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: 10.1126/science.abg3074
  • Primary Citation of Related Structures:  
    7LBM

  • PubMed Abstract: 
  • Eukaryotic transcription requires the assembly of a multi-subunit preinitiation complex (PIC) comprised of RNA polymerase II (Pol II) and the general transcription factors. The co-activator 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 ...

    Eukaryotic transcription requires the assembly of a multi-subunit preinitiation complex (PIC) comprised of RNA polymerase II (Pol II) and the general transcription factors. The co-activator 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 sub-4 Å. 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

    Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Northwestern University, Chicago, IL, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isoform 2 of Mediator of RNA polymerase II transcription subunit 16A [auth 0]841Homo sapiensMutation(s): 0 
Gene Names: MED16DRIP92THRAP5
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 23B [auth 1]1368Homo sapiensMutation(s): 0 
Gene Names: MED23ARC130CRSP3DRIP130KIAA1216SUR2
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 24C [auth 2]989Homo sapiensMutation(s): 0 
Gene Names: MED24ARC100CRSP4DRIP100KIAA0130THRAP4TRAP100
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 25D [auth 3]747Homo sapiensMutation(s): 0 
Gene Names: MED25ACID1ARC92PTOV2TCBAP0758
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1E [auth A]1970Homo sapiensMutation(s): 0 
Gene Names: POLR2APOLR2
EC: 2.7.7.6 (PDB Primary Data), 2.7.7.48 (UniProt)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2F [auth B]1174Homo sapiensMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3G [auth C]275Homo sapiensMutation(s): 0 
Gene Names: POLR2CA-152E5.7
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4H [auth D]142Homo sapiensMutation(s): 0 
Gene Names: POLR2D
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB5I [auth E]210Homo sapiensMutation(s): 0 
Gene Names: POLR2E
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2J [auth F]127Homo sapiensMutation(s): 0 
Gene Names: POLR2FPOLRF
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7K [auth G]172Homo sapiensMutation(s): 0 
Gene Names: POLR2GRPB7
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3L [auth H]150Homo sapiensMutation(s): 0 
Gene Names: POLR2H
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9M [auth I]125Homo sapiensMutation(s): 0 
Gene Names: POLR2I
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5N [auth J]67Homo sapiensMutation(s): 0 
Gene Names: POLR2L
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11-aO [auth K]117Homo sapiensMutation(s): 0 
Gene Names: POLR2JPOLR2J1
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4P [auth L]58Homo sapiensMutation(s): 0 
Gene Names: POLR2K
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 1Q [auth M]376Homo sapiensMutation(s): 0 
Gene Names: GTF2A1TF2A1
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2R [auth N]109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIBS [auth O]316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
EC: 2.3.1.48
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-box-binding proteinT [auth P]339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIE subunit 1U [auth Q]439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1TF2E1
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaV [auth R]291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2TF2E2
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIF subunit 1W [auth S]517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
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Entity ID: 24
MoleculeChainsSequence 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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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
TFIIH basal transcription factor complex helicase XPB subunitAA [auth W]782Homo sapiensMutation(s): 0 
Gene Names: ERCC3XPBXPBC
EC: 3.6.4.12
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
TFIIH basal transcription factor complex helicase XPD subunitBA [auth X]760Homo sapiensMutation(s): 0 
Gene Names: ERCC2XPDXPDC
EC: 3.6.4.12
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 1CA [auth Y]548Homo sapiensMutation(s): 0 
Gene Names: GTF2H1BTF2
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4, p52DA [auth Z]462Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2EA [auth a]395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2BTF2P44
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 3FA [auth b]308Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 5GA [auth c]71Homo sapiensMutation(s): 0 
Gene Names: GTF2H5C6orf175TTDA
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Entity ID: 34
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CDK-activating kinase assembly factor MAT1HA [auth d]309Homo sapiensMutation(s): 0 
Gene Names: MNAT1CAP35MAT1RNF66
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 7IA [auth e]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: 36
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Cyclin-HJA [auth f]323Homo sapiensMutation(s): 0 
Gene Names: CCNH
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Entity ID: 37
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Mediator of RNA polymerase II transcription subunit 6KA [auth g]246Homo sapiensMutation(s): 0 
Gene Names: MED6ARC33
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Entity ID: 38
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Mediator of RNA polymerase II transcription subunit 8LA [auth h]268Homo sapiensMutation(s): 0 
Gene Names: MED8
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Entity ID: 39
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Mediator of RNA polymerase II transcription subunit 11MA [auth i]117Homo sapiensMutation(s): 0 
Gene Names: MED11HSPC296
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Entity ID: 40
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Mediator of RNA polymerase II transcription subunit 17NA [auth j]651Homo sapiensMutation(s): 0 
Gene Names: MED17ARC77CRSP6DRIP77DRIP80TRAP80
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Entity ID: 41
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Mediator of RNA polymerase II transcription subunit 18OA [auth k]208Homo sapiensMutation(s): 0 
Gene Names: MED18
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20PA [auth l]212Homo sapiensMutation(s): 0 
Gene Names: MED20TRFP
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22QA [auth m]200Homo sapiensMutation(s): 0 
Gene Names: MED22SURF5
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 27RA [auth n]311Homo sapiensMutation(s): 0 
Gene Names: MED27CRSP34CRSP8
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 28SA [auth o]178Homo sapiensMutation(s): 0 
Gene Names: MED28EG1FKSG20
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 29TA [auth p]200Homo sapiensMutation(s): 0 
Gene Names: MED29IXL
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 30UA [auth q]178Homo sapiensMutation(s): 0 
Gene Names: MED30THRAP6TRAP25
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 14VA [auth r]1454Homo sapiensMutation(s): 0 
Gene Names: MED14ARC150CRSP2CXorf4DRIP150EXLM1RGR1TRAP170
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Entity ID: 49
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Mediator of RNA polymerase II transcription subunit 4WA [auth s]270Homo sapiensMutation(s): 0 
Gene Names: MED4ARC36DRIP36VDRIPHSPC126
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Entity ID: 50
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Mediator of RNA polymerase II transcription subunit 7XA [auth t]233Homo sapiensMutation(s): 0 
Gene Names: MED7ARC34CRSP9
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Entity ID: 51
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Mediator of RNA polymerase II transcription subunit 9YA [auth u]146Homo sapiensMutation(s): 0 
Gene Names: MED9MED25
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Entity ID: 52
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Mediator of RNA polymerase II transcription subunit 10ZA [auth v]135Homo sapiensMutation(s): 0 
Gene Names: MED10L6TRG17TRG20
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Entity ID: 53
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Mediator of RNA polymerase II transcription subunit 19AB [auth w]244Homo sapiensMutation(s): 0 
Gene Names: MED19LCMR1
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21BB [auth x]144Homo sapiensMutation(s): 0 
Gene Names: MED21SRB7SURB7
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31CB [auth y]131Homo sapiensMutation(s): 0 
Gene Names: MED31SOH1CGI-125
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 15DB [auth z]788Homo sapiensMutation(s): 0 
Gene Names: MED15ARC105CTG7APCQAPTIG1TNRC7
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Entity ID: 25
MoleculeChainsLengthOrganismImage
super core promoter sense strandY [auth U]100Homo sapiens
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Entity ID: 26
MoleculeChainsLengthOrganismImage
super core promoter antisense strandZ [auth V]100Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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QB [auth X]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
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
 Ligand Interaction
MG
Query on MG

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

Experimental Data

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

Structure Validation

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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