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 1.1 of the entry. See complete history


Literature

Structure of the human Mediator-RNA polymerase II pre-initiation complex.

Rengachari, S.Schilbach, S.Aibara, S.Dienemann, C.Cramer, P.

(2021) Nature 

  • DOI: 10.1038/s41586-021-03555-7
  • Primary Citation of Related Structures:  
    7NVR

  • PubMed Abstract: 
  • Mediator is a conserved coactivator that enables regulated transcription initiation at eukaryotic genes 1-3 . Mediator is recruited by transcriptional activators and binds the pre-initiation complex (PIC) to stimulate RNA polymerase II (Pol II) phosphorylation and promoter escape 1-6 ...

    Mediator is a conserved coactivator that enables regulated transcription initiation at eukaryotic genes 1-3 . Mediator is recruited by transcriptional activators and binds the pre-initiation complex (PIC) to stimulate RNA polymerase II (Pol II) phosphorylation and promoter escape 1-6 . Here we prepare a recombinant human Mediator, reconstitute a 50-subunit Mediator-PIC complex, and determine the structure of the complex by cryo-EM. Mediator uses its head module to contact the Pol II stalk and the general transcription factors TFIIB and TFIIE, resembling the Mediator-PIC interactions in the corresponding yeast complex 7-9 . 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 CDK-activating kinase (CAK) of the general transcription factor TFIIH near the linker to the C-terminal repeat domain (CTD) of Pol II. The Mediator shoulder domain holds the CAK subunit CDK7, whereas the hook domain contacts a CDK7 element that flanks the kinase active site. The shoulder and hook 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 CTD phosphorylation.


    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
Find proteins for P32780 (Homo sapiens)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4C [auth 2]462Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
Find proteins for Q92759 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CDK-activating kinase assembly factor MAT1D [auth 3]309Homo sapiensMutation(s): 0 
Gene Names: MNAT1CAP35MAT1RNF66
Find proteins for P51948 (Homo sapiens)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 3E [auth 4]308Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
Find proteins for Q13889 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 5F [auth 5]71Homo sapiensMutation(s): 0 
Gene Names: GTF2H5C6orf175TTDA
Find proteins for Q6ZYL4 (Homo sapiens)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2G [auth 6]395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2BTF2P44
Find proteins for Q13888 (Homo sapiens)
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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
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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
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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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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3R [auth H]150Sus scrofaMutation(s): 0 
Gene Names: POLR2H
Find proteins for A0A4X1ULF2 (Sus scrofa)
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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
Find proteins for P60899 (Sus scrofa)
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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
Find proteins for A0A4X1VYD0 (Sus scrofa)
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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
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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
Find proteins for Q00403 (Homo sapiens)
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-box-binding proteinY [auth O]339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
Find proteins for P20226 (Homo sapiens)
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIF subunit 1Z [auth Q]517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
Find proteins for P35269 (Homo sapiens)
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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
Find proteins for P13984 (Homo sapiens)
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 1CA [auth U]376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1TF2A1
Find proteins for P52655 (Homo sapiens)
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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
Find proteins for P29083 (Homo sapiens)
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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
Find proteins for O75586 (Homo sapiens)
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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
Find proteins for Q96G25 (Homo sapiens)
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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
Find proteins for Q9P086 (Homo sapiens)
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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
Find proteins for Q9NVC6 (Homo sapiens)
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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
Find proteins for Q9BUE0 (Homo sapiens)
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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
Find proteins for Q9H944 (Homo sapiens)
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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
Find proteins for Q15528 (Homo sapiens)
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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
Find proteins for O43513 (Homo sapiens)
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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
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 10SA [auth k]135Homo sapiensMutation(s): 0 
Gene Names: MED10L6TRG17TRG20
Find proteins for Q9BTT4 (Homo sapiens)
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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
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 19UA [auth m]244Homo sapiensMutation(s): 0 
Gene Names: MED19LCMR1
Find proteins for A0JLT2 (Homo sapiens)
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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
Find proteins for Q13503 (Homo sapiens)
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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
Find proteins for Q9Y3C7 (Homo sapiens)
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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
Find proteins for Q6P2C8 (Homo sapiens)
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 28YA [auth q]178Homo sapiensMutation(s): 0 
Gene Names: MED28EG1FKSG20
Find proteins for Q9H204 (Homo sapiens)
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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
Find proteins for Q96HR3 (Homo sapiens)
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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 
Protein Feature View
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
unassigned peptide (MED29 or MED30)FB [auth z]23Trichoplusia niMutation(s): 0 
Protein Feature View
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Entity ID: 24
MoleculeChainsLengthOrganismImage
NTX [auth N]106Human mastadenovirus C
Protein Feature View
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Entity ID: 28
MoleculeChainsLengthOrganismImage
TEMPLATEBA [auth T]106Human mastadenovirus C
Protein Feature View
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  • Reference Sequence
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] , MB [auth 6] , NB [auth 6] , OB [auth A] , 
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

View Full Validation Report



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