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Open data
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Basic information
Entry | Database: PDB / ID: 6o9l | ||||||
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Title | Human holo-PIC in the closed state | ||||||
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![]() | TRANSCRIPTION/DNA / Transcription initiation / Molecular dynamics / Gene regulation / Community network analysis / Global protein dynamics / RNA polymerase / TRANSCRIPTION-DNA complex | ||||||
Function / homology | ![]() LRR domain binding / microfibril binding / RNA Polymerase III Chain Elongation / core TFIIH complex portion of holo TFIIH complex / MMXD complex / RNA Polymerase III Transcription Termination / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination ...LRR domain binding / microfibril binding / RNA Polymerase III Chain Elongation / core TFIIH complex portion of holo TFIIH complex / MMXD complex / RNA Polymerase III Transcription Termination / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / positive regulation of mitotic recombination / positive regulation of core promoter binding / RPAP3/R2TP/prefoldin-like complex / meiotic sister chromatid cohesion / hair follicle maturation / hair cell differentiation / ventricular system development / nucleotide-excision repair factor 3 complex / cyclin-dependent protein kinase activating kinase holoenzyme complex / transcription factor TFIIE complex / snRNA transcription by RNA polymerase II / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / regulation of transcription by RNA polymerase I / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIK complex / UV protection / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / RNA polymerase transcription factor SL1 complex / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase II core complex assembly / TFIIH-class transcription factor complex binding / Cytosolic sensors of pathogen-associated DNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / adult heart development / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / G protein-coupled receptor internalization / female germ cell nucleus / DNA 3'-5' helicase / male pronucleus / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / female pronucleus / transcription factor TFIIH holo complex / Abortive elongation of HIV-1 transcript in the absence of Tat / germinal vesicle / RNA polymerase II general transcription initiation factor binding / [RNA-polymerase]-subunit kinase / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / transcription preinitiation complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of mitotic cell cycle phase transition / Viral Messenger RNA Synthesis / hematopoietic stem cell proliferation / Signaling by FGFR2 IIIa TM / regulation of cyclin-dependent protein serine/threonine kinase activity / 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 / PIWI-interacting RNA (piRNA) biogenesis / protein acetylation / : / : / 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 / cell division site / mRNA Splicing - Minor Pathway / erythrocyte maturation / RNA polymerase II complex binding / regulation of G1/S transition of mitotic cell cycle / viral transcription / 3'-5' DNA helicase activity / RNA Polymerase I Transcription Initiation / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / transcription by RNA polymerase I / DNA topological change / aryl hydrocarbon receptor binding / ATPase activator activity Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.2 Å | ||||||
![]() | Yan, C.L. / Dodd, T. / He, Y. / Tainer, J.A. / Tsutakawa, S.E. / Ivanov, I. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of promoter-bound TFIID and model of human pre-initiation complex assembly. Authors: Robert K Louder / Yuan He / José Ramón López-Blanco / Jie Fang / Pablo Chacón / Eva Nogales / ![]() ![]() Abstract: The general transcription factor IID (TFIID) plays a central role in the initiation of RNA polymerase II (Pol II)-dependent transcription by nucleating pre-initiation complex (PIC) assembly at the ...The general transcription factor IID (TFIID) plays a central role in the initiation of RNA polymerase II (Pol II)-dependent transcription by nucleating pre-initiation complex (PIC) assembly at the core promoter. TFIID comprises the TATA-binding protein (TBP) and 13 TBP-associated factors (TAF1-13), which specifically interact with a variety of core promoter DNA sequences. Here we present the structure of human TFIID in complex with TFIIA and core promoter DNA, determined by single-particle cryo-electron microscopy at sub-nanometre resolution. All core promoter elements are contacted by subunits of TFIID, with TAF1 and TAF2 mediating major interactions with the downstream promoter. TFIIA bridges the TBP-TATA complex with lobe B of TFIID. We also present the cryo-electron microscopy reconstruction of a fully assembled human TAF-less PIC. Superposition of common elements between the two structures provides novel insights into the general role of TFIID in promoter recognition, PIC assembly, and transcription initiation. | ||||||
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 | ![]() | 1.8 MB | Display | ![]() |
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PDB format | ![]() | 1.4 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 244.1 KB | Display | |
Data in CIF | ![]() | 376.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3307M ![]() 6o9mC 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
-DNA-directed RNA polymerase II subunit ... , 8 types, 8 molecules ABCDEGIK
#1: Protein | Mass: 217420.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P24928, DNA-directed RNA polymerase, RNA-directed RNA polymerase |
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#2: Protein | Mass: 134071.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 31478.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: Protein | Mass: 24584.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein | Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#9: Protein | Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: Protein | Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-DNA-directed RNA polymerases I, II, and III subunit ... , 4 types, 4 molecules FHJL
#6: Protein | Mass: 14491.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#8: Protein | Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#10: Protein | Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Transcription initiation factor ... , 4 types, 4 molecules MNOR
#13: Protein | Mass: 34877.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#14: Protein | Mass: 41544.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#15: Protein | Mass: 12469.091 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#18: Protein | Mass: 33106.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Protein , 6 types, 6 molecules PQU389
#16: Protein | Mass: 37729.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#17: Protein | Mass: 49516.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#21: Protein | Mass: 34022.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#25: Protein | Mass: 35873.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#30: Protein | Mass: 39090.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() References: UniProt: P50613, cyclin-dependent kinase, [RNA-polymerase]-subunit kinase |
#31: Protein | Mass: 37695.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-General transcription factor IIF subunit ... , 2 types, 2 molecules ST
#19: Protein | Mass: 58343.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#20: Protein | Mass: 28427.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-TFIIH basal transcription factor complex helicase ... , 2 types, 2 molecules 07
#22: Protein | Mass: 87021.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#29: Protein | Mass: 89404.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-General transcription factor IIH subunit ... , 5 types, 5 molecules 12456
#23: Protein | Mass: 62116.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#24: Protein | Mass: 52245.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#26: Protein | Mass: 34416.008 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#27: Protein | Mass: 8060.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#28: Protein | Mass: 44481.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-DNA chain , 2 types, 2 molecules XY
#32: DNA chain | Mass: 20214.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#33: DNA chain | Mass: 19867.658 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 20 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
#34: Chemical | #35: Chemical | ChemComp-ZN / #36: Chemical | ChemComp-SF4 / | |
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-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: holo-PIC in the closed state / Type: COMPLEX / Entity ID: #1-#33 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: C-flat |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Model: FEI TITAN |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 46 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
EM software |
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3D reconstruction | Resolution: 7.2 Å / Num. of particles: 24290 | |||||||||||||||||||||||||
Atomic model building | Protocol: 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. |