision repair, DNA duplex unwinding / global genome nucleotide-excision repair / nucleotide-excision repair, preincision complex assembly / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / nucleotide-excision repair, DNA incision, 5'-to lesion / positive regulation of DNA binding / Dual Incision in GG-NER / base-excision repair / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nucleotide-excision repair, DNA incision / chromosome segregation / Dual incision in TC-NER / Formation of Incision Complex in GG-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to gamma radiation / protein-macromolecule adaptor activity / multicellular organism growth / spindle / transcription by RNA polymerase II / transcription-coupled nucleotide-excision repair / cell population proliferation / 4 iron, 4 sulfur cluster binding / DNA helicase / sequence-specific double-stranded DNA binding / DNA helicase activity / extracellular matrix organization / protein localization / double-stranded DNA binding / protein N-terminus binding / in utero embryonic development
Similarity search - Function
TFB5-like / XPA protein N-terminal / XPA / Zinc finger, XPA-type, conserved site / XPA protein C-terminus / XPA, conserved site / XPA, C-terminal / XPA protein signature 2. / XPA protein signature 1. / XPA domain superfamily ...TFB5-like / XPA protein N-terminal / XPA / Zinc finger, XPA-type, conserved site / XPA protein C-terminus / XPA, conserved site / XPA, C-terminal / XPA protein signature 2. / XPA protein signature 1. / XPA domain superfamily / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH C1-like domain / RAD3/XPD family / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Helical and beta-bridge domain / Helical and beta-bridge domain / ATP-dependent helicase Rad3/Chl1-like / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / Helicase XPB/Ssl2 / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / ERCC3/RAD25/XPB helicase, C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / TFIIH subunit TTDA/Tfb5 / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / Helicase-like, DEXD box c2 type / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / HELICc2 / Helicase C-terminal domain / DEAD_2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD2 / DEXDc2 / Putative DNA-binding domain superfamily / Type III restriction enzyme, res subunit / Helicase/UvrB, N-terminal / DEAH-box subfamily ATP-dependent helicases signature. / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / 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 / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Helicase, C-terminal / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / Alpha-Beta Plaits / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
General transcription factor IIH subunit 5 / General transcription factor IIH subunit 3 / DNA repair protein complementing XP-A cells / General transcription factor IIH subunit 2 / IRON/SULFUR CLUSTER / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription and DNA repair factor IIH helicase subunit XPD / DNA (> 10) / DNA / General transcription factor IIH subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKokic, G. / Chernev, A. / Tegunov, D. / Dienemann, C. / Urlaub, H. / Cramer, P.
Funding support Germany, 4items
OrganizationGrant numberCountry
German Research FoundationSFB860 Germany
German Research FoundationSPP1935 Germany
European Research Council693023
Volkswagen Foundation
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis of TFIIH activation for nucleotide excision repair.
Authors: Goran Kokic / Aleksandar Chernev / Dimitry Tegunov / Christian Dienemann / Henning Urlaub / Patrick Cramer /
Abstract: Nucleotide excision repair (NER) is the major DNA repair pathway that removes UV-induced and bulky DNA lesions. There is currently no structure of NER intermediates, which form around the large ...Nucleotide excision repair (NER) is the major DNA repair pathway that removes UV-induced and bulky DNA lesions. There is currently no structure of NER intermediates, which form around the large multisubunit transcription factor IIH (TFIIH). Here we report the cryo-EM structure of an NER intermediate containing TFIIH and the NER factor XPA. Compared to its transcription conformation, the TFIIH structure is rearranged such that its ATPase subunits XPB and XPD bind double- and single-stranded DNA, consistent with their translocase and helicase activities, respectively. XPA releases the inhibitory kinase module of TFIIH, displaces a 'plug' element from the DNA-binding pore in XPD, and together with the NER factor XPG stimulates XPD activity. Our results explain how TFIIH is switched from a transcription to a repair factor, and provide the basis for a mechanistic analysis of the NER pathway.
History
DepositionMay 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_seq_map_depositor_info.one_letter_code_mod

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Structure visualization

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Assembly

Deposited unit
J: DNA1
K: DNA2
A: General transcription and DNA repair factor IIH helicase subunit XPB
F: General transcription factor IIH subunit 5
B: TFIIH basal transcription factor complex helicase XPD subunit
E: General transcription factor IIH subunit 3
D: General transcription factor IIH subunit 2
C: General transcription factor IIH subunit 4
G: DNA repair protein complementing XP-A cells
hetero molecules


Theoretical massNumber of molelcules
Total (without water)377,90816
Polymers377,1649
Non-polymers7447
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, The complex formation and composition was further validated by crosslinking mass spectrometry and cryo-EM.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area25980 Å2
ΔGint-157 kcal/mol
Surface area109550 Å2
MethodPISA

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Components

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DNA chain , 2 types, 2 molecules JK

#1: DNA chain DNA1


Mass: 15036.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA2


Mass: 15075.698 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Protein , 3 types, 3 molecules ABG

#3: Protein General transcription and DNA repair factor IIH helicase subunit XPB / TFIIH subunit XPB / Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair ...TFIIH subunit XPB / Basic transcription factor 2 89 kDa subunit / BTF2 p89 / DNA excision repair protein ERCC-3 / DNA repair protein complementing XP-B cells / TFIIH basal transcription factor complex 89 kDa subunit / TFIIH p89 / Xeroderma pigmentosum group B-complementing protein


Mass: 89404.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC3, XPB, XPBC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P19447, DNA helicase
#5: Protein TFIIH basal transcription factor complex helicase XPD subunit / Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision repair protein ERCC-2 ...Basic transcription factor 2 80 kDa subunit / BTF2 p80 / CXPD / DNA excision repair protein ERCC-2 / DNA repair protein complementing XP-D cells / TFIIH basal transcription factor complex 80 kDa subunit / TFIIH p80 / Xeroderma pigmentosum group D-complementing protein


Mass: 87021.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERCC2, XPD, XPDC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P18074, DNA helicase
#9: Protein DNA repair protein complementing XP-A cells / / Xeroderma pigmentosum group A-complementing protein


Mass: 31422.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPA, XPAC / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P23025

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General transcription factor IIH subunit ... , 4 types, 4 molecules FEDC

#4: Protein General transcription factor IIH subunit 5 / General transcription factor IIH polypeptide 5 / TFB5 ortholog / TFIIH basal transcription factor ...General transcription factor IIH polypeptide 5 / TFB5 ortholog / TFIIH basal transcription factor complex TTD-A subunit


Mass: 8060.362 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H5, C6orf175, TTDA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6ZYL4
#6: Protein General transcription factor IIH subunit 3 / Basic transcription factor 2 34 kDa subunit / BTF2 p34 / General transcription factor IIH ...Basic transcription factor 2 34 kDa subunit / BTF2 p34 / General transcription factor IIH polypeptide 3 / TFIIH basal transcription factor complex p34 subunit


Mass: 34416.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13889
#7: Protein General transcription factor IIH subunit 2 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH ...Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH polypeptide 2 / TFIIH basal transcription factor complex p44 subunit


Mass: 44481.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H2, BTF2P44 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13888
#8: Protein General transcription factor IIH subunit 4 / Basic transcription factor 2 52 kDa subunit / BTF2 p52 / General transcription factor IIH ...Basic transcription factor 2 52 kDa subunit / BTF2 p52 / General transcription factor IIH polypeptide 4 / TFIIH basal transcription factor complex p52 subunit


Mass: 52245.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92759

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Non-polymers , 2 types, 7 molecules

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


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


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Core TFIIH-XPA-DNA complexCOMPLEX#1-#90MULTIPLE SOURCES
2TFIIH-XPACOMPLEX#3-#91RECOMBINANT
3DNACOMPLEX#1-#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Trichoplusia ni (cabbage looper)7111
33synthetic construct (others)32630
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: 4 ul of sample was applied to glow-discharged grids which were blotted for 5s and plunge-frozen in liquid ethane.

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Cs: 2.7 mm
Image recordingElectron dose: 41 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227776 / Symmetry type: POINT

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