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- EMDB-12609: Human Mediator with RNA Polymerase II Stalk -

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Entry
Database: EMDB / ID: EMD-12609
TitleHuman Mediator with RNA Polymerase II Stalk
Map data
SampleHuman Mediator with RNA Polymerase II Stalk
Function / homology
Function and homology information


negative regulation of smooth muscle cell differentiation / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase I Transcription Termination / RNA Polymerase I Promoter Escape / cyclin-dependent protein kinase activating kinase holoenzyme complex / MMXD complex / core mediator complex / core TFIIH complex portion of holo TFIIH complex ...negative regulation of smooth muscle cell differentiation / RNA Polymerase I Transcription Initiation / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase I Transcription Termination / RNA Polymerase I Promoter Escape / cyclin-dependent protein kinase activating kinase holoenzyme complex / MMXD complex / core mediator complex / core TFIIH complex portion of holo TFIIH complex / positive regulation of DNA helicase activity / central nervous system myelin formation / B-WICH complex positively regulates rRNA expression / CAK-ERCC2 complex / hair follicle maturation / Cytosolic iron-sulfur cluster assembly / ventricular system development / positive regulation of mitotic recombination / transcription factor TFIIK complex / Estrogen-dependent gene expression / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / RNA Pol II CTD phosphorylation and interaction with CE / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Promoter Escape / mRNA Splicing - Minor Pathway / mRNA Splicing - Major Pathway / mRNA Capping / RNA polymerase II transcribes snRNA genes / FGFR2 alternative splicing / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / Transcriptional regulation by small RNAs / Processing of Capped Intron-Containing Pre-mRNA / Gap-filling DNA repair synthesis and ligation in TC-NER / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / RNA polymerase II core complex assembly / adult heart development / hair cell differentiation / nucleotide-excision repair factor 3 complex / embryonic cleavage / phosphatase activator activity / transcription factor TFIIE complex / TFIIF-class transcription factor complex binding / [RNA-polymerase]-subunit kinase / negative regulation of DNA helicase activity / transcription factor TFIIH core complex / positive regulation of core promoter binding / transcription factor TFIIH holo complex / UV protection / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIF complex / transcriptional start site selection at RNA polymerase II promoter / G protein-coupled receptor internalization / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription elongation from RNA polymerase I promoter / cyclin-dependent protein serine/threonine kinase activator activity / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA Polymerase III Abortive And Retractive Initiation / phosphorylation of RNA polymerase II C-terminal domain / Abortive elongation of HIV-1 transcript in the absence of Tat / transcription factor TFIIA complex / 5'-3' DNA helicase activity / RNA polymerase III general transcription initiation factor activity / limb development / nuclear-transcribed mRNA catabolic process, exonucleolytic / RNA Polymerase I Transcription Termination / general transcription initiation factor activity / RNA polymerase II general transcription initiation factor binding / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / Formation of the HIV-1 Early Elongation Complex / Formation of the Early Elongation Complex / mRNA Capping / FGFR2 alternative splicing / Generic Transcription Pathway / male pronucleus / female pronucleus / Viral Messenger RNA Synthesis / mediator complex / mRNA export from nucleus in response to heat stress / 3'-5' DNA helicase activity / positive regulation of viral transcription / transcription initiation from RNA polymerase I promoter / RNA polymerase II preinitiation complex assembly / bone mineralization / thyroid hormone receptor binding / Processing of Capped Intron-Containing Pre-mRNA / cyclin-dependent protein serine/threonine kinase regulator activity / vitamin D receptor binding / cortical actin cytoskeleton / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Initiation And Promoter Clearance
Similarity search - Function
Mediator complex, subunit Med6, metazoa/plant / Mediator complex subunit 30 / Mediator of RNA polymerase II transcription subunit 9, metazoan / Mediator of RNA pol II transcription subunit 19 / Mediator complex, subunit Med28 / Mediator complex, subunit Med30, metazoa / Mediator complex, subunit Med19, metazoa / Mediator complex subunit 27 / Mediator complex, subunit Med10 / Mediator complex, subunit Med27 ...Mediator complex, subunit Med6, metazoa/plant / Mediator complex subunit 30 / Mediator of RNA polymerase II transcription subunit 9, metazoan / Mediator of RNA pol II transcription subunit 19 / Mediator complex, subunit Med28 / Mediator complex, subunit Med30, metazoa / Mediator complex, subunit Med19, metazoa / Mediator complex subunit 27 / Mediator complex, subunit Med10 / Mediator complex, subunit Med27 / Transcription factor subunit Med10 of Mediator complex / RNA polymerase II transcription mediator complex subunit 9 / Mediator of RNA polymerase II transcription subunit 9 / Vitamin-D-receptor interacting Mediator subunit 4 / Mediator complex, subunit Med4 / Mediator complex, subunit Med14 / Mediator complex subunit MED14 / Subunit 21 of Mediator complex / SOH1 / Mediator complex, subunit Med21 / Mediator complex, subunit Med31 / Mediator of RNA polymerase II, subunit Med31 superfamily / CyclinH/Ccl1 / Mediator complex protein / Mediator complex, subunit Med11 / Mediator complex, subunit Med7/Med21-like / Cyclin-dependent kinase 7 / MED7 protein / Mediator complex, subunit Med7 / Cyclin, C-terminal domain 2 / Cyclin C-terminal domain / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex, subunit Med20 / Subunit 17 of Mediator complex / Mediator complex, subunit Med17 / MED6 mediator sub complex component / Mediator complex, subunit Med6 superfamily / Mediator complex, subunit Med6 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription complex subunit 8 / Surfeit locus protein 5 subunit 22 of Mediator complex / : / Mediator complex, subunit Med8, fungi/metazoa / Med18 protein / Mediator complex, subunit Med18 / Zinc finger, C3HC4 type (RING finger) / Cdk-activating kinase assembly factor MAT1, centre / Cdk-activating kinase assembly factor MAT1/Tfb3 / CDK-activating kinase assembly factor MAT1 / Transcription factor TFIIE alpha subunit, C-terminal / Transcription factor Tfb4 / TFIIH subunit Tfb4/GTF2H3 / C-terminal general transcription factor TFIIE alpha / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / TFIIH p62 subunit, N-terminal / Ssl1-like / TFIIH C1-like domain / BSD domain / Ssl1-like / TFIIH subunit Ssl1/p44 / domain in transcription factors and synapse-associated proteins / TFIIH C1-like domain / TFIIH C1-like domain / BSD domain / RAD3/XPD family / BSD domain profile. / Helical and beta-bridge domain / Helical and beta-bridge domain / ATP-dependent helicase Rad3/Chl1-like / Helicase XPB/Ssl2 / Helicase conserved C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Transcription factor Tfb2, C-terminal domain / Transcription factor TFIIH subunit p52/Tfb2 / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / ERCC3/RAD25/XPB helicase, C-terminal domain / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / TFIIH subunit TTDA/Tfb5 / Helicase-like, DEXD box c2 type / Helicase C-terminal domain / DEAD2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / DEAD_2 / HELICc2 / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2 / TFIIE beta subunit core domain / TFIIE beta central core DNA-binding domain profile. / TFA2, Winged helix domain 2 / Transcription factor TFIIE beta subunit, DNA-binding domain / TFA2 Winged helix domain 2 / Transcription initiation factor TFIIE, beta subunit / Cyclin/Cyclin-like subunit Ssn8 / Transcription initiation factor IIE subunit alpha, N-terminal
Similarity search - Domain/homology
General transcription factor IIH subunit 2 / Mediator of RNA polymerase II transcription subunit 22 / General transcription factor IIH subunit 3 / Transcription initiation factor IIA subunit 2 / Mediator of RNA polymerase II transcription subunit 21 / Transcription initiation factor IIB / DNA-directed RNA polymerase II subunit RPB9 / General transcription factor IIH subunit 5 / Mediator of RNA polymerase II transcription subunit 27 / Mediator of RNA polymerase II transcription subunit 18 ...General transcription factor IIH subunit 2 / Mediator of RNA polymerase II transcription subunit 22 / General transcription factor IIH subunit 3 / Transcription initiation factor IIA subunit 2 / Mediator of RNA polymerase II transcription subunit 21 / Transcription initiation factor IIB / DNA-directed RNA polymerase II subunit RPB9 / General transcription factor IIH subunit 5 / Mediator of RNA polymerase II transcription subunit 27 / Mediator of RNA polymerase II transcription subunit 18 / General transcription factor IIH subunit 4 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 30 / Mediator of RNA polymerase II transcription subunit 10 / CDK-activating kinase assembly factor MAT1 / Mediator of RNA polymerase II transcription subunit 28 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 4 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 9 / Mediator of RNA polymerase II transcription subunit 11 / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIE subunit beta / Cyclin-H / RNA polymerase II subunit K / RNA polymerase II subunit D / RNA_pol_L_2 domain-containing protein / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Mediator of RNA polymerase II transcription subunit 19 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit E / Cyclin-dependent kinase 7 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 6 / General transcription factor IIF subunit 2 / General transcription and DNA repair factor IIH helicase subunit XPD / General transcription and DNA repair factor IIH helicase subunit XPB / TATA-box-binding protein / General transcription factor IIE subunit 1 / General transcription factor IIH subunit 1 / General transcription factor IIF subunit 1 / Mediator of RNA polymerase II transcription subunit 31
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsRengachari S / Schilbach S / Aibara S / Cramer P
Funding supportEuropean Union, Germany, 5 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission894862European Union
German Research Foundation (DFG)EXC 2067/1 39072994 Germany
European Research Council (ERC)882357European Union
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP2191 Germany
CitationJournal: Nature / Year: 2021
Title: Structure of the human Mediator-RNA polymerase II pre-initiation complex.
Authors: Srinivasan Rengachari / Sandra Schilbach / Shintaro Aibara / Christian Dienemann / Patrick Cramer /
Abstract: Mediator is a conserved coactivator complex that enables the regulated initiation of transcription at eukaryotic genes. Mediator is recruited by transcriptional activators and binds the pre- ...Mediator is a conserved coactivator complex that enables the regulated initiation of transcription at eukaryotic genes. Mediator is recruited by transcriptional activators and binds the pre-initiation complex (PIC) to stimulate the phosphorylation of RNA polymerase II (Pol II) and promoter escape. Here we prepare a recombinant version of human Mediator, reconstitute a 50-subunit Mediator-PIC complex and determine the structure of the complex by cryo-electron microscopy. The head module of Mediator contacts the stalk of Pol II and the general transcription factors TFIIB and TFIIE, resembling the Mediator-PIC interactions observed in the corresponding complex in yeast. The metazoan subunits MED27-MED30 associate with exposed regions in MED14 and MED17 to form the proximal part of the Mediator tail module that binds activators. Mediator positions the flexibly linked cyclin-dependent kinase (CDK)-activating kinase of the general transcription factor TFIIH near the linker to the C-terminal repeat domain of Pol II. The Mediator shoulder domain holds the CDK-activating kinase subunit CDK7, whereas the hook domain contacts a CDK7 element that flanks the kinase active site. The shoulder and hook domains reside in the Mediator head and middle modules, respectively, which can move relative to each other and may induce an active conformation of the CDK7 kinase to allosterically stimulate phosphorylation of the C-terminal domain.
History
DepositionMar 15, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateJun 16, 2021-
Current statusJun 16, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5.25
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_12609.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.05 Å/pix.
x 420 pix.
= 441. Å
1.05 Å/pix.
x 420 pix.
= 441. Å
1.05 Å/pix.
x 420 pix.
= 441. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 5.25 / Movie #1: 5.25
Minimum - Maximum-27.963213 - 46.90356
Average (Standard dev.)-0.00048153268 (±0.99334824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 440.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z441.000441.000441.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ420420420
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-27.96346.904-0.000

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Supplemental data

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Segmentation: #1

Fileemd_12609_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Unfiltered half map 1

Fileemd_12609_half_map_1.map
AnnotationUnfiltered half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Unfiltered half map 2

Fileemd_12609_half_map_2.map
AnnotationUnfiltered half map 2
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Sample components

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Entire Human Mediator with RNA Polymerase II Stalk

EntireName: Human Mediator with RNA Polymerase II Stalk / Number of components: 1

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Component #1: protein, Human Mediator with RNA Polymerase II Stalk

ProteinName: Human Mediator with RNA Polymerase II Stalk / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 58.56 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 85186
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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