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Yorodumi- EMDB-12618: RNA polymerase II pre-initiation complex with closed promoter DNA... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12618 | ||||||||||||||||||
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Title | RNA polymerase II pre-initiation complex with closed promoter DNA in distal position | ||||||||||||||||||
Map data | Local resolution filtered and sharpened map | ||||||||||||||||||
Sample |
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Keywords | Initiation / TRANSCRIPTION | ||||||||||||||||||
Function / homology | Function and homology information MMXD complex / core TFIIH complex portion of holo TFIIH complex / 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 / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion ...MMXD complex / core TFIIH complex portion of holo TFIIH complex / 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 / RNA polymerase II core complex assembly / meiotic sister chromatid cohesion / ventricular system development / hair follicle maturation / RNA polymerase transcription factor SL1 complex / hair cell differentiation / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / UV protection / transcription factor TFIIK complex / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / 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 I core promoter sequence-specific DNA binding / transcriptional start site selection at RNA polymerase II promoter / 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 / 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 - 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 / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / transcription factor TFIIF complex / DNA 5'-3' helicase / RNA Polymerase III Abortive And Retractive Initiation / G protein-coupled receptor internalization / adult heart development / transcription factor TFIIA complex / female germ cell nucleus / transcription factor TFIIH holo complex / transcription factor TFIIH core complex / male pronucleus / female pronucleus / cyclin-dependent protein serine/threonine kinase activator activity / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA polymerase II general transcription initiation factor binding / germinal vesicle / DNA 3'-5' helicase / transcription preinitiation complex / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / Signaling by FGFR2 IIIa TM / regulation of mitotic cell cycle phase transition / Viral Messenger RNA Synthesis / hematopoietic stem cell proliferation / 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 / regulation of cyclin-dependent protein serine/threonine kinase activity / transcription factor TFIID complex / bone mineralization / RNA polymerase II general transcription initiation factor activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / organelle membrane / mRNA Capping / spinal cord development / protein acetylation / cell division site / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) / Sus scrofa (pig) / Human mastadenovirus C | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.2 Å | ||||||||||||||||||
Authors | Aibara S / Schilbach S | ||||||||||||||||||
Funding support | Germany, 5 items
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Citation | Journal: Nature / Year: 2021 Title: Structures of mammalian RNA polymerase II pre-initiation complexes. Authors: Shintaro Aibara / Sandra Schilbach / Patrick Cramer / Abstract: The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) ...The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. To initiate transcription, RNA polymerase II (Pol II) assembles with general transcription factors into a pre-initiation complex (PIC) that opens promoter DNA. Previous work provided the molecular architecture of the yeast and human PIC and a topological model for DNA opening by the general transcription factor TFIIH. Here we report the high-resolution cryo-electron microscopy structure of PIC comprising human general factors and Sus scrofa domesticus Pol II, which is 99.9% identical to human Pol II. We determine the structures of PIC with closed and opened promoter DNA at 2.5-2.8 Å resolution, and resolve the structure of TFIIH at 2.9-4.0 Å resolution. We capture the TFIIH translocase XPB in the pre- and post-translocation states, and show that XPB induces and propagates a DNA twist to initiate the opening of DNA approximately 30 base pairs downstream of the TATA box. We also provide evidence that DNA opening occurs in two steps and leads to the detachment of TFIIH from the core PIC, which may stop DNA twisting and enable RNA chain initiation. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12618.map.gz | 320.3 MB | EMDB map data format | |
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Header (meta data) | emd-12618-v30.xml emd-12618.xml | 58.8 KB 58.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12618_fsc.xml | 16.1 KB | Display | FSC data file |
Images | emd_12618.png | 147.5 KB | ||
Masks | emd_12618_msk_1.map | 347.6 MB | Mask map | |
Filedesc metadata | emd-12618.cif.gz | 14.5 KB | ||
Others | emd_12618_additional_1.map.gz emd_12618_half_map_1.map.gz emd_12618_half_map_2.map.gz | 204.7 MB 278 MB 278.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12618 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12618 | HTTPS FTP |
-Validation report
Summary document | emd_12618_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_12618_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_12618_validation.xml.gz | 24 KB | Display | |
Data in CIF | emd_12618_validation.cif.gz | 32.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12618 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12618 | HTTPS FTP |
-Related structure data
Related structure data | 7nvzMC 7nvrC 7nvsC 7nvtC 7nvuC 7nvvC 7nvwC 7nvxC 7nvyC 7nw0C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_12618.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Local resolution filtered and sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_12618_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Local resolution filtered map, unsharpened
File | emd_12618_additional_1.map | ||||||||||||
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Annotation | Local resolution filtered map, unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map 1
File | emd_12618_half_map_1.map | ||||||||||||
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Annotation | Unfiltered half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map 2
File | emd_12618_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : RNA polymerase II pre-initiation complex with closed promoter DNA...
+Supramolecule #1: RNA polymerase II pre-initiation complex with closed promoter DNA...
+Macromolecule #1: TFIIH basal transcription factor complex helicase XPD subunit
+Macromolecule #2: General transcription factor IIH subunit 1
+Macromolecule #3: General transcription factor IIH subunit 4
+Macromolecule #4: CDK-activating kinase assembly factor MAT1
+Macromolecule #5: General transcription factor IIH subunit 3
+Macromolecule #6: General transcription factor IIH subunit 5
+Macromolecule #7: General transcription factor IIH subunit 2
+Macromolecule #8: General transcription and DNA repair factor IIH helicase subunit XPB
+Macromolecule #9: RPB1
+Macromolecule #10: DNA-directed RNA polymerase subunit beta
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #12: RPOL4c domain-containing protein
+Macromolecule #13: DNA-directed RNA polymerase II subunit E
+Macromolecule #14: DNA-directed RNA polymerase II subunit F
+Macromolecule #15: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #16: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #17: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #18: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #19: RNA_pol_L_2 domain-containing protein
+Macromolecule #20: RNA polymerase II subunit K
+Macromolecule #21: Transcription initiation factor IIB
+Macromolecule #23: TATA-box-binding protein
+Macromolecule #24: General transcription factor IIF subunit 1
+Macromolecule #25: General transcription factor IIF subunit 2
+Macromolecule #27: Transcription initiation factor IIA subunit 1
+Macromolecule #28: Transcription initiation factor IIA subunit 2
+Macromolecule #29: General transcription factor IIE subunit 1
+Macromolecule #30: Transcription initiation factor IIE subunit beta
+Macromolecule #31: Unassigned peptide, likely TFIIE-beta
+Macromolecule #32: Unassigned peptide, likely XPB
+Macromolecule #22: Non-template DNA
+Macromolecule #26: Template DNA
+Macromolecule #33: IRON/SULFUR CLUSTER
+Macromolecule #34: ZINC ION
+Macromolecule #35: 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 | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 41.1 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |