7NVR

Human Mediator with RNA Polymerase II Pre-initiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of mammalian RNA polymerase II pre-initiation complexes.

Aibara, S.Schilbach, S.Cramer, P.

(2021) Nature 594: 124-128

  • DOI: 10.1038/s41586-021-03554-8
  • Primary Citation of Related Structures:  
    7NVR, 7NVS, 7NVT, 7NVU, 7NVV, 7NVW, 7NVX, 7NVY, 7NVZ, 7NW0

  • PubMed Abstract: 
  • The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. For transcription initiation, RNA polymerase II (Pol II) assembles with general transcription factors into a pre-initiation complex (PIC) that opens promoter DNA ...

    The initiation of transcription is a focal point for the regulation of gene activity during mammalian cell differentiation and development. For transcription initiation, 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 1-9 and human 10,11 PIC and a topological model for DNA opening by the general factor TFIIH 12-14 . Here we report the high-resolution cryo-EM PIC structure comprising human general factors and Sus scrofa domesticus Pol II, which is 99.9% identical to human Pol II. We determine PIC structures with closed and opened promoter DNA at 2.5-2.8 Å resolution, and resolve 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 DNA opening ~30 base pairs downstream of the TATA box. We also provide evidence that DNA opening occurs in two steps and leads to TFIIH detachment from the core PIC, which may stop DNA twisting and enable RNA chain initiation.


    Organizational Affiliation

    Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany. patrick.cramer@mpibpc.mpg.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TFIIH basal transcription factor complex helicase XPD subunitA [auth 0]760Homo sapiensMutation(s): 0 
Gene Names: ERCC2XPDXPDC
EC: 3.6.4.12
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 1B [auth 1]548Homo sapiensMutation(s): 0 
Gene Names: GTF2H1BTF2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4C [auth 2]462Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CDK-activating kinase assembly factor MAT1D [auth 3]309Homo sapiensMutation(s): 0 
Gene Names: MNAT1CAP35MAT1RNF66
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UniProt GroupP51948
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 3E [auth 4]308Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 5F [auth 5]71Homo sapiensMutation(s): 0 
Gene Names: GTF2H5C6orf175TTDA
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2G [auth 6]395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2BTF2P44
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPBH [auth 7]782Homo sapiensMutation(s): 0 
Gene Names: ERCC3XPBXPBC
EC: 3.6.4.12
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 7I [auth 8]346Homo sapiensMutation(s): 0 
Gene Names: CDK7CAKCAK1CDKN7MO15STK1
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-HJ [auth 9]323Homo sapiensMutation(s): 0 
Gene Names: CCNH
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunitK [auth A]1970Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaL [auth B]1174Sus scrofaMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3M [auth C]275Sus scrofaMutation(s): 0 
Gene Names: POLR2C
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
RPOL4c domain-containing proteinN [auth D]142Sus scrofaMutation(s): 0 
Gene Names: POLR2D
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit EO [auth E]210Sus scrofaMutation(s): 0 
Gene Names: POLR2E
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit FP [auth F]127Sus scrofaMutation(s): 0 
Gene Names: POLR2F
UniProt
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7Q [auth G]172Sus scrofaMutation(s): 0 
Gene Names: POLR2G
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Find proteins for I3LJZ9 (Sus scrofa)
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3R [auth H]150Sus scrofaMutation(s): 0 
Gene Names: POLR2H
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9S [auth I]125Sus scrofaMutation(s): 0 
Gene Names: POLR2I
UniProt
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5T [auth J]67Sus scrofaMutation(s): 0 
Gene Names: POLR2L
UniProt
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing proteinU [auth K]117Sus scrofaMutation(s): 0 
Gene Names: POLR2J
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase II subunit KV [auth L]58Sus scrofaMutation(s): 0 
Gene Names: POLR2K
UniProt
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIBW [auth M]316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
EC: 2.3.1.48
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-box-binding proteinY [auth O]339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIF subunit 1Z [auth Q]517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIF subunit 2AA [auth R]249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2RAP30
EC: 3.6.4.12
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 1CA [auth U]376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1TF2A1
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2DA [auth V]109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIE subunit 1EA [auth W]439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1TF2E1
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaFA [auth X]291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2TF2E2
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned peptide, likely TFIIE-betaGA [auth Y]19Homo sapiensMutation(s): 0 
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Unassigned peptide, likely XPBHA [auth Z]8Homo sapiensMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6IA [auth a]246Homo sapiensMutation(s): 0 
Gene Names: MED6ARC33
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 8JA [auth b]268Homo sapiensMutation(s): 0 
Gene Names: MED8
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11KA [auth c]117Homo sapiensMutation(s): 0 
Gene Names: MED11HSPC296
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17LA [auth d]651Homo sapiensMutation(s): 0 
Gene Names: MED17ARC77CRSP6DRIP77DRIP80TRAP80
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18MA [auth e]208Homo sapiensMutation(s): 0 
Gene Names: MED18
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20NA [auth f]212Homo sapiensMutation(s): 0 
Gene Names: MED20TRFP
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22OA [auth g]200Homo sapiensMutation(s): 0 
Gene Names: MED22SURF5
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4PA [auth h]270Homo sapiensMutation(s): 0 
Gene Names: MED4ARC36DRIP36VDRIPHSPC126
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7QA [auth i]233Homo sapiensMutation(s): 0 
Gene Names: MED7ARC34CRSP9
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 9RA [auth j]146Homo sapiensMutation(s): 0 
Gene Names: MED9MED25
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Entity ID: 45
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Mediator of RNA polymerase II transcription subunit 10SA [auth k]135Homo sapiensMutation(s): 0 
Gene Names: MED10L6TRG17TRG20
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 14TA [auth l]1454Homo sapiensMutation(s): 0 
Gene Names: MED14ARC150CRSP2CXorf4DRIP150EXLM1RGR1TRAP170
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Entity ID: 47
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Mediator of RNA polymerase II transcription subunit 19UA [auth m]244Homo sapiensMutation(s): 0 
Gene Names: MED19LCMR1
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21VA [auth n]144Homo sapiensMutation(s): 0 
Gene Names: MED21SRB7SURB7
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31WA [auth o]131Homo sapiensMutation(s): 0 
Gene Names: MED31SOH1CGI-125
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 27XA [auth p]311Homo sapiensMutation(s): 0 
Gene Names: MED27CRSP34CRSP8
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Entity ID: 51
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Mediator of RNA polymerase II transcription subunit 28YA [auth q]178Homo sapiensMutation(s): 0 
Gene Names: MED28EG1FKSG20
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
unassigned peptide (MED29 or MED30)ZA [auth r]20Homo sapiensMutation(s): 0 
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 30AB [auth s]178Homo sapiensMutation(s): 0 
Gene Names: MED30THRAP6TRAP25
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
unassigned peptide (MED14)BB [auth v]22Homo sapiensMutation(s): 0 
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
unassigned peptide (MED6)CB [auth w]16Homo sapiensMutation(s): 0 
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
unassigned peptide (MED17)DB [auth x]11Homo sapiensMutation(s): 0 
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
unassigned peptide (MED29 or MED30)EB [auth y]18Trichoplusia niMutation(s): 0 
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
unassigned peptide (MED29 or MED30)FB [auth z]23Trichoplusia niMutation(s): 0 
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Entity ID: 24
MoleculeChainsLengthOrganismImage
NTX [auth N]106Human mastadenovirus C
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Entity ID: 28
MoleculeChainsLengthOrganismImage
TEMPLATEBA [auth T]106Human mastadenovirus C
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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GB [auth 0]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

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HB [auth 3],
IB [auth 3],
JB [auth 4],
KB [auth 4],
LB [auth 6],
HB [auth 3],
IB [auth 3],
JB [auth 4],
KB [auth 4],
LB [auth 6],
MB [auth 6],
NB [auth 6],
OB [auth A],
PB [auth A],
RB [auth B],
SB [auth C],
TB [auth I],
UB [auth I],
VB [auth J],
WB [auth L],
XB [auth M],
YB [auth W],
ZB [auth p]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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QB [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyEXC 2067/1 39072994
German Research Foundation (DFG)GermanySFB860
German Research Foundation (DFG)GermanySPP2191
European Research Council (ERC)European Union882357
H2020 Marie Curie Actions of the European CommissionEuropean Union894862

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-06-02
    Changes: Database references
  • Version 1.2: 2021-06-16
    Changes: Database references, Derived calculations