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- EMDB-12610: Human Mediator with RNA Polymerase II Pre-initiation complex -

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Basic information

Entry
Database: EMDB / ID: EMD-12610
TitleHuman Mediator with RNA Polymerase II Pre-initiation complex
Map data
SampleHuman Mediator with RNA Polymerase II Pre-initiation complex
  • Pol Complex and Mediator of RNA polymerase II transcription
  • DNA-directed RNA polymerasePolymerase
  • NT and Template
  • unassigned peptides (MED29 or MED30)
  • Transcription initiation factors
  • TFIIH basal transcription factor complex helicase XPD subunit
  • (General transcription ...) x 9
  • CDK-activating kinase assembly factor MAT1
  • Cyclin-dependent kinase 7
  • Cyclin-H
  • (DNA-directed RNA polymerase ...Polymerase) x 7
  • RPOL4c domain-containing protein
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 2
  • RNA_pol_L_2 domain-containing protein
  • RNA polymerase II subunit K
  • (Transcription initiation factor ...) x 4
  • (nucleic-acidNucleic acid) x 2
  • TATA-box-binding protein
  • (Unassigned peptide, likely ...) x 2
  • (Mediator of RNA polymerase II transcription subunit ...) x 18
  • (unassigned peptide ...) x 6
  • (ligand) x 3
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) / Sus scrofa (pig) / Human mastadenovirus C / Trichoplusia ni (cabbage looper) / Pig (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsRengachari S / Schilbach S / Aibara S / Cramer P
Funding support Germany, European Union, 5 items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2067/1 39072994 Germany
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SPP2191 Germany
European Research Council (ERC)882357European Union
H2020 Marie Curie Actions of the European Commission894862European Union
CitationJournal: Nature / Year: 2021
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
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: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nvr
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_12610.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: 3.0 / Movie #1: 3
Minimum - Maximum-17.335718 - 40.087654
Average (Standard dev.)-3.3155442e-12 (±1.0)
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-17.33640.088-0.000

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Supplemental data

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Segmentation: #1

Fileemd_12610_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: #1

Fileemd_12610_additional_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Half map: #2

Fileemd_12610_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Half map: #1

Fileemd_12610_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire Human Mediator with RNA Polymerase II Pre-initiation complex

EntireName: Human Mediator with RNA Polymerase II Pre-initiation complex
Number of components: 67

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Component #1: protein, Human Mediator with RNA Polymerase II Pre-initiation complex

ProteinName: Human Mediator with RNA Polymerase II Pre-initiation complex
Recombinant expression: No

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Component #2: protein, Pol Complex and Mediator of RNA polymerase II transcription

ProteinName: Pol Complex and Mediator of RNA polymerase II transcription
Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #3: protein, DNA-directed RNA polymerase

ProteinName: DNA-directed RNA polymerasePolymerase / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)

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Component #4: protein, NT and Template

ProteinName: NT and Template / Recombinant expression: No
SourceSpecies: Human mastadenovirus C
Source (engineered)Expression System: synthetic construct (others)

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Component #5: protein, unassigned peptides (MED29 or MED30)

ProteinName: unassigned peptides (MED29 or MED30) / Recombinant expression: No
SourceSpecies: Trichoplusia ni (cabbage looper)

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Component #6: protein, Transcription initiation factors

ProteinName: Transcription initiation factors / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, TFIIH basal transcription factor complex helicase XPD subunit

ProteinName: TFIIH basal transcription factor complex helicase XPD subunit
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 87.021078 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #8: protein, General transcription factor IIH subunit 1

ProteinName: General transcription factor IIH subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 62.116492 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #9: protein, General transcription factor IIH subunit 4

ProteinName: General transcription factor IIH subunit 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.245156 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #10: protein, CDK-activating kinase assembly factor MAT1

ProteinName: CDK-activating kinase assembly factor MAT1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.873965 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #11: protein, General transcription factor IIH subunit 3

ProteinName: General transcription factor IIH subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.416008 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #12: protein, General transcription factor IIH subunit 5

ProteinName: General transcription factor IIH subunit 5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.060362 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #13: protein, General transcription factor IIH subunit 2

ProteinName: General transcription factor IIH subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.481996 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #14: protein, General transcription and DNA repair factor IIH helicase...

ProteinName: General transcription and DNA repair factor IIH helicase subunit XPB
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 89.404734 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #15: protein, Cyclin-dependent kinase 7

ProteinName: Cyclin-dependent kinase 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.090344 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #16: protein, Cyclin-H

ProteinName: Cyclin-H / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.695473 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #17: protein, DNA-directed RNA polymerase subunit

ProteinName: DNA-directed RNA polymerase subunitPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 217.450078 kDa
SourceSpecies: Pig (pig)

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Component #18: protein, DNA-directed RNA polymerase subunit beta

ProteinName: DNA-directed RNA polymerase subunit betaPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 134.041422 kDa
SourceSpecies: Pig (pig)

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Component #19: protein, DNA-directed RNA polymerase II subunit RPB3

ProteinName: DNA-directed RNA polymerase II subunit RPB3Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.439074 kDa
SourceSpecies: Pig (pig)

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Component #20: protein, RPOL4c domain-containing protein

ProteinName: RPOL4c domain-containing protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.331255 kDa
SourceSpecies: Pig (pig)

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Component #21: protein, DNA-directed RNA polymerase II subunit E

ProteinName: DNA-directed RNA polymerase II subunit EPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.644318 kDa
SourceSpecies: Pig (pig)

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Component #22: protein, DNA-directed RNA polymerase II subunit F

ProteinName: DNA-directed RNA polymerase II subunit FPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.477001 kDa
SourceSpecies: Pig (pig)

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Component #23: protein, DNA-directed RNA polymerase II subunit RPB7

ProteinName: DNA-directed RNA polymerase II subunit RPB7Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.314283 kDa
SourceSpecies: Pig (pig)

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Component #24: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.162273 kDa
SourceSpecies: Pig (pig)

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Component #25: protein, DNA-directed RNA polymerase II subunit RPB9

ProteinName: DNA-directed RNA polymerase II subunit RPB9Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.541221 kDa
SourceSpecies: Pig (pig)

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Component #26: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC5

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.655123 kDa
SourceSpecies: Pig (pig)

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Component #27: protein, RNA_pol_L_2 domain-containing protein

ProteinName: RNA_pol_L_2 domain-containing protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.310284 kDa
SourceSpecies: Pig (pig)

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Component #28: protein, RNA polymerase II subunit K

ProteinName: RNA polymerase II subunit K / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.018244 kDa
SourceSpecies: Pig (pig)

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Component #29: protein, Transcription initiation factor IIB

ProteinName: Transcription initiation factor IIB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.877949 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #30: nucleic-acid, NT

nucleic acidName: NT / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DC)(DG)(DG)(DG)(DT)(DG)(DT)(DT)(DC)(DC) (DT)(DG)(DA)(DA)(DG)(DG)(DG)(DG)(DG)(DG) (DC)(DT)(DA)(DT)(DA)(DA)(DA)(DA)(DG)(DG) (DG)(DG)(DG)(DT)(DG)(DG)(DG)(DG)(DG)(DC) (DG)(DC)(DG)(DT)(DT)(DC) ...Sequence:
(DC)(DG)(DG)(DG)(DT)(DG)(DT)(DT)(DC)(DC) (DT)(DG)(DA)(DA)(DG)(DG)(DG)(DG)(DG)(DG) (DC)(DT)(DA)(DT)(DA)(DA)(DA)(DA)(DG)(DG) (DG)(DG)(DG)(DT)(DG)(DG)(DG)(DG)(DG)(DC) (DG)(DC)(DG)(DT)(DT)(DC)(DG)(DT)(DC)(DC) (DT)(DC)(DA)(DC)(DT)(DC)(DT)(DC)(DT)(DT) (DC)(DC)(DG)(DC)(DA)(DT)(DC)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DG)(DC)(DG)(DA)(DG)(DG) (DG)(DC)(DC)(DA)(DG)(DC)(DT)(DG)(DT)(DT) (DG)(DG)(DG)(DG)(DT)(DG)(DA)(DG)(DT)(DA) (DC)(DT)(DC)(DC)(DC)(DT)
MassTheoretical: 32.911859 kDa
SourceSpecies: Human mastadenovirus C

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Component #31: protein, TATA-box-binding protein

ProteinName: TATA-box-binding protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.729938 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #32: protein, General transcription factor IIF subunit 1

ProteinName: General transcription factor IIF subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 58.343578 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #33: protein, General transcription factor IIF subunit 2

ProteinName: General transcription factor IIF subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.427309 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #34: nucleic-acid, TEMPLATE

nucleic acidName: TEMPLATE / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DC)(DT) (DC)(DA)(DC)(DC)(DC)(DC)(DA)(DA)(DC)(DA) (DG)(DC)(DT)(DG)(DG)(DC)(DC)(DC)(DT)(DC) (DG)(DC)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DG) (DA)(DT)(DG)(DC)(DG)(DG) ...Sequence:
(DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA)(DC)(DT) (DC)(DA)(DC)(DC)(DC)(DC)(DA)(DA)(DC)(DA) (DG)(DC)(DT)(DG)(DG)(DC)(DC)(DC)(DT)(DC) (DG)(DC)(DA)(DG)(DA)(DC)(DA)(DG)(DC)(DG) (DA)(DT)(DG)(DC)(DG)(DG)(DA)(DA)(DG)(DA) (DG)(DA)(DG)(DT)(DG)(DA)(DG)(DG)(DA)(DC) (DG)(DA)(DA)(DC)(DG)(DC)(DG)(DC)(DC)(DC) (DC)(DC)(DA)(DC)(DC)(DC)(DC)(DC)(DT)(DT) (DT)(DT)(DA)(DT)(DA)(DG)(DC)(DC)(DC)(DC) (DC)(DC)(DT)(DT)(DC)(DA)(DG)(DG)(DA)(DA) (DC)(DA)(DC)(DC)(DC)(DG)
MassTheoretical: 32.508752 kDa
SourceSpecies: Human mastadenovirus C

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Component #35: protein, Transcription initiation factor IIA subunit 1

ProteinName: Transcription initiation factor IIA subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.544551 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #36: protein, Transcription initiation factor IIA subunit 2

ProteinName: Transcription initiation factor IIA subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.469091 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #37: protein, General transcription factor IIE subunit 1

ProteinName: General transcription factor IIE subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.516094 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #38: protein, Transcription initiation factor IIE subunit beta

ProteinName: Transcription initiation factor IIE subunit beta / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.106824 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #39: protein, Unassigned peptide, likely TFIIE-beta

ProteinName: Unassigned peptide, likely TFIIE-beta / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.635006 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

+
Component #40: protein, Unassigned peptide, likely XPB

ProteinName: Unassigned peptide, likely XPB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.698854 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #41: protein, Mediator of RNA polymerase II transcription subunit 6

ProteinName: Mediator of RNA polymerase II transcription subunit 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.464627 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #42: protein, Mediator of RNA polymerase II transcription subunit 8

ProteinName: Mediator of RNA polymerase II transcription subunit 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.112906 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #43: protein, Mediator of RNA polymerase II transcription subunit 11

ProteinName: Mediator of RNA polymerase II transcription subunit 11
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.145829 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #44: protein, Mediator of RNA polymerase II transcription subunit 17

ProteinName: Mediator of RNA polymerase II transcription subunit 17
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 72.984047 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #45: protein, Mediator of RNA polymerase II transcription subunit 18

ProteinName: Mediator of RNA polymerase II transcription subunit 18
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.69373 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #46: protein, Mediator of RNA polymerase II transcription subunit 20

ProteinName: Mediator of RNA polymerase II transcription subunit 20
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.243762 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #47: protein, Mediator of RNA polymerase II transcription subunit 22

ProteinName: Mediator of RNA polymerase II transcription subunit 22
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.243713 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #48: protein, Mediator of RNA polymerase II transcription subunit 4

ProteinName: Mediator of RNA polymerase II transcription subunit 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.781424 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #49: protein, Mediator of RNA polymerase II transcription subunit 7

ProteinName: Mediator of RNA polymerase II transcription subunit 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.285281 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #50: protein, Mediator of RNA polymerase II transcription subunit 9

ProteinName: Mediator of RNA polymerase II transcription subunit 9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.42275 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #51: protein, Mediator of RNA polymerase II transcription subunit 10

ProteinName: Mediator of RNA polymerase II transcription subunit 10
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.710969 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #52: protein, Mediator of RNA polymerase II transcription subunit 14

ProteinName: Mediator of RNA polymerase II transcription subunit 14
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 160.787594 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #53: protein, Mediator of RNA polymerase II transcription subunit 19

ProteinName: Mediator of RNA polymerase II transcription subunit 19
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.321146 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #54: protein, Mediator of RNA polymerase II transcription subunit 21

ProteinName: Mediator of RNA polymerase II transcription subunit 21
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.575234 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #55: protein, Mediator of RNA polymerase II transcription subunit 31

ProteinName: Mediator of RNA polymerase II transcription subunit 31
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.826116 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #56: protein, Mediator of RNA polymerase II transcription subunit 27

ProteinName: Mediator of RNA polymerase II transcription subunit 27
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.478742 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #57: protein, Mediator of RNA polymerase II transcription subunit 28

ProteinName: Mediator of RNA polymerase II transcription subunit 28
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.540107 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #58: protein, unassigned peptide (MED29 or MED30)

ProteinName: unassigned peptide (MED29 or MED30) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.720111 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #59: protein, Mediator of RNA polymerase II transcription subunit 30

ProteinName: Mediator of RNA polymerase II transcription subunit 30
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 20.301229 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #60: protein, unassigned peptide (MED14)

ProteinName: unassigned peptide (MED14) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.890321 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #61: protein, unassigned peptide (MED6)

ProteinName: unassigned peptide (MED6) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.379692 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #62: protein, unassigned peptide (MED17)

ProteinName: unassigned peptide (MED17) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.954168 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

+
Component #63: protein, unassigned peptide (MED29 or MED30)

ProteinName: unassigned peptide (MED29 or MED30) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.549902 kDa
SourceSpecies: Trichoplusia ni (cabbage looper)

+
Component #64: protein, unassigned peptide (MED29 or MED30)

ProteinName: unassigned peptide (MED29 or MED30) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.975426 kDa
SourceSpecies: Trichoplusia ni (cabbage looper)

+
Component #65: ligand, IRON/SULFUR CLUSTER

LigandName: IRON/SULFUR CLUSTERIron–sulfur cluster / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.35164 kDa

+
Component #66: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 18 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #67: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

-
Experimental details

-
Sample preparation

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

-
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

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 25967
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Output model

+
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