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- PDB-7nvw: TFIIH in a pre-translocated state (without ADP-BeF3) -

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Entry
Database: PDB / ID: 7nvw
TitleTFIIH in a pre-translocated state (without ADP-BeF3)
Components
  • (General transcription ...) x 7
  • (Unassigned Peptide, likely ...) x 2
  • CDK-activating kinase assembly factor MAT1
  • Non-template DNA
  • TFIIH basal transcription factor complex helicase XPD subunit
  • Template DNA
KeywordsTRANSCRIPTION / Initiation
Function / homology
Function and homology information


cyclin-dependent protein kinase activating kinase holoenzyme complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / central nervous system myelin formation / CAK-ERCC2 complex / hair follicle maturation / Cytosolic iron-sulfur cluster assembly / ventricular system development / positive regulation of mitotic recombination ...cyclin-dependent protein kinase activating kinase holoenzyme complex / MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / central nervous system myelin formation / CAK-ERCC2 complex / hair follicle maturation / Cytosolic iron-sulfur cluster assembly / ventricular system development / positive regulation of mitotic recombination / transcription factor TFIIK complex / adult heart development / hair cell differentiation / nucleotide-excision repair factor 3 complex / embryonic cleavage / transcription factor TFIIE complex / negative regulation of DNA helicase activity / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / UV protection / transcription open complex formation at RNA polymerase II promoter / G protein-coupled receptor internalization / transcription elongation from RNA polymerase I promoter / cyclin-dependent protein serine/threonine kinase activator activity / phosphorylation of RNA polymerase II C-terminal domain / 5'-3' DNA helicase activity / RNA Polymerase I Transcription Termination / RNA Pol II CTD phosphorylation and interaction with CE / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / 3'-5' DNA helicase activity / transcription initiation from RNA polymerase I promoter / bone mineralization / thyroid hormone receptor binding / RNA Polymerase II Transcription Initiation And Promoter Clearance / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II HIV Promoter Escape / HIV Transcription Initiation / termination of RNA polymerase I transcription / ATPase activator activity / RNA polymerase II general transcription initiation factor activity / snRNA transcription by RNA polymerase II / nucleotide-excision repair, preincision complex stabilization / nucleotide-excision repair, DNA incision, 3'-to lesion / transcription factor TFIID complex / RNA Polymerase I Transcription Initiation / spinal cord development / Tat-mediated elongation of the HIV-1 transcript / RNA polymerase II transcribes snRNA genes / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / hematopoietic stem cell differentiation / erythrocyte maturation / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / DNA topological change / transcription by RNA polymerase I / 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 / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription elongation from RNA polymerase II promoter / Cyclin A:Cdk2-associated events at S phase entry / post-embryonic development / hormone-mediated signaling pathway / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / nucleotide-excision repair / 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 / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Dual Incision in GG-NER / positive regulation of DNA binding / nucleotide-excision repair, DNA incision / chromosome segregation / Formation of Incision Complex in GG-NER / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / positive regulation of smooth muscle cell proliferation / cellular response to gamma radiation / protein-macromolecule adaptor activity / G1/S transition of mitotic cell cycle / transcription by RNA polymerase II / multicellular organism growth / spindle
Similarity search - Function
Zinc finger, C3HC4 type (RING finger) / CDK-activating kinase assembly factor MAT1 / Cdk-activating kinase assembly factor MAT1, centre / Cdk-activating kinase assembly factor MAT1/Tfb3 / TFIIH p62 subunit, N-terminal domain / Transcription factor TFIIE alpha subunit, C-terminal / TFIIH subunit Tfb1/GTF2H1 / C-terminal general transcription factor TFIIE alpha / Transcription factor Tfb4 / TFIIH p62 subunit, N-terminal ...Zinc finger, C3HC4 type (RING finger) / CDK-activating kinase assembly factor MAT1 / Cdk-activating kinase assembly factor MAT1, centre / Cdk-activating kinase assembly factor MAT1/Tfb3 / TFIIH p62 subunit, N-terminal domain / Transcription factor TFIIE alpha subunit, C-terminal / TFIIH subunit Tfb1/GTF2H1 / C-terminal general transcription factor TFIIE alpha / Transcription factor Tfb4 / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb4/GTF2H3 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / TFIIH C1-like domain / domain in transcription factors and synapse-associated proteins / RAD3/XPD family / BSD domain / BSD domain / Ssl1-like / TFIIH subunit Ssl1/p44 / BSD domain profile. / Helical and beta-bridge domain / Helical and beta-bridge domain / ATP-dependent helicase Rad3/Chl1-like / Helicase XPB/Ssl2, N-terminal domain / Helicase XPB/Ssl2 / Helicase conserved C-terminal domain / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2 / Transcription factor Tfb2, C-terminal domain / 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 / ATP-dependent helicase, C-terminal / Helicase-like, DEXD box c2 type / DEXDc2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / DEAD_2 / HELICc2 / DEAD2 / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / TFE/IIEalpha-type HTH domain profile. / Transcription factor TFE/TFIIEalpha HTH domain / TFIIEalpha/SarR/Rpc3 HTH domain / Transcription factor E / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription initiation factor IIE / TFIIE alpha subunit / Zinc finger, TFIIB-type / TFIIB zinc-binding / Type III restriction enzyme, res subunit / Helicase/UvrB, N-terminal / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Ubiquitin-interacting motif (UIM) domain profile. / Ubiquitin interacting motif / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / Zinc finger RING-type signature. / Zinc finger, RING-type, conserved site / von Willebrand factor A-like domain superfamily / Zinc finger C2H2-type / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-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 / PH-like domain superfamily / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
General transcription factor IIH subunit 3 / General transcription factor IIH subunit 2 / CDK-activating kinase assembly factor MAT1 / General transcription factor IIE subunit 1 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 1 / IRON/SULFUR CLUSTER / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription and DNA repair factor IIH helicase subunit XPD / DNA (> 100) ...General transcription factor IIH subunit 3 / General transcription factor IIH subunit 2 / CDK-activating kinase assembly factor MAT1 / General transcription factor IIE subunit 1 / General transcription factor IIH subunit 5 / General transcription factor IIH subunit 1 / IRON/SULFUR CLUSTER / General transcription and DNA repair factor IIH helicase subunit XPB / General transcription and DNA repair factor IIH helicase subunit XPD / DNA (> 100) / DNA (> 10) / DNA / : / General transcription factor IIH subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Human mastadenovirus C
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsAibara, S. / Schilbach, S. / Cramer, P.
Funding support Germany, 5items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission894862 Germany
German Research Foundation (DFG)EXC 2067/1 39072994 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP2191 Germany
European Research Council (ERC)882357 Germany
CitationJournal: Nature / Year: 2021
Title: Structures of mammalian RNA polymerase II pre-initiation complexes.
Authors: Shintaro Aibara / Sandra Schilbach / Patrick Cramer /
Abstract: The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) ...The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) assembles with general transcription factors into a pre-initiation complex (PIC) that opens promoter DNA. Previous work provided the molecular architecture of the yeast and human PIC and a topological model for DNA opening by the general transcription factor TFIIH. Here we report the high-resolution cryo-electron microscopy structure of PIC comprising human general factors and Sus scrofa domesticus Pol II, which is 99.9% identical to human Pol II. We determine the structures of PIC with closed and opened promoter DNA at 2.5-2.8 Å resolution, and resolve the structure of TFIIH at 2.9-4.0 Å resolution. We capture the TFIIH translocase XPB in the pre- and post-translocation states, and show that XPB induces and propagates a DNA twist to initiate the opening of DNA approximately 30 base pairs downstream of the TATA box. We also provide evidence that DNA opening occurs in two steps and leads to the detachment of TFIIH from the core PIC, which may stop DNA twisting and enable RNA chain initiation.
History
DepositionMar 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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  • Deposited structure unit
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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
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: General transcription and DNA repair factor IIH helicase subunit XPB
N: Non-template DNA
T: Template DNA
W: General transcription factor IIE subunit 1
Y: Unassigned Peptide, likely XPB
Z: Unassigned Peptide, likely TFIIE-Beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)531,70021
Polymers530,89013
Non-polymers8108
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules 03

#1: 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
#4: Protein CDK-activating kinase assembly factor MAT1 / CDK7/cyclin-H assembly factor / Cyclin-G1-interacting protein / Menage a trois / RING finger ...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 genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MNAT1, CAP35, MAT1, RNF66 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P51948

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General transcription ... , 7 types, 7 molecules 124567W

#2: 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
#3: 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
#5: 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
#6: 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
#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 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
#11: Protein General transcription factor IIE subunit 1 / General transcription factor IIE 56 kDa subunit / Transcription initiation factor IIE subunit alpha ...General transcription factor IIE 56 kDa subunit / Transcription initiation factor IIE subunit alpha / TFIIE-alpha


Mass: 49516.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2E1, TF2E1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29083

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DNA chain , 2 types, 2 molecules NT

#9: DNA chain Non-template DNA


Mass: 32911.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human mastadenovirus C / References: GenBank: 1706691521
#10: DNA chain Template DNA


Mass: 32508.752 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human mastadenovirus C / References: GenBank: 1706691521

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Unassigned Peptide, likely ... , 2 types, 2 molecules YZ

#12: Protein/peptide Unassigned Peptide, likely XPB


Mass: 698.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)
#13: Protein/peptide Unassigned Peptide, likely TFIIE-Beta


Mass: 1635.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 2 types, 8 molecules

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


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


Mass: 65.409 Da / Num. of mol.: 7 / 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

ComponentName: TFIIH (without ADP-BeF3) / Type: COMPLEX / Entity ID: #1-#13 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.49 MDa / Experimental value: NO
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 FIELDBright-field microscopy
Image recordingElectron dose: 41.1 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 129156 / Symmetry type: POINT

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