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- PDB-6o9m: Structure of the human apo TFIIH -

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Entry
Database: PDB / ID: 6o9m
TitleStructure of the human apo TFIIH
Components
  • (General transcription factor IIH subunit ...) x 5
  • (TFIIH basal transcription factor complex helicase ...) x 2
  • CDK-activating kinase assembly factor MAT1
KeywordsTRANSCRIPTION / Transcription initiation / Molecular dynamics / Gene regulation / Community network analysis / Global protein dynamics / RNA polymerase
Function / homology
Function and homology information


Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Formation of HIV elongation complex in the absence of HIV Tat / Formation of the HIV-1 Early Elongation Complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Polymerase II HIV Promoter Escape / HIV Transcription Initiation / Transcription of the HIV genome / RNA Polymerase I Transcription Termination / Cyclin A/B1/B2 associated events during G2/M transition ...Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Formation of HIV elongation complex in the absence of HIV Tat / Formation of the HIV-1 Early Elongation Complex / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Polymerase II HIV Promoter Escape / HIV Transcription Initiation / Transcription of the HIV genome / RNA Polymerase I Transcription Termination / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / mRNA Capping / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase II Promoter Escape / rt:r-hsa-73777: / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Cyclin D associated events in G1 / Cyclin E associated events during G1/S transition / Dual Incision in GG-NER / Formation of HIV-1 elongation complex containing HIV-1 Tat / Tat-mediated elongation of the HIV-1 transcript / Cytosolic iron-sulfur cluster assembly / NoRC negatively regulates rRNA expression / Formation of Incision Complex in GG-NER / RNA Polymerase II Pre-transcription Events / Formation of TC-NER Pre-Incision Complex / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / TP53 Regulates Transcription of DNA Repair Genes / cyclin-dependent protein kinase activating kinase holoenzyme complex / negative regulation of DNA helicase activity / ventricular system development / CAK-ERCC2 complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / positive regulation of mitotic recombination / central nervous system myelin formation / 5'-3' DNA helicase activity / regulation of mitotic recombination / erythrocyte maturation / hair follicle maturation / nucleotide-excision repair factor 3 complex / adult heart development / hair cell differentiation / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / embryonic cleavage / 3'-5' DNA helicase activity / cyclin-dependent protein serine/threonine kinase activator activity / phosphorylation of RNA polymerase II C-terminal domain / transcription initiation from RNA polymerase I promoter / UV protection / G protein-coupled receptor internalization / hematopoietic stem cell differentiation / go:0043141: / rDNA binding / transcription elongation from RNA polymerase I promoter / termination of RNA polymerase I transcription / RNA polymerase II general transcription initiation factor activity / ATPase activator activity / nucleotide-excision repair, preincision complex stabilization / nucleotide-excision repair, DNA incision, 3'-to lesion / transcription factor TFIID complex / go:0004003: / spinal cord development / bone mineralization / transcription by RNA polymerase I / DNA-dependent ATPase activity / DNA topological change / 7-methylguanosine mRNA capping / transcriptional preinitiation complex / embryonic organ development / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of mitotic cell cycle phase transition / transcription elongation from RNA polymerase II promoter / response to UV / post-embryonic development / ec:3.6.4.12: / protein localization / nucleotide-excision repair, DNA duplex unwinding / global genome nucleotide-excision repair / chromosome segregation / nucleotide-excision repair, preincision complex assembly / nucleotide-excision repair / nucleotide-excision repair, DNA incision, 5'-to lesion / helicase activity / protein binding, bridging / nucleotide-excision repair, DNA incision / rRNA processing / positive regulation of DNA binding / cellular response to gamma radiation / spindle
BSD domain / Helicase/UvrB, N-terminal / DEAH-box subfamily ATP-dependent helicases signature. / Zinc finger RING-type profile. / Ssl1-like / VWFA domain profile. / Helicase-like, DEXD box c2 type / Ubiquitin-interacting motif (UIM) domain profile. / ATP-dependent helicase, C-terminal / BSD domain profile. ...BSD domain / Helicase/UvrB, N-terminal / DEAH-box subfamily ATP-dependent helicases signature. / Zinc finger RING-type profile. / Ssl1-like / VWFA domain profile. / Helicase-like, DEXD box c2 type / Ubiquitin-interacting motif (UIM) domain profile. / ATP-dependent helicase, C-terminal / BSD domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / TFIIH subunit Tfb4/GTF2H3 / Ssl1-like / TFIIH subunit TTDA/Tfb5 / DEAD2 / Superfamilies 1 and 2 helicase C-terminal domain profile. / Helical and beta-bridge domain / BSD domain / Zinc finger RING-type signature. / TFIIH C1-like domain / Type III restriction enzyme, res subunit / Transcription factor TFIIH complex subunit Tfb5 / Helicase XPB/Ssl2 / CDK-activating kinase assembly factor MAT1 / Helicase, C-terminal / Zinc finger, RING-type / DEAD_2 / Helical and beta-bridge domain / RAD3/XPD family / von Willebrand factor, type A / Transcription factor Tfb2 (p52) C-terminal domain / TFIIH p62 subunit, N-terminal domain / Helicase C-terminal domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Zinc finger, C3HC4 type (RING finger) / Ubiquitin interacting motif / Cdk-activating kinase assembly factor MAT1/Tfb3 / TFIIH C1-like domain / Transcription factor TFIIH subunit p52/Tfb2 / PH-like domain superfamily / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / TFIIH subunit Tfb1/GTF2H1 / TFB5-like superfamily / von Willebrand factor A-like domain superfamily / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb4 / P-loop containing nucleoside triphosphate hydrolase / TFIIH subunit Ssl1/p44 / ATP-dependent helicase Rad3/Chl1-like / Zinc finger, RING/FYVE/PHD-type / Zinc finger C2H2-type / TFIIH p62 subunit, N-terminal / Helicase superfamily 1/2, ATP-binding domain / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Cdk-activating kinase assembly factor MAT1, centre / Zinc finger, RING-type, conserved site
General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription factor IIH subunit 1 / CDK-activating kinase assembly factor MAT1 / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 4
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsYan, C.L. / Dodd, T. / He, Y. / Tainer, J.A. / Tsutakawa, S.E. / Ivanov, I.
Funding supportUnited States , 1件
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM110387United States
CitationJournal: Nature / Year: 2017
Title: The cryo-electron microscopy structure of human transcription factor IIH.
Authors: Basil J Greber / Thi Hoang Duong Nguyen / Jie Fang / Pavel V Afonine / Paul D Adams / Eva Nogales /
Abstract: Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcription. Composed of ten subunits ...Human transcription factor IIH (TFIIH) is part of the general transcriptional machinery required by RNA polymerase II for the initiation of eukaryotic gene transcription. Composed of ten subunits that add up to a molecular mass of about 500 kDa, TFIIH is also essential for nucleotide excision repair. The seven-subunit TFIIH core complex formed by XPB, XPD, p62, p52, p44, p34, and p8 is competent for DNA repair, while the CDK-activating kinase subcomplex, which includes the kinase activity of CDK7 as well as the cyclin H and MAT1 subunits, is additionally required for transcription initiation. Mutations in the TFIIH subunits XPB, XPD, and p8 lead to severe premature ageing and cancer propensity in the genetic diseases xeroderma pigmentosum, Cockayne syndrome, and trichothiodystrophy, highlighting the importance of TFIIH for cellular physiology. Here we present the cryo-electron microscopy structure of human TFIIH at 4.4 Å resolution. The structure reveals the molecular architecture of the TFIIH core complex, the detailed structures of its constituent XPB and XPD ATPases, and how the core and kinase subcomplexes of TFIIH are connected. Additionally, our structure provides insight into the conformational dynamics of TFIIH and the regulation of its activity.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 14, 2019 / Release: May 29, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0May 29, 2019Structure modelrepositoryInitial release
1.1Jun 5, 2019Structure modelData collection / Database referencescitation_citation.pdbx_database_id_PubMed / _citation.title
1.2Jun 19, 2019Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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Assembly

Deposited unit
0: TFIIH basal transcription factor complex helicase XPD subunit
1: General transcription factor IIH subunit 1
2: General transcription factor IIH subunit 4, p52
3: CDK-activating kinase assembly factor MAT1
4: General transcription factor IIH subunit 3
5: General transcription factor IIH subunit 5
6: General transcription factor IIH subunit 2
7: TFIIH basal transcription factor complex helicase XPB subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)414,36415
Polymers413,6208
Non-polymers7447
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area41810 Å2
ΔGint-346 kcal/mol
Surface area156200 Å2

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Components

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TFIIH basal transcription factor complex helicase ... , 2 types, 2 molecules 07

#1: Protein/peptide TFIIH basal transcription factor complex helicase XPD subunit / 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18074, EC: 3.6.4.12
#8: Protein/peptide TFIIH basal transcription factor complex helicase XPB subunit / 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P19447, EC: 3.6.4.12

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General transcription factor IIH subunit ... , 5 types, 5 molecules 12456

#2: Protein/peptide General transcription factor IIH subunit 1 / 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P32780
#3: Protein/peptide General transcription factor IIH subunit 4, p52 / 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92759
#5: Protein/peptide General transcription factor IIH subunit 3 / p34 / Basic transcription factor 2 44 kDa subunit / BTF2 p44 / General transcription factor IIH polypeptide 2 / TFIIH basal transcription factor complex p44 subunit


Mass: 34416.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13889
#6: Protein/peptide General transcription factor IIH subunit 5 / 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6ZYL4
#7: Protein/peptide General transcription factor IIH subunit 2 / 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 natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13888

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Protein/peptide , 1 types, 1 molecules 3

#4: Protein/peptide CDK-activating kinase assembly factor MAT1 / CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger protein 66 / RING finger protein MAT1 / p35 / p36


Mass: 35873.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P51948

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Non-polymers , 2 types, 7 molecules

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


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Iron–sulfur cluster
#10: Chemical
ChemComp-ZN / ZINC ION


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

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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

ComponentName: apo TFIIH / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8 / Source: NATURAL
Source (natural)Organism: Homo sapiens (human)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
7NAMD2.12model fittingMolecular dynamics flexible fitting
8UCSF Chimera1.12model fittingRigid body fit
20Coot0.8.9.1model refinementmodel building and refinement
21PHENIX1.14model refinementreal-space refinement
CTF correctionType: NONE
3D reconstructionResolution: 4.4 Å / Num. of particles: 122900 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: Initial model assembled from high-resolution structures and homology models, subsequently rebuilt in COOT, refined into the Cryo-EM map using Phenix and fully validated.

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