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- EMDB-12619: RNA polymerase II pre-initiation complex with open promoter DNA -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12619 | ||||||||||||||||||
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Title | RNA polymerase II pre-initiation complex with open promoter DNA | ||||||||||||||||||
![]() | Local filtered and sharpened map | ||||||||||||||||||
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Function / homology | ![]() MMXD complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / negative regulation of DNA helicase activity / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | ![]() ![]() | ||||||||||||||||||
![]() | Aibara S / Schilbach S / Cramer P | ||||||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 325.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 54.9 KB 54.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.1 KB | Display | ![]() |
Images | ![]() | 131.6 KB | ||
Masks | ![]() | 347.6 MB | ![]() | |
Others | ![]() ![]() | 277.2 MB 277.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nw0MC ![]() 7nvrC ![]() 7nvsC ![]() 7nvtC ![]() 7nvuC ![]() 7nvvC ![]() 7nvwC ![]() 7nvxC ![]() 7nvyC ![]() 7nvzC 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
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Annotation | Local filtered and sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Projections & Slices |
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Density Histograms |
-Half map: Unfiltered half map 1
File | emd_12619_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 1
File | emd_12619_half_map_2.map | ||||||||||||
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Annotation | Unfiltered half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
+Entire : RNA polymerase II pre-initiation complex with open promoter DNA
+Supramolecule #1: RNA polymerase II pre-initiation complex with open 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: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #36: MAGNESIUM ION
+Macromolecule #37: BERYLLIUM TRIFLUORIDE ION
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 43.0 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |