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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-12610 | ||||||||||||||||||
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Title | Human Mediator with RNA Polymerase II Pre-initiation complex | ||||||||||||||||||
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![]() | Mediator complex / RNA polymerase II / TFIIH / Pre-initiation complex / TRANSCRIPTION | ||||||||||||||||||
Function / homology | ![]() negative regulation of smooth muscle cell differentiation / core TFIIH complex portion of holo TFIIH complex / MMXD 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 / core mediator complex / meiotic sister chromatid cohesion ...negative regulation of smooth muscle cell differentiation / core TFIIH complex portion of holo TFIIH complex / MMXD 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 / core mediator complex / meiotic sister chromatid cohesion / hair follicle maturation / hair cell differentiation / ventricular system development / nucleotide-excision repair factor 3 complex / cyclin-dependent protein kinase activating kinase holoenzyme complex / transcription factor TFIIE complex / snRNA transcription by RNA polymerase II / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / CAK-ERCC2 complex / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIK complex / UV protection / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / RNA polymerase transcription factor SL1 complex / 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 I core promoter sequence-specific DNA binding / RNA polymerase II core complex assembly / TFIIH-class transcription factor complex binding / 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 / 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 Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / mediator complex / adult heart development / Generic Transcription Pathway / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / G protein-coupled receptor internalization / female germ cell nucleus / DNA 3'-5' helicase / male pronucleus / transcription factor TFIIH core complex / cyclin-dependent protein serine/threonine kinase activator activity / female pronucleus / transcription factor TFIIH holo complex / Abortive elongation of HIV-1 transcript in the absence of Tat / nuclear vitamin D receptor binding / germinal vesicle / RNA polymerase II general transcription initiation factor binding / [RNA-polymerase]-subunit kinase / limb development / FGFR2 alternative splicing / transcription preinitiation complex / RNA Polymerase I Transcription Termination / nuclear thyroid hormone receptor binding / cyclin-dependent protein serine/threonine kinase regulator activity / regulation of mitotic cell cycle phase transition / Viral Messenger RNA Synthesis / hematopoietic stem cell proliferation / Signaling by FGFR2 IIIa TM / cortical actin cytoskeleton / regulation of cyclin-dependent protein serine/threonine kinase activity / spinal cord development / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / termination of RNA polymerase II transcription / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping Similarity search - Function | ||||||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | ||||||||||||||||||
![]() | Rengachari S / Schilbach S | ||||||||||||||||||
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 | ![]() | 243.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 100.3 KB 100.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15 KB | Display | ![]() |
Images | ![]() | 159.7 KB | ||
Masks | ![]() | 282.6 MB | ![]() | |
Filedesc metadata | ![]() | 20 KB | ||
Others | ![]() ![]() ![]() | 160.7 MB 225.6 MB 225.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 862.1 KB | Display | ![]() |
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Full document | ![]() | 861.6 KB | Display | |
Data in XML | ![]() | 22.7 KB | Display | |
Data in CIF | ![]() | 29.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7nvrMC ![]() 7nvsC ![]() 7nvtC ![]() 7nvuC ![]() 7nvvC ![]() 7nvwC ![]() 7nvxC ![]() 7nvyC ![]() 7nvzC ![]() 7nw0C M: atomic model generated by this map C: citing same article ( |
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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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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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Density Histograms |
-Additional map: #1
File | emd_12610_additional_1.map | ||||||||||||
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Density Histograms |
-Half map: #2
File | emd_12610_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_12610_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
+Entire : Human Mediator with RNA Polymerase II Pre-initiation complex
+Supramolecule #1: Human Mediator with RNA Polymerase II Pre-initiation complex
+Supramolecule #2: Pol Complex and Mediator of RNA polymerase II transcription
+Supramolecule #3: DNA-directed RNA polymerase
+Supramolecule #4: NT and Template
+Supramolecule #5: unassigned peptides (MED29 or MED30)
+Supramolecule #6: Transcription initiation factors
+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: Cyclin-dependent kinase 7
+Macromolecule #10: Cyclin-H
+Macromolecule #11: DNA-directed RNA polymerase subunit
+Macromolecule #12: DNA-directed RNA polymerase subunit beta
+Macromolecule #13: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #14: RPOL4c domain-containing protein
+Macromolecule #15: DNA-directed RNA polymerase II subunit E
+Macromolecule #16: DNA-directed RNA polymerase II subunit F
+Macromolecule #17: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #18: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #19: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #20: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #21: RNA_pol_L_2 domain-containing protein
+Macromolecule #22: RNA polymerase II subunit K
+Macromolecule #23: Transcription initiation factor IIB
+Macromolecule #25: TATA-box-binding protein
+Macromolecule #26: General transcription factor IIF subunit 1
+Macromolecule #27: General transcription factor IIF subunit 2
+Macromolecule #29: Transcription initiation factor IIA subunit 1
+Macromolecule #30: Transcription initiation factor IIA subunit 2
+Macromolecule #31: General transcription factor IIE subunit 1
+Macromolecule #32: Transcription initiation factor IIE subunit beta
+Macromolecule #33: Unassigned peptide, likely TFIIE-beta
+Macromolecule #34: Unassigned peptide, likely XPB
+Macromolecule #35: Mediator of RNA polymerase II transcription subunit 6
+Macromolecule #36: Mediator of RNA polymerase II transcription subunit 8
+Macromolecule #37: Mediator of RNA polymerase II transcription subunit 11
+Macromolecule #38: Mediator of RNA polymerase II transcription subunit 17
+Macromolecule #39: Mediator of RNA polymerase II transcription subunit 18
+Macromolecule #40: Mediator of RNA polymerase II transcription subunit 20
+Macromolecule #41: Mediator of RNA polymerase II transcription subunit 22
+Macromolecule #42: Mediator of RNA polymerase II transcription subunit 4
+Macromolecule #43: Mediator of RNA polymerase II transcription subunit 7
+Macromolecule #44: Mediator of RNA polymerase II transcription subunit 9
+Macromolecule #45: Mediator of RNA polymerase II transcription subunit 10
+Macromolecule #46: Mediator of RNA polymerase II transcription subunit 14
+Macromolecule #47: Mediator of RNA polymerase II transcription subunit 19
+Macromolecule #48: Mediator of RNA polymerase II transcription subunit 21
+Macromolecule #49: Mediator of RNA polymerase II transcription subunit 31
+Macromolecule #50: Mediator of RNA polymerase II transcription subunit 27
+Macromolecule #51: Mediator of RNA polymerase II transcription subunit 28
+Macromolecule #52: unassigned peptide (MED29 or MED30)
+Macromolecule #53: Mediator of RNA polymerase II transcription subunit 30
+Macromolecule #54: unassigned peptide (MED14)
+Macromolecule #55: unassigned peptide (MED6)
+Macromolecule #56: unassigned peptide (MED17)
+Macromolecule #57: unassigned peptide (MED29 or MED30)
+Macromolecule #58: unassigned peptide (MED29 or MED30)
+Macromolecule #24: NT
+Macromolecule #28: TEMPLATE
+Macromolecule #59: IRON/SULFUR CLUSTER
+Macromolecule #60: ZINC ION
+Macromolecule #61: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
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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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.56 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |