7LBM

Structure of the human Mediator-bound transcription pre-initiation complex

  • Classification: TRANSCRIPTION/DNA
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2021-01-08 Released: 2021-03-24 
  • Deposition Author(s): Abdella, R., Talyzina, A., He, Y.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), American Cancer Society, National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 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-bound transcription preinitiation complex.

Abdella, R.Talyzina, A.Chen, S.Inouye, C.J.Tjian, R.He, Y.

(2021) Science 372: 52-56

  • DOI: https://doi.org/10.1126/science.abg3074
  • Primary Citation of Related Structures:  
    7LBM

  • PubMed Abstract: 

    Eukaryotic transcription requires the assembly of a multisubunit preinitiation complex (PIC) composed of RNA polymerase II (Pol II) and the general transcription factors. The coactivator Mediator is recruited by transcription factors, facilitates the assembly of the PIC, and stimulates phosphorylation of the Pol II C-terminal domain (CTD) by the TFIIH subunit CDK7. Here, we present the cryo-electron microscopy structure of the human Mediator-bound PIC at a resolution below 4 angstroms. Transcription factor binding sites within Mediator are primarily flexibly tethered to the tail module. CDK7 is stabilized by multiple contacts with Mediator. Two binding sites exist for the Pol II CTD, one between the head and middle modules of Mediator and the other in the active site of CDK7, providing structural evidence for Pol II CTD phosphorylation within the Mediator-bound PIC.


  • Organizational Affiliation

    Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of Mediator of RNA polymerase II transcription subunit 16A [auth 0]841Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175221 
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UniProt GroupQ9Y2X0
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 23B [auth 1]1,368Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000112282 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 24C [auth 2]989Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000008838 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 25D [auth 3]747Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000104973 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1E [auth A]1,970Homo sapiensMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2F [auth B]1,174Homo sapiensMutation(s): 0 
EC: 2.7.7.6
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GTEx:  ENSG00000047315 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3G [auth C]275Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000102978 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4H [auth D]142Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000144231 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB5I [auth E]210Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099817 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2J [auth F]127Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100142 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7K [auth G]172Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168002 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3L [auth H]150Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163882 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9M [auth I]125Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000105258 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5N [auth J]67Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000177700 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11-aO [auth K]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000005075 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4P [auth L]58Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000147669 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 1Q [auth M]376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1TF2A1
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GTEx:  ENSG00000165417 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2R [auth N]109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
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GTEx:  ENSG00000140307 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIBS [auth O]316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
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GTEx:  ENSG00000137947 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box-binding proteinT [auth P]339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
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GTEx:  ENSG00000112592 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIE subunit 1U [auth Q]439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1TF2E1
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GTEx:  ENSG00000153767 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaV [auth R]291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2TF2E2
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GTEx:  ENSG00000197265 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIF subunit 1W [auth S]517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
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GTEx:  ENSG00000125651 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIF subunit 2X [auth T]249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2RAP30
EC: 3.6.4.12
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GTEx:  ENSG00000188342 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
TFIIH basal transcription factor complex helicase XPB subunitAA [auth W]782Homo sapiensMutation(s): 0 
EC: 3.6.4.12
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GTEx:  ENSG00000163161 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
TFIIH basal transcription factor complex helicase XPD subunitBA [auth X]760Homo sapiensMutation(s): 0 
EC: 3.6.4.12
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GTEx:  ENSG00000104884 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 1CA [auth Y]548Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000110768 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4, p52DA [auth Z]462Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000213780 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2EA [auth a]395Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000145736 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 3FA [auth b]308Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000111358 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
General transcription factor IIH subunit 5GA [auth c]71Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000272047 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
CDK-activating kinase assembly factor MAT1HA [auth d]309Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000020426 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-dependent kinase 7IA [auth e]346Homo sapiensMutation(s): 0 
EC: 2.7.11.22 (PDB Primary Data), 2.7.11.23 (PDB Primary Data)
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GTEx:  ENSG00000134058 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclin-HJA [auth f]323Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000134480 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6KA [auth g]246Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000133997 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 8LA [auth h]268Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159479 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11MA [auth i]117Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161920 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17NA [auth j]651Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000042429 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18OA [auth k]208Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000130772 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20PA [auth l]212Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000124641 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22QA [auth m]200Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000148297 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 27RA [auth n]311Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000160563 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 28SA [auth o]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000118579 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 29TA [auth p]200Homo sapiensMutation(s): 0 
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Find proteins for Q9NX70 (Homo sapiens)
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GTEx:  ENSG00000063322 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 30UA [auth q]178Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000164758 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 14VA [auth r]1,454Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000180182 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4WA [auth s]270Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000136146 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7XA [auth t]233Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000155868 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 9YA [auth u]146Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000141026 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 10ZA [auth v]135Homo sapiensMutation(s): 0 
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Find proteins for Q9BTT4 (Homo sapiens)
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GTEx:  ENSG00000133398 
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 19AB [auth w]244Homo sapiensMutation(s): 0 
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Find proteins for A0JLT2 (Homo sapiens)
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GTEx:  ENSG00000156603 
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21BB [auth x]144Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000152944 
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31CB [auth y]131Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108590 
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 15DB [auth z]788Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099917 
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Entity ID: 25
MoleculeChains LengthOrganismImage
super core promoter sense strandY [auth U]100Homo sapiens
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Entity ID: 26
MoleculeChains LengthOrganismImage
super core promoter antisense strandZ [auth V]100Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
QB [auth X]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
ZN
Query on ZN

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FB [auth A]
GB [auth A]
IB [auth B]
JB [auth C]
KB [auth I]
FB [auth A],
GB [auth A],
IB [auth B],
JB [auth C],
KB [auth I],
LB [auth I],
MB [auth J],
NB [auth L],
OB [auth O],
PB [auth Q],
RB [auth a],
SB [auth a],
TB [auth a],
UB [auth b],
VB [auth d],
WB [auth d]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
EB [auth A],
HB [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
American Cancer SocietyUnited StatesIRG-15-173-21
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP01-CA092584
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesU54-CA193419
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32-GM008382

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-24
    Type: Initial release
  • Version 1.1: 2021-04-14
    Changes: Database references