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Yorodumi- EMDB-23255: Structure of the human Mediator-bound transcription pre-initiatio... -
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-Basic information
Entry | Database: EMDB / ID: EMD-23255 | ||||||||||||||||||
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Title | Structure of the human Mediator-bound transcription pre-initiation complex | ||||||||||||||||||
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Function / homology | Function and homology information positive regulation of mediator complex assembly / positive regulation of T cell extravasation / LRR domain binding / negative regulation of smooth muscle cell differentiation / microfibril binding / RNA Polymerase III Chain Elongation / MMXD complex / core TFIIH complex portion of holo TFIIH complex / RNA Polymerase III Transcription Termination / Cytosolic iron-sulfur cluster assembly ...positive regulation of mediator complex assembly / positive regulation of T cell extravasation / LRR domain binding / negative regulation of smooth muscle cell differentiation / microfibril binding / RNA Polymerase III Chain Elongation / MMXD complex / core TFIIH complex portion of holo TFIIH complex / RNA Polymerase III Transcription Termination / Cytosolic iron-sulfur cluster assembly / nucleotide-excision repair, DNA duplex unwinding / central nervous system myelin formation / regulation of transcription by RNA polymerase I / positive regulation of mitotic recombination / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / core mediator complex / hair follicle maturation / ventricular system development / hair cell differentiation / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / snRNA transcription by RNA polymerase II / RPAP3/R2TP/prefoldin-like complex / RNA polymerase transcription factor SL1 complex / 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 / TFIIF-class transcription factor complex binding / RNA polymerase I core promoter sequence-specific DNA binding / transcriptional start site selection at RNA polymerase II promoter / Cytosolic sensors of pathogen-associated DNA / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / DNA 5'-3' helicase / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / mediator complex / RNA Polymerase III Abortive And Retractive Initiation / nuclear retinoic acid receptor binding / G protein-coupled receptor internalization / adult heart development / Generic Transcription Pathway / transcription factor TFIIA complex / female germ cell nucleus / male pronucleus / transcription factor TFIIH core complex / female pronucleus / transcription factor TFIIH holo complex / cyclin-dependent protein serine/threonine kinase activator activity / Abortive elongation of HIV-1 transcript in the absence of Tat / DNA 3'-5' helicase / positive regulation of chromatin binding / RNA polymerase II general transcription initiation factor binding / germinal vesicle / nuclear vitamin D receptor binding / [RNA-polymerase]-subunit kinase / limb development / transcription preinitiation complex / MicroRNA (miRNA) biogenesis / RNA Polymerase I Transcription Termination / FGFR2 alternative splicing / nuclear thyroid hormone receptor binding / cyclin-dependent protein serine/threonine kinase regulator activity / Viral Messenger RNA Synthesis / regulation of mitotic cell cycle phase transition / Signaling by FGFR2 IIIa TM / hematopoietic stem cell proliferation / cortical actin cytoskeleton / 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 / transcription factor TFIID complex / termination of RNA polymerase II transcription / RNA polymerase II general transcription initiation factor activity / regulation of cyclin-dependent protein serine/threonine kinase activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / PIWI-interacting RNA (piRNA) biogenesis / cell division site / spinal cord development / RSV-host interactions / protein acetylation / bone mineralization / 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 / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / erythrocyte maturation Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) / Human (human) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 Å | ||||||||||||||||||
Authors | Abdella R / Talyzina A / He Y | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Science / Year: 2021 Title: Structure of the human Mediator-bound transcription preinitiation complex. Authors: R Abdella / A Talyzina / S Chen / C J Inouye / R Tjian / Y He / Abstract: Eukaryotic transcription requires the assembly of a multisubunit preinitiation complex (PIC) composed of RNA polymerase II (Pol II) and the general transcription factors. The coactivator Mediator is ...Eukaryotic transcription requires the assembly of a multisubunit preinitiation complex (PIC) composed of RNA polymerase II (Pol II) and the general transcription factors. The coactivator Mediator is recruited by transcription factors, facilitates the assembly of the PIC, and stimulates phosphorylation of the Pol II C-terminal domain (CTD) by the TFIIH subunit CDK7. Here, we present the cryo-electron microscopy structure of the human Mediator-bound PIC at a resolution below 4 angstroms. Transcription factor binding sites within Mediator are primarily flexibly tethered to the tail module. CDK7 is stabilized by multiple contacts with Mediator. Two binding sites exist for the Pol II CTD, one between the head and middle modules of Mediator and the other in the active site of CDK7, providing structural evidence for Pol II CTD phosphorylation within the Mediator-bound PIC. | ||||||||||||||||||
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_23255.map.gz | 254 MB | EMDB map data format | |
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Header (meta data) | emd-23255-v30.xml emd-23255.xml | 87.4 KB 87.4 KB | Display Display | EMDB header |
Images | emd_23255.png | 168.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23255 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23255 | HTTPS FTP |
-Validation report
Summary document | emd_23255_validation.pdf.gz | 359.2 KB | Display | EMDB validaton report |
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Full document | emd_23255_full_validation.pdf.gz | 358.8 KB | Display | |
Data in XML | emd_23255_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | emd_23255_validation.cif.gz | 8.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23255 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23255 | HTTPS FTP |
-Related structure data
Related structure data | 7lbmMC M: atomic model generated by this map C: citing same article (ref.) |
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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_23255.map.gz / Format: CCP4 / Size: 282.6 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: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Mediator-bound pre-initiation complex
+Supramolecule #1: Mediator-bound pre-initiation complex
+Supramolecule #2: RNA Polymerase II
+Supramolecule #3: Mediator
+Supramolecule #4: TFIIH
+Supramolecule #5: General transcription factors
+Supramolecule #6: promoter DNA
+Supramolecule #7: cyclin-H and associated factors
+Macromolecule #1: Isoform 2 of Mediator of RNA polymerase II transcription subunit 16
+Macromolecule #2: Mediator of RNA polymerase II transcription subunit 23
+Macromolecule #3: Mediator of RNA polymerase II transcription subunit 24
+Macromolecule #4: Mediator of RNA polymerase II transcription subunit 25
+Macromolecule #5: DNA-directed RNA polymerase II subunit RPB1
+Macromolecule #6: DNA-directed RNA polymerase II subunit RPB2
+Macromolecule #7: DNA-directed RNA polymerase II subunit RPB3
+Macromolecule #8: DNA-directed RNA polymerase II subunit RPB4
+Macromolecule #9: DNA-directed RNA polymerase II subunit RPB5
+Macromolecule #10: DNA-directed RNA polymerases I, II, and III subunit RPABC2
+Macromolecule #11: DNA-directed RNA polymerase II subunit RPB7
+Macromolecule #12: DNA-directed RNA polymerases I, II, and III subunit RPABC3
+Macromolecule #13: DNA-directed RNA polymerase II subunit RPB9
+Macromolecule #14: DNA-directed RNA polymerases I, II, and III subunit RPABC5
+Macromolecule #15: DNA-directed RNA polymerase II subunit RPB11-a
+Macromolecule #16: DNA-directed RNA polymerases I, II, and III subunit RPABC4
+Macromolecule #17: Transcription initiation factor IIA subunit 1
+Macromolecule #18: Transcription initiation factor IIA subunit 2
+Macromolecule #19: Transcription initiation factor IIB
+Macromolecule #20: TATA-box-binding protein
+Macromolecule #21: General transcription factor IIE subunit 1
+Macromolecule #22: Transcription initiation factor IIE subunit beta
+Macromolecule #23: General transcription factor IIF subunit 1
+Macromolecule #24: General transcription factor IIF subunit 2
+Macromolecule #27: TFIIH basal transcription factor complex helicase XPB subunit
+Macromolecule #28: TFIIH basal transcription factor complex helicase XPD subunit
+Macromolecule #29: General transcription factor IIH subunit 1
+Macromolecule #30: General transcription factor IIH subunit 4, p52
+Macromolecule #31: General transcription factor IIH subunit 2
+Macromolecule #32: General transcription factor IIH subunit 3
+Macromolecule #33: General transcription factor IIH subunit 5
+Macromolecule #34: CDK-activating kinase assembly factor MAT1
+Macromolecule #35: Cyclin-dependent kinase 7
+Macromolecule #36: Cyclin-H
+Macromolecule #37: Mediator of RNA polymerase II transcription subunit 6
+Macromolecule #38: Mediator of RNA polymerase II transcription subunit 8
+Macromolecule #39: Mediator of RNA polymerase II transcription subunit 11
+Macromolecule #40: Mediator of RNA polymerase II transcription subunit 17
+Macromolecule #41: Mediator of RNA polymerase II transcription subunit 18
+Macromolecule #42: Mediator of RNA polymerase II transcription subunit 20
+Macromolecule #43: Mediator of RNA polymerase II transcription subunit 22
+Macromolecule #44: Mediator of RNA polymerase II transcription subunit 27
+Macromolecule #45: Mediator of RNA polymerase II transcription subunit 28
+Macromolecule #46: Mediator of RNA polymerase II transcription subunit 29
+Macromolecule #47: Mediator of RNA polymerase II transcription subunit 30
+Macromolecule #48: Mediator of RNA polymerase II transcription subunit 14
+Macromolecule #49: Mediator of RNA polymerase II transcription subunit 4
+Macromolecule #50: Mediator of RNA polymerase II transcription subunit 7
+Macromolecule #51: Mediator of RNA polymerase II transcription subunit 9
+Macromolecule #52: Mediator of RNA polymerase II transcription subunit 10
+Macromolecule #53: Mediator of RNA polymerase II transcription subunit 19
+Macromolecule #54: Mediator of RNA polymerase II transcription subunit 21
+Macromolecule #55: Mediator of RNA polymerase II transcription subunit 31
+Macromolecule #56: Mediator of RNA polymerase II transcription subunit 15
+Macromolecule #25: super core promoter sense strand
+Macromolecule #26: super core promoter antisense strand
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: ZINC ION
+Macromolecule #59: IRON/SULFUR CLUSTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
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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 K2 SUMMIT (4k x 4k) / Average electron dose: 31.5 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 |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 156383 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |