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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8132 | |||||||||||||||
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Title | Human holo-PIC in the open state | |||||||||||||||
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![]() | initiation / RNA polymerase II / human / TRANSCRIPTION / TRANSFERASE-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 / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / 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 / 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 / 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 / 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 / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / transcription preinitiation complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / regulation of mitotic cell cycle phase transition / Viral Messenger RNA Synthesis / hematopoietic stem cell proliferation / Signaling by FGFR2 IIIa TM / 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 / 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 / transcription by RNA polymerase III / Processing of Capped Intron-Containing Pre-mRNA / acetyltransferase activity / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RNA polymerase II transcribes snRNA genes / transcription factor TFIID complex / TFIIB-class transcription factor binding / intrinsic apoptotic signaling pathway by p53 class mediator / RNA polymerase II general transcription initiation factor activity Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.6 Å | |||||||||||||||
![]() | He Y / Yan C | |||||||||||||||
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
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 1.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 54.9 KB 54.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.9 KB | Display | ![]() |
Images | ![]() | 151.4 KB | ||
Filedesc metadata | ![]() | 14.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 379.3 KB | Display | ![]() |
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Full document | ![]() | 378.9 KB | Display | |
Data in XML | ![]() | 9.4 KB | Display | |
Data in CIF | ![]() | 12.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5iy7MC ![]() 8131C ![]() 8133C ![]() 8134C ![]() 8135C ![]() 8136C ![]() 8137C ![]() 8138C ![]() 5ivwC ![]() 5iy6C ![]() 5iy8C ![]() 5iy9C ![]() 5iyaC ![]() 5iybC ![]() 5iycC ![]() 5iydC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.62 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Human holo-PIC in the open state
+Supramolecule #1: Human holo-PIC in the open state
+Supramolecule #2: RNA polymerase II
+Supramolecule #3: General transcription factors
+Supramolecule #4: Super core promoter
+Macromolecule #1: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #2: DNA-directed RNA polymerase II subunit RPB2
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #4: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #5: DNA-directed RNA polymerase II subunit RPB5
+Macromolecule #6: DNA-directed RNA polymerase II subunit RPB6
+Macromolecule #7: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #8: DNA-directed RNA polymerase II subunit RPB8
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #10: DNA-directed RNA polymerase II subunit RPB10
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB11-a
+Macromolecule #12: DNA-directed RNA polymerase II subunit RPB12
+Macromolecule #13: Transcription initiation factor IIB
+Macromolecule #14: Transcription initiation factor IIA subunit 1
+Macromolecule #15: Transcription initiation factor IIA subunit 2
+Macromolecule #16: TATA-box-binding protein
+Macromolecule #17: General transcription factor IIE subunit 1
+Macromolecule #18: Transcription initiation factor IIE subunit beta
+Macromolecule #19: General transcription factor IIF subunit 1
+Macromolecule #20: General transcription factor IIF subunit 2
+Macromolecule #21: Transcription elongation factor TFIIS
+Macromolecule #22: TFIIH basal transcription factor complex helicase XPB subunit
+Macromolecule #23: TFIIH basal transcription factor complex helicase XPD subunit
+Macromolecule #24: General transcription factor IIH subunit 2
+Macromolecule #25: General transcription factor IIH subunit 5
+Macromolecule #26: General transcription factor IIH subunit 4
+Macromolecule #27: General transcription factor IIH subunit 3
+Macromolecule #28: SCP-X
+Macromolecule #29: SCP-Y
+Macromolecule #30: MAGNESIUM ION
+Macromolecule #31: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.9 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV Details: Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 27500 |
Sample stage | Specimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-5iy7: |