+Open data
-Basic information
Entry | Database: PDB / ID: 5ivw | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Human core TFIIH bound to DNA within the PIC | |||||||||||||||
Components |
| |||||||||||||||
Keywords | TRANSCRIPTION/DNA / initiation / RNA polymerase II / human / TRANSCRIPTION-DNA complex | |||||||||||||||
Function / homology | Function and homology information MMXD complex / core TFIIH complex portion of holo TFIIH 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 ...MMXD complex / core TFIIH complex portion of holo TFIIH 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 / DNA 5'-3' helicase / G protein-coupled receptor internalization / transcription factor TFIIH core complex / transcription factor TFIIH holo complex / DNA 3'-5' helicase / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / hematopoietic stem cell proliferation / 3'-5' DNA helicase activity / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / transcription factor TFIID complex / spinal cord development / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / RNA polymerase II general transcription initiation factor activity / 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 / RNA Polymerase I Transcription Initiation / DNA topological change / ATPase activator activity / intrinsic apoptotic signaling pathway by p53 class mediator / 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 / Formation of HIV elongation complex in the absence of HIV Tat / embryonic organ development / transcription-coupled nucleotide-excision repair / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / response to UV / RNA Polymerase II Pre-transcription Events / DNA helicase activity / extracellular matrix organization / insulin-like growth factor receptor signaling pathway / isomerase activity / post-embryonic development / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chromosome segregation / RNA Polymerase I Promoter Escape / determination of adult lifespan / promoter-specific chromatin binding / nucleotide-excision repair / transcription initiation at RNA polymerase II promoter / TP53 Regulates Transcription of DNA Repair Genes / transcription elongation by RNA polymerase II / NoRC negatively regulates rRNA expression / multicellular organism growth / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Dual Incision in GG-NER / cellular response to gamma radiation / Formation of Incision Complex in GG-NER / spindle / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / protein localization / double-stranded DNA binding / protein-macromolecule adaptor activity / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / 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 / regulation of transcription by RNA polymerase II / regulation of DNA-templated transcription / nucleolus / apoptotic process / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 10 Å | |||||||||||||||
Authors | He, Y. / Yan, C. / Fang, J. / Inouye, C. / Tjian, R. / Ivanov, I. / Nogales, E. | |||||||||||||||
Funding support | United States, 4items
| |||||||||||||||
Citation | Journal: Nature / Year: 2016 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5ivw.cif.gz | 382.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ivw.ent.gz | 276.6 KB | Display | PDB format |
PDBx/mmJSON format | 5ivw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ivw_validation.pdf.gz | 765.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5ivw_full_validation.pdf.gz | 963.7 KB | Display | |
Data in XML | 5ivw_validation.xml.gz | 80.5 KB | Display | |
Data in CIF | 5ivw_validation.cif.gz | 114.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iv/5ivw ftp://data.pdbj.org/pub/pdb/validation_reports/iv/5ivw | 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 (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-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) Homo sapiens (human) / References: UniProt: P19447, DNA helicase |
---|---|
#2: Protein | Mass: 87021.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P18074, DNA helicase |
-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) Homo sapiens (human) / References: UniProt: Q13888 |
---|---|
#4: Protein | Mass: 8060.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6ZYL4 |
#5: Protein | Mass: 52245.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92759 |
#6: Protein | Mass: 34416.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13889 |
-DNA chain , 2 types, 2 molecules XY
#7: DNA chain | Mass: 5879.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
---|---|
#8: DNA chain | Mass: 6071.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Human core TFIIH bound to DNA within the PIC / Type: COMPLEX / Entity ID: all / Source: NATURAL |
---|---|
Molecular weight | Value: 0.49 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
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). |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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 |
-Processing
EM software | Name: RELION / Version: 1.4beta / Category: 3D reconstruction |
---|---|
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 |