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

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Basic information

Entry
Database: EMDB / ID: EMD-12609
TitleHuman Mediator with RNA Polymerase II Stalk
Map dataPostprocessed map
Sample
  • Complex: Human Mediator with RNA Polymerase II Stalk
Function / homology
Function and homology information


negative regulation of smooth muscle cell differentiation / 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 / central nervous system myelin formation / positive regulation of mitotic recombination / core mediator complex ...negative regulation of smooth muscle cell differentiation / 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 / central nervous system myelin formation / positive regulation of mitotic recombination / core mediator complex / positive regulation of core promoter binding / meiotic sister chromatid cohesion / RNA polymerase II core complex assembly / hair cell differentiation / ventricular system development / hair follicle maturation / cyclin-dependent protein kinase activating kinase holoenzyme complex / RNA polymerase transcription factor SL1 complex / snRNA transcription by RNA polymerase II / nucleotide-excision repair factor 3 complex / transcription factor TFIIE complex / nucleotide-excision repair, preincision complex assembly / phosphatase activator activity / UV protection / CAK-ERCC2 complex / transcription factor TFIIK complex / RNA polymerase III general transcription initiation factor activity / embryonic cleavage / transcription open complex formation at RNA polymerase II promoter / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / mediator complex / 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 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 / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIF complex / 5'-3' DNA helicase activity / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Generic Transcription Pathway / adult heart development / RNA Polymerase III Abortive And Retractive Initiation / transcription factor TFIIA complex / G protein-coupled receptor internalization / : / 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 / nuclear vitamin D receptor binding / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / germinal vesicle / [RNA-polymerase]-subunit kinase / RNA polymerase II general transcription initiation factor binding / limb development / 3'-5' DNA helicase activity / nuclear thyroid hormone receptor binding / transcription preinitiation complex / RNA Polymerase I Transcription Termination / regulation of mitotic cell cycle phase transition / cyclin-dependent protein serine/threonine kinase regulator activity / : / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Viral Messenger RNA Synthesis / hematopoietic stem cell proliferation / Signaling by FGFR2 IIIa TM / termination of RNA polymerase II transcription / cell division site / cortical actin cytoskeleton / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE
Similarity search - Function
Mediator complex subunit 28 / Mediator complex, subunit Med6, metazoa/plant / Mediator complex, subunit Med19, metazoa / Mediator complex, subunit Med30, metazoa / Mediator complex, subunit Med28 / Mediator of RNA polymerase II transcription subunit 9, metazoan / Mediator of RNA pol II transcription subunit 19 / Mediator complex subunit 30 / Mediator complex, subunit Med27 / Mediator complex subunit 27 ...Mediator complex subunit 28 / Mediator complex, subunit Med6, metazoa/plant / Mediator complex, subunit Med19, metazoa / Mediator complex, subunit Med30, metazoa / Mediator complex, subunit Med28 / Mediator of RNA polymerase II transcription subunit 9, metazoan / Mediator of RNA pol II transcription subunit 19 / Mediator complex subunit 30 / Mediator complex, subunit Med27 / Mediator complex subunit 27 / Mediator complex, subunit Med10 / Transcription factor subunit Med10 of Mediator complex / Mediator of RNA polymerase II transcription subunit 9 / RNA polymerase II transcription mediator complex subunit 9 / Mediator complex, subunit Med4 / Vitamin-D-receptor interacting Mediator subunit 4 / Mediator complex, subunit Med7 superfmaily / Mediator complex, subunit Med31 / Mediator complex, subunit Med21 / Mediator of RNA polymerase II, subunit Med31 superfamily / SOH1 / Subunit 21 of Mediator complex / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / MED7 protein / Mediator complex, subunit Med20 / Mediator complex, subunit Med14 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex subunit MED14 / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex / Mediator of RNA polymerase II transcription subunit 22 / Mediator complex, subunit Med8, fungi/metazoa / Mediator complex, subunit Med11 / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex protein / Mediator complex, subunit Med18 / Med18 protein / Transcription factor TFIIE alpha subunit, C-terminal / C-terminal general transcription factor TFIIE alpha / CyclinH/Ccl1 / Cyclin-dependent kinase 7 / TFIIH subunit Tfb4/GTF2H3 / Transcription factor Tfb4 / TFIIH C1-like domain / Ssl1-like / TFIIH subunit Ssl1/p44 / Ssl1-like / TFIIH C1-like domain / TFIIH C1-like domain / TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / RAD3/XPD family / Helicase XPB/Ssl2 / Helical and beta-bridge domain / ERCC3/RAD25/XPB helicase, C-terminal domain / Helicase XPB/Ssl2, N-terminal domain / Helical and beta-bridge domain / Helicase conserved C-terminal domain / ERCC3/RAD25/XPB C-terminal helicase / Transcription factor TFIIH subunit p52/Tfb2 / ATP-dependent helicase Rad3/Chl1-like / Transcription factor Tfb2, C-terminal domain / Transcription factor Tfb2 / Transcription factor Tfb2 (p52) C-terminal domain / Transcription factor TFIIE beta subunit, DNA-binding domain / Transcription initiation factor TFIIE, beta subunit / TFA2, Winged helix domain 2 / TFIIE beta subunit core domain / TFA2 Winged helix domain 2 / TFIIE beta central core DNA-binding domain profile. / TFIIH subunit TTDA/Tfb5 / TFB5-like superfamily / Transcription factor TFIIH complex subunit Tfb5 / Transcription factor TFIIH complex subunit Tfb5 / Cdk-activating kinase assembly factor MAT1/Tfb3 / Cdk-activating kinase assembly factor MAT1, centre / CDK-activating kinase assembly factor MAT1 / Zinc finger, C3HC4 type (RING finger) / Helicase superfamily 1/2, DinG/Rad3-like / Helicase-like, DEXD box c2 type / ATP-dependent helicase, C-terminal / DEAD2 / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Cyclin, C-terminal domain 2 / DEAD_2 / Helicase C-terminal domain / Cyclin C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / DEXDc2
Similarity search - Domain/homology
RNA polymerase II subunit D / DNA-directed RNA polymerase II subunit RPB11-a / 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 polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II, I and III subunit K ...RNA polymerase II subunit D / DNA-directed RNA polymerase II subunit RPB11-a / 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 polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II, I and III subunit K / DNA-directed RNA polymerase II subunit E / 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 / Transcription initiation factor IIE subunit beta / General transcription factor IIH subunit 1 / General transcription factor IIF subunit 1 / Cyclin-dependent kinase 7 / Cyclin-H / CDK-activating kinase assembly factor MAT1 / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / Mediator of RNA polymerase II transcription subunit 21 / General transcription factor IIH subunit 2 / General transcription factor IIH subunit 3 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 27 / General transcription factor IIH subunit 5 / 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 / Mediator of RNA polymerase II transcription subunit 18 / 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 / Mediator of RNA polymerase II transcription subunit 31
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 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
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  • Surface view colored by radius
  • Surface level: 5.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12609.png

Downloads & links

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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)
AnnotationPostprocessed map
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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Mask #1

Fileemd_12609_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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

Histogram

Histogram (log scale)

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Half map: Unfiltered half map 2

Fileemd_12609_half_map_2.map
AnnotationUnfiltered half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
Components
  • Complex: Human Mediator with RNA Polymerase II Stalk

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Supramolecule #1: Human Mediator with RNA Polymerase II Stalk

SupramoleculeName: Human Mediator with RNA Polymerase II Stalk / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.56 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 85186
FSC plot (resolution estimation)

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