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- PDB-7zxe: Structure of SNAPc containing Pol II pre-initiation complex bound... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7zxe | |||||||||||||||
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Title | Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (OC) | |||||||||||||||
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![]() | TRANSCRIPTION / RNA polymerase II / Pol II / PIC / SNAPc / snRNA / U1 promoter | |||||||||||||||
Function / homology | ![]() snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of core promoter binding / meiotic sister chromatid cohesion / snRNA transcription by RNA polymerase II / RNA polymerase III general transcription initiation factor activity / RNA polymerase transcription factor SL1 complex ...snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / RNA polymerase III type 3 promoter sequence-specific DNA binding / positive regulation of core promoter binding / meiotic sister chromatid cohesion / snRNA transcription by RNA polymerase II / RNA polymerase III general transcription initiation factor activity / RNA polymerase transcription factor SL1 complex / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase II core complex assembly / 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 / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / female pronucleus / germinal vesicle / RNA polymerase II general transcription initiation factor binding / transcription preinitiation complex / nuclear thyroid hormone receptor binding / RNA Polymerase I Transcription Termination / protein acetylation / 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 / RNA polymerase II complex binding / transcription initiation at RNA polymerase III promoter / viral transcription / RNA Polymerase I Transcription Initiation / aryl hydrocarbon receptor binding / transcription by RNA polymerase III / acetyltransferase activity / RNA polymerase II transcribes snRNA genes / transcription factor TFIID complex / TFIIB-class transcription factor binding / RNA polymerase II general transcription initiation factor activity / positive regulation of transcription initiation by RNA polymerase II / spindle assembly / RNA polymerase II core promoter sequence-specific DNA binding / core promoter sequence-specific DNA binding / histone acetyltransferase activity / RNA polymerase II preinitiation complex assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / SIRT1 negatively regulates rRNA expression / male germ cell nucleus / DNA-templated transcription initiation / promoter-specific chromatin binding / RNA Polymerase I Promoter Escape / transcription initiation at RNA polymerase II promoter / protein-DNA complex / euchromatin / mRNA transcription by RNA polymerase II / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / kinetochore / RNA polymerase II transcription regulator complex / cell junction / chromosome / spermatogenesis / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Regulation of TP53 Activity through Phosphorylation / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / nuclear body / transcription cis-regulatory region binding / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / nucleolus / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
![]() | Rengachari, S. / Schilbach, S. / Kaliyappan, T. / Gouge, J. / Zumer, K. / Schwarz, J. / Urlaub, H. / Dienemann, C. / Vannini, A. / Cramer, P. | |||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II. Authors: Srinivasan Rengachari / Sandra Schilbach / Thangavelu Kaliyappan / Jerome Gouge / Kristina Zumer / Juliane Schwarz / Henning Urlaub / Christian Dienemann / Alessandro Vannini / Patrick Cramer / ![]() ![]() ![]() Abstract: RNA polymerase II (Pol II) carries out transcription of both protein-coding and non-coding genes. Whereas Pol II initiation at protein-coding genes has been studied in detail, Pol II initiation at ...RNA polymerase II (Pol II) carries out transcription of both protein-coding and non-coding genes. Whereas Pol II initiation at protein-coding genes has been studied in detail, Pol II initiation at non-coding genes, such as small nuclear RNA (snRNA) genes, is less well understood at the structural level. Here, we study Pol II initiation at snRNA gene promoters and show that the snRNA-activating protein complex (SNAPc) enables DNA opening and transcription initiation independent of TFIIE and TFIIH in vitro. We then resolve cryo-EM structures of the SNAPc-containing Pol IIpre-initiation complex (PIC) assembled on U1 and U5 snRNA promoters. The core of SNAPc binds two turns of DNA and recognizes the snRNA promoter-specific proximal sequence element (PSE), located upstream of the TATA box-binding protein TBP. Two extensions of SNAPc, called wing-1 and wing-2, bind TFIIA and TFIIB, respectively, explaining how SNAPc directs Pol II to snRNA promoters. Comparison of structures of closed and open promoter complexes elucidates TFIIH-independent DNA opening. These results provide the structural basis of Pol II initiation at non-coding RNA gene promoters. #1: ![]() Title: Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II Authors: Rengachari, S. / Schilbach, S. / Kaliyappan, T. / Gouge, J. / Zumer, K. / Schwarz, J. / Urlaub, H. / Dienemann, C. / Vannini, A. / Cramer, P. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 363.9 KB | Display | ![]() |
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PDB format | ![]() | 267.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 58.5 KB | Display | |
Data in CIF | ![]() | 88.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 15009MC ![]() 7zwcC ![]() 7zwdC ![]() 7zx7C ![]() 7zx8C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 2 types, 2 molecules MO
#1: Protein | Mass: 34877.949 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#3: Protein | Mass: 37729.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules NT
#2: DNA chain | Mass: 29969.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#4: DNA chain | Mass: 29261.691 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Transcription initiation factor IIA subunit ... , 2 types, 2 molecules UV
#5: Protein | Mass: 41544.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#6: Protein | Mass: 12469.091 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-SnRNA-activating protein complex subunit ... , 4 types, 4 molecules abcd
#7: Protein | Mass: 43074.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#8: Protein | Mass: 46812.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#9: Protein | Mass: 159645.172 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#10: Protein | Mass: 11343.449 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Non-polymers , 1 types, 2 molecules ![](data/chem/img/ZN.gif)
#11: Chemical |
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-Details
Has ligand of interest | Y |
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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
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 300 nm |
Image recording | Electron dose: 54.45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 137246 / Symmetry type: POINT |