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- PDB-7ad8: Core TFIIH-XPA-DNA complex with modelled p62 subunit -

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Entry
Database: PDB / ID: 7ad8
TitleCore TFIIH-XPA-DNA complex with modelled p62 subunit
Components
  • (DNA (49-MER)) x 2
  • (General transcription factor IIH subunit ...) x 5
  • DNA repair protein complementing XP-A cells
  • General transcription and DNA repair factor IIH helicase subunit XPB
  • TFIIH basal transcription factor complex helicase XPD subunit
KeywordsDNA BINDING PROTEIN / DNA repair / transcription factor
Function / homology
Function and homology information


nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / nucleotide-excision repair factor 3 complex ...nucleotide-excision repair factor 1 complex / nucleotide-excision repair involved in interstrand cross-link repair / nucleotide-excision repair, DNA damage recognition / MMXD complex / core TFIIH complex portion of holo TFIIH complex / Cytosolic iron-sulfur cluster assembly / central nervous system myelin formation / positive regulation of mitotic recombination / hair cell differentiation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / hair follicle maturation / CAK-ERCC2 complex / embryonic cleavage / UV protection / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / DNA 5'-3' helicase / G protein-coupled receptor internalization / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / UV-damage excision repair / transcription factor TFIID complex / regulation of mitotic cell cycle phase transition / RNA polymerase II general transcription initiation factor activity / erythrocyte maturation / hematopoietic stem cell proliferation / spinal cord development / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / bone mineralization / mRNA Capping / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / ATPase activator activity / 3'-5' DNA helicase activity / DNA 3'-5' helicase / DNA topological change / intrinsic apoptotic signaling pathway by p53 class mediator / RNA Polymerase I Transcription Initiation / hematopoietic stem cell differentiation / embryonic organ development / positive regulation of transcription initiation by RNA polymerase II / protein localization to nucleus / Tat-mediated elongation of the HIV-1 transcript / transcription elongation by RNA polymerase I / Formation of HIV-1 elongation complex containing HIV-1 Tat / response to UV / Formation of HIV elongation complex in the absence of HIV Tat / transcription by RNA polymerase I / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / transcription-coupled nucleotide-excision repair / extracellular matrix organization / hormone-mediated signaling pathway / RNA Polymerase II Pre-transcription Events / insulin-like growth factor receptor signaling pathway / DNA helicase activity / determination of adult lifespan / regulation of autophagy / post-embryonic development / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nucleotide-excision repair / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / chromosome segregation / promoter-specific chromatin binding / transcription elongation by RNA polymerase II / RNA Polymerase I Promoter Escape / cellular response to gamma radiation / base-excision repair / NoRC negatively regulates rRNA expression / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / multicellular organism growth / response to toxic substance / spindle / Formation of TC-NER Pre-Incision Complex / intrinsic apoptotic signaling pathway in response to DNA damage / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / sequence-specific double-stranded DNA binding / intracellular protein localization / 4 iron, 4 sulfur cluster binding / response to oxidative stress / double-stranded DNA binding / transcription by RNA polymerase II / 5'-3' DNA helicase activity / in utero embryonic development / damaged DNA binding
Similarity search - Function
XPA protein N-terminal / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site / XPA protein C-terminus / XPA protein signature 1. / XPA protein signature 2. / XPA domain superfamily / TFIIH subunit Tfb4/GTF2H3 ...XPA protein N-terminal / XPA / Zinc finger, XPA-type, conserved site / XPA, C-terminal / XPA, conserved site / XPA protein C-terminus / XPA protein signature 1. / XPA protein signature 2. / XPA domain 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 / Helicase XPB/Ssl2, N-terminal domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / TFIIH subunit TTDA/Tfb5 / Helical and beta-bridge domain / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Helical and beta-bridge domain / Transcription factor TFIIH complex subunit Tfb5 / ATP-dependent helicase Rad3/Chl1-like / ERCC3/RAD25/XPB helicase, C-terminal domain / : / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / HELICc2 / ATP-dependent helicase, C-terminal / Helicase C-terminal domain / Putative DNA-binding domain superfamily / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-type / PH-like domain 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 / 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 / General transcription and DNA repair factor IIH helicase/translocase subunit XPB / DNA repair protein complementing XP-A cells / General transcription factor IIH subunit 1 / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsKoelmel, W. / Kuper, J. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KI 562/11-1 Germany
CitationJournal: Nucleic Acids Res / Year: 2020
Title: The TFIIH subunits p44/p62 act as a damage sensor during nucleotide excision repair.
Authors: Jamie T Barnett / Jochen Kuper / Wolfgang Koelmel / Caroline Kisker / Neil M Kad /
Abstract: Nucleotide excision repair (NER) in eukaryotes is orchestrated by the core form of the general transcription factor TFIIH, containing the helicases XPB, XPD and five 'structural' subunits, p62, p44, ...Nucleotide excision repair (NER) in eukaryotes is orchestrated by the core form of the general transcription factor TFIIH, containing the helicases XPB, XPD and five 'structural' subunits, p62, p44, p34, p52 and p8. Recent cryo-EM structures show that p62 makes extensive contacts with p44 and in part occupies XPD's DNA binding site. While p44 is known to regulate the helicase activity of XPD during NER, p62 is thought to be purely structural. Here, using helicase and adenosine triphosphatase assays we show that a complex containing p44 and p62 enhances XPD's affinity for dsDNA 3-fold over p44 alone. Remarkably, the relative affinity is further increased to 60-fold by dsDNA damage. Direct binding studies show this preference derives from p44/p62's high affinity (20 nM) for damaged ssDNA. Single molecule imaging of p44/p62 complexes without XPD reveals they bind to and randomly diffuse on DNA, however, in the presence of UV-induced DNA lesions these complexes stall. Combined with the analysis of a recent cryo-EM structure, we suggest that p44/p62 acts as a novel DNA-binding entity that enhances damage recognition in TFIIH. This revises our understanding of TFIIH and prompts investigation into the core subunits for an active role during DNA repair and/or transcription.
History
DepositionSep 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
J: DNA (49-MER)
K: DNA (49-MER)
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
I: General transcription factor IIH subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)440,02417
Polymers439,28010
Non-polymers7447
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area31990 Å2
ΔGint-279 kcal/mol
Surface area119360 Å2
MethodPISA

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Components

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DNA chain , 2 types, 2 molecules JK

#1: DNA chain DNA (49-MER)


Mass: 15036.663 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (49-MER)


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 ... , 5 types, 5 molecules FEDCI

#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
#10: Protein General transcription factor IIH subunit 1 / Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH ...Basic transcription factor 2 62 kDa subunit / BTF2 p62 / General transcription factor IIH polypeptide 1 / TFIIH basal transcription factor complex p62 subunit


Mass: 62116.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2H1, BTF2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P32780

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Non-polymers , 2 types, 7 molecules

#11: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


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


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

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Details

Has ligand of interestN

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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 complex with modelled p62 subunitCOMPLEX#1-#100MULTIPLE SOURCES
2TFIIHCOMPLEX#3-#101RECOMBINANT
3DNACOMPLEX#1-#21RECOMBINANT
Molecular weightExperimental value: NO
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
VitrificationCryogen name: 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 FIELD
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
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 227776 / Symmetry type: POINT

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