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Open data
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Basic information
Entry | Database: PDB / ID: 5ivw | |||||||||||||||
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Title | Human core TFIIH bound to DNA within the PIC | |||||||||||||||
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![]() | TRANSCRIPTION/DNA / initiation / RNA polymerase II / human / TRANSCRIPTION-DNA complex | |||||||||||||||
Function / homology | ![]() core TFIIH complex portion of holo TFIIH complex / MMXD complex / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / hair follicle maturation / hair cell differentiation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly ...core TFIIH complex portion of holo TFIIH complex / MMXD complex / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / hair follicle maturation / hair cell differentiation / nucleotide-excision repair factor 3 complex / nucleotide-excision repair, preincision complex assembly / CAK-ERCC2 complex / UV protection / embryonic cleavage / G protein-coupled receptor internalization / DNA 3'-5' helicase / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / 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 / mRNA Capping / bone mineralization / 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 / erythrocyte maturation / 3'-5' DNA helicase activity / RNA Polymerase I Transcription Initiation / DNA topological change / ATPase activator activity / transcription factor TFIID complex / intrinsic apoptotic signaling pathway by p53 class mediator / RNA polymerase II general transcription initiation factor activity / hematopoietic stem cell differentiation / transcription elongation by RNA polymerase I / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / embryonic organ development / transcription-coupled nucleotide-excision repair / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / response to UV / DNA helicase activity / RNA Polymerase II Pre-transcription Events / extracellular matrix organization / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / insulin-like growth factor receptor signaling pathway / post-embryonic development / chromosome segregation / transcription elongation by RNA polymerase II / determination of adult lifespan / promoter-specific chromatin binding / nucleotide-excision repair / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / NoRC negatively regulates rRNA expression / protein localization / multicellular organism growth / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / cellular response to gamma radiation / Formation of TC-NER Pre-Incision Complex / Formation of Incision Complex in GG-NER / spindle / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein-macromolecule adaptor activity / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / double-stranded DNA binding / DNA helicase / in utero embryonic development / response to oxidative stress / transcription by RNA polymerase II / damaged DNA binding / response to hypoxia / nuclear speck / positive regulation of apoptotic process / DNA repair / apoptotic process / regulation of DNA-templated transcription / nucleolus / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 Å | |||||||||||||||
![]() | He, Y. / Yan, C. / Fang, J. / Inouye, C. / Tjian, R. / Ivanov, I. / Nogales, E. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Near-atomic resolution visualization of human transcription promoter opening. Authors: Yuan He / Chunli Yan / Jie Fang / Carla Inouye / Robert Tjian / Ivaylo Ivanov / Eva Nogales / ![]() Abstract: In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the ...In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA-RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB. | |||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 382.2 KB | Display | ![]() |
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PDB format | ![]() | 276.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 765.6 KB | Display | ![]() |
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Full document | ![]() | 963.7 KB | Display | |
Data in XML | ![]() | 80.5 KB | Display | |
Data in CIF | ![]() | 114.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8131MC ![]() 8132C ![]() 8133C ![]() 8134C ![]() 8135C ![]() 8136C ![]() 8137C ![]() 8138C ![]() 5iy6C ![]() 5iy7C ![]() 5iy8C ![]() 5iy9C ![]() 5iyaC ![]() 5iybC ![]() 5iycC ![]() 5iydC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-TFIIH basal transcription factor complex helicase ... , 2 types, 2 molecules VW
#1: Protein | Mass: 89404.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 87021.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-General transcription factor IIH subunit ... , 4 types, 4 molecules 0123
#3: Protein | Mass: 44481.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#4: Protein | Mass: 8060.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: Protein | Mass: 52245.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#6: Protein | Mass: 34416.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-DNA chain , 2 types, 2 molecules XY
#7: DNA chain | Mass: 5879.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#8: DNA chain | Mass: 6071.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Human core TFIIH bound to DNA within the PIC / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Molecular weight | Value: 0.49 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.9 |
Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % Details: Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 27500 X / Nominal defocus max: 4000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm |
Specimen holder | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Image recording | Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 30 |
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Processing
EM software | Name: RELION / Version: 1.4beta / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 10 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 219771 / Symmetry type: POINT |
Atomic model building | Protocol: FLEXIBLE FIT |