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Yorodumi- EMDB-15006: Structure of SNAPc containing Pol II pre-initiation complex bound... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-15006 | |||||||||||||||
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Title | Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (CC) | |||||||||||||||
Map data | ||||||||||||||||
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Function / homology | Function and homology information 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 / RNA polymerase II core complex assembly / RNA polymerase transcription factor SL1 complex / snRNA transcription by RNA polymerase II ...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 / RNA polymerase II core complex assembly / RNA polymerase transcription factor SL1 complex / snRNA transcription by RNA polymerase II / phosphatase activator activity / RNA polymerase III general transcription initiation factor activity / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / B-WICH complex positively regulates rRNA expression / RNA Polymerase I Transcription Initiation / RNA Polymerase I Promoter Escape / RNA Polymerase I Transcription Termination / 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 Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA Polymerase III Abortive And Retractive Initiation / nuclear lumen / transcription factor TFIIA complex / : / female germ cell nucleus / male pronucleus / female pronucleus / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / germinal vesicle / RNA polymerase II general transcription initiation factor binding / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Viral Messenger RNA Synthesis / Signaling by FGFR2 IIIa TM / cell division site / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / RNA polymerase II complex binding / mRNA Splicing - Minor Pathway / 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 / transcription initiation at RNA polymerase III promoter / viral transcription / acetyltransferase activity / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of translational initiation / RNA polymerase II activity / organelle membrane / aryl hydrocarbon receptor binding / RNA polymerase II transcribes snRNA genes / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / TFIIB-class transcription factor binding / transcription-coupled nucleotide-excision repair / positive regulation of transcription initiation by RNA polymerase II Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / pig (pig) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||
Authors | Rengachari S / Schilbach S / Kaliyappan T / Gouge J / Zumer K / Schwarz J / Urlaub H / Dienemann C / Vannini A / Cramer P | |||||||||||||||
Funding support | Germany, United Kingdom, 4 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 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: Journal: Biorxiv / Year: 2022 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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_15006.map.gz | 141.6 MB | EMDB map data format | |
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Header (meta data) | emd-15006-v30.xml emd-15006.xml | 49.4 KB 49.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_15006_fsc.xml | 14.1 KB | Display | FSC data file |
Images | emd_15006.png | 94.1 KB | ||
Masks | emd_15006_msk_1.map | 244.1 MB | Mask map | |
Others | emd_15006_half_map_1.map.gz emd_15006_half_map_2.map.gz | 193.9 MB 194.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-15006 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-15006 | HTTPS FTP |
-Related structure data
Related structure data | 7zx7MC 7zwcC 7zwdC 7zx8C 7zxeC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_15006.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_15006_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_15006_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_15006_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Pre-initiation complex of RNA polymerase II with general transcri...
+Supramolecule #1: Pre-initiation complex of RNA polymerase II with general transcri...
+Supramolecule #2: SNAPc
+Supramolecule #3: TATA-box-binding protein and transcription factors
+Supramolecule #4: Promoter
+Supramolecule #5: RNA polymerase II
+Macromolecule #1: DNA-directed RNA polymerase subunit
+Macromolecule #2: DNA-directed RNA polymerase subunit beta
+Macromolecule #3: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #4: RNA polymerase II subunit D
+Macromolecule #5: DNA-directed RNA polymerase II subunit E
+Macromolecule #6: DNA-directed RNA polymerase II subunit F
+Macromolecule #7: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #8: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #11: RNA polymerase II subunit J
+Macromolecule #12: RNA polymerase II subunit K
+Macromolecule #13: Transcription initiation factor IIB
+Macromolecule #15: TATA-box-binding protein
+Macromolecule #16: General transcription factor IIF subunit 1
+Macromolecule #17: General transcription factor IIF subunit 2
+Macromolecule #19: Transcription initiation factor IIA subunit 1
+Macromolecule #20: Transcription initiation factor IIA subunit 2
+Macromolecule #21: snRNA-activating protein complex subunit 1
+Macromolecule #22: snRNA-activating protein complex subunit 3
+Macromolecule #23: snRNA-activating protein complex subunit 4
+Macromolecule #24: snRNA-activating protein complex subunit 5
+Macromolecule #14: Non-template strand
+Macromolecule #18: Template strand
+Macromolecule #25: ZINC ION
+Macromolecule #26: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.3 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.45 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |