+Open data
-Basic information
Entry | Database: PDB / ID: 5iy9 | |||||||||||||||
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Title | Human holo-PIC in the initial transcribing state (no IIS) | |||||||||||||||
Components |
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Keywords | TRANSCRIPTION / TRANSFERASE/DNA/RNA / initiation / RNA polymerase II / human / TRANSFERASE-DNA-RNA complex | |||||||||||||||
Function / homology | Function and homology information LRR domain binding / microfibril binding / RNA Polymerase III Chain Elongation / MMXD complex / core TFIIH complex portion of holo TFIIH complex / RNA Polymerase III Transcription Termination / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / regulation of transcription by RNA polymerase I ...LRR domain binding / microfibril binding / RNA Polymerase III Chain Elongation / MMXD complex / core TFIIH complex portion of holo TFIIH complex / RNA Polymerase III Transcription Termination / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / regulation of transcription by RNA polymerase I / positive regulation of mitotic recombination / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / hair follicle maturation / hair cell differentiation / nucleotide-excision repair factor 3 complex / RPAP3/R2TP/prefoldin-like complex / transcription factor TFIIE complex / RNA polymerase transcription factor SL1 complex / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / UV protection / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / RNA polymerase I core promoter sequence-specific DNA binding / DNA 5'-3' helicase / transcriptional start site selection at RNA polymerase II promoter / 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 / female germ cell nucleus / G protein-coupled receptor internalization / 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 / DNA 3'-5' helicase / germinal vesicle / RNA polymerase II general transcription initiation factor binding / MicroRNA (miRNA) biogenesis / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / Viral Messenger RNA Synthesis / hematopoietic stem cell proliferation / Signaling by FGFR2 IIIa TM / 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 / PIWI-interacting RNA (piRNA) biogenesis / protein acetylation / bone mineralization / cell division site / 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 II complex binding / mRNA Splicing - Minor Pathway / viral transcription / acetyltransferase activity / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA Polymerase I Transcription Initiation / transcription by RNA polymerase I / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / aryl hydrocarbon receptor binding / DNA topological change / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / nuclear-transcribed mRNA catabolic process / ATPase activator activity / transcription by RNA polymerase III / Processing of Capped Intron-Containing Pre-mRNA / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / TFIIB-class transcription factor binding / RNA polymerase II transcribes snRNA genes / intrinsic apoptotic signaling pathway by p53 class mediator / RNA polymerase II activity Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.3 Å | |||||||||||||||
Authors | He, Y. / Yan, C. / Fang, J. / Inouye, C. / Tjian, R. / Ivanov, I. / Nogales, E. | |||||||||||||||
Funding support | United States, 4items
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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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5iy9.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5iy9.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 5iy9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5iy9_validation.pdf.gz | 1000.5 KB | Display | wwPDB validaton report |
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Full document | 5iy9_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5iy9_validation.xml.gz | 226.1 KB | Display | |
Data in CIF | 5iy9_validation.cif.gz | 341.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/5iy9 ftp://data.pdbj.org/pub/pdb/validation_reports/iy/5iy9 | HTTPS FTP |
-Related structure data
Related structure data | 8134MC 8131C 8132C 8133C 8135C 8136C 8137C 8138C 5ivwC 5iy6C 5iy7C 5iy8C 5iyaC 5iybC 5iycC 5iydC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-DNA-directed RNA polymerase II subunit ... , 12 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 217420.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) 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) Homo sapiens (human) / References: UniProt: P30876, DNA-directed RNA polymerase |
#3: Protein | Mass: 31478.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P19387 |
#4: Protein | Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O15514 |
#5: Protein | Mass: 24584.223 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P19388 |
#6: Protein | Mass: 14491.026 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61218 |
#7: Protein | Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62487 |
#8: Protein | Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52434 |
#9: Protein | Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P36954 |
#10: Protein | Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P62875 |
#11: Protein | Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P52435 |
#12: Protein | Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P53803 |
-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.) Homo sapiens (human) / Gene: GTF2B, TF2B, TFIIB / Production host: Escherichia coli (E. coli) / References: UniProt: Q00403 |
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#14: Protein | Mass: 41544.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A1, TF2A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52655 |
#15: Protein | Mass: 12469.091 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A2, TF2A2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52657 |
#18: Protein | Mass: 33106.824 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2E2, TF2E2 / Production host: Escherichia coli (E. coli) / References: UniProt: P29084 |
-Protein , 2 types, 2 molecules PQ
#16: Protein | Mass: 37729.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TBP, GTF2D1, TF2D, TFIID / Production host: Escherichia coli (E. coli) / References: UniProt: P20226 |
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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.) Homo sapiens (human) / Gene: GTF2E1, TF2E1 / Production host: Escherichia coli (E. coli) / References: UniProt: P29083 |
-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.) Homo sapiens (human) / Gene: GTF2F1, RAP74 / Production host: Escherichia coli (E. coli) / References: UniProt: P35269 |
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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.) Homo sapiens (human) / Gene: GTF2F2, RAP30 / Production host: Escherichia coli (E. coli) / References: UniProt: P13984, DNA helicase |
-TFIIH basal transcription factor complex helicase ... , 2 types, 2 molecules VW
#21: 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 |
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#22: 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
#23: Protein | Mass: 44481.996 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13888 |
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#24: Protein | Mass: 8060.362 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q6ZYL4 |
#25: Protein | Mass: 52245.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q92759 |
#26: 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
#27: DNA chain | Mass: 25772.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#28: DNA chain | Mass: 25381.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-RNA chain , 1 types, 1 molecules Z
#29: RNA chain | Mass: 1891.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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-Non-polymers , 2 types, 12 molecules
#30: Chemical | #31: Chemical | ChemComp-ZN / |
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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 |
-Sample preparation
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Molecular weight |
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Source (natural) |
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Buffer solution | pH: 7.9 | ||||||||||||||||||||||||||||||
Specimen | Conc.: 0.3 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 |
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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 |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 91642 / Symmetry type: POINT |
Atomic model building | Protocol: FLEXIBLE FIT |