7ENA

TFIID-based PIC-Mediator holo-complex in pre-assembled state (pre-hPIC-MED)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.07 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

Structures of the human Mediator and Mediator-bound preinitiation complex.

Chen, X.Yin, X.Li, J.Wu, Z.Qi, Y.Wang, X.Liu, W.Xu, Y.

(2021) Science 372

  • DOI: 10.1126/science.abg0635
  • Primary Citation of Related Structures:  
    7EMF, 7ENA, 7ENC, 7ENJ

  • PubMed Abstract: 
  • The 1.3-MDa transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)-mediated transcription initiation on almost all genes. The 26-subunit Mediator stimulates transcription and cyclin-dependent kinase 7 (CDK7)-mediated phosphorylation of Pol II C-terminal domain (CTD) ...

    The 1.3-MDa transcription factor IID (TFIID) is required for preinitiation complex (PIC) assembly and RNA polymerase II (Pol II)-mediated transcription initiation on almost all genes. The 26-subunit Mediator stimulates transcription and cyclin-dependent kinase 7 (CDK7)-mediated phosphorylation of Pol II C-terminal domain (CTD). We determined the structures of human Mediator in the Tail module-extended (at near-atomic resolution) and Tail-bent conformations and structures of TFIID-based PIC-Mediator (76 polypeptides, ~4.1 MDa) in four distinct conformations. PIC-Mediator assembly induces concerted reorganization (Head-tilting and Middle-down) of Mediator and creates a Head-Middle sandwich, which stabilizes two CTD segments and brings CTD to CDK7 for phosphorylation, suggesting a CTD-gating mechanism favorable for phosphorylation. The TFIID-based PIC architecture modulates Mediator organization and TFIIH stabilization, underscoring the significance of TFIID in orchestrating PIC-Mediator assembly.


    Organizational Affiliation

    Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CDK-activating kinase assembly factor MAT1A [auth 0]309Homo sapiensMutation(s): 0 
Gene Names: MNAT1CAP35MAT1RNF66
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-dependent kinase 7B [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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Cyclin-HC [auth 9]323Homo sapiensMutation(s): 0 
Gene Names: CCNH
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2D [auth DO]109Homo sapiensMutation(s): 0 
Gene Names: GTF2A2TF2A2
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-box-binding proteinE [auth DP]339Homo sapiensMutation(s): 0 
Gene Names: TBPGTF2D1TF2DTFIID
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
TFIIA-aF [auth DQ]307Homo sapiensMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIBG [auth BA]316Homo sapiensMutation(s): 0 
Gene Names: GTF2BTF2BTFIIB
EC: 2.3.1.48
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIF subunit 1H [auth FA]517Homo sapiensMutation(s): 0 
Gene Names: GTF2F1RAP74
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIF subunit 2I [auth FB]249Homo sapiensMutation(s): 0 
Gene Names: GTF2F2RAP30
EC: 3.6.4.12
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
RPB1J [auth PA]1970Sus scrofaMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaK [auth PB]1174Sus scrofaMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3L [auth PC]275Sus scrofaMutation(s): 0 
Gene Names: POLR2C
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4M [auth PD]142Sus scrofaMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit EN [auth PE]210Sus scrofaMutation(s): 0 
Gene Names: POLR2E
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit FO [auth PF]127Sus scrofaMutation(s): 0 
Gene Names: POLR2F
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7P [auth PG]172Sus scrofaMutation(s): 0 
Gene Names: POLR2G
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3Q [auth PH]150Sus scrofaMutation(s): 0 
Gene Names: POLR2H
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9R [auth PI]125Sus scrofaMutation(s): 0 
Gene Names: POLR2I
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
RPB10S [auth PJ]67Sus scrofaMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing proteinT [auth PK]117Sus scrofaMutation(s): 0 
Gene Names: POLR2J
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
RPB12U [auth PL]58Sus scrofaMutation(s): 0 
Gene Names: POLR2K
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 1V [auth DA]1872Homo sapiensMutation(s): 0 
Gene Names: TAF1BA2RCCG1CCGSTAF2A
EC: 2.3.1.48 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 2W [auth DB]1199Homo sapiensMutation(s): 0 
Gene Names: TAF2CIF150TAF2B
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 4X [auth DD], GA [auth Dd]1085Homo sapiensMutation(s): 0 
Gene Names: TAF4TAF2CTAF2C1TAF4ATAFII130TAFII135
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 5Y [auth DE], HA [auth De]800Homo sapiensMutation(s): 0 
Gene Names: TAF5TAF2D
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 6Z [auth DF], IA [auth Df]677Homo sapiensMutation(s): 0 
Gene Names: TAF6TAF2ETAFII70
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 7AA [auth DG]349Homo sapiensMutation(s): 0 
Gene Names: TAF7TAF2FTAFII55
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 8BA [auth DH]310Homo sapiensMutation(s): 0 
Gene Names: TAF8TAFII43TBN
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 9CA [auth DI], JA [auth Di]264Homo sapiensMutation(s): 0 
Gene Names: TAF9TAF2GTAFII31
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 10DA [auth DJ], KA [auth Dj]218Homo sapiensMutation(s): 0 
Gene Names: TAF10TAF2ATAF2HTAFII30
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 12EA [auth DL], MA [auth Dl]161Homo sapiensMutation(s): 0 
Gene Names: TAF12TAF15TAF2JTAFII20
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 3FA [auth Dc]929Homo sapiensMutation(s): 0 
Gene Names: TAF3
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 11LA [auth Dk]211Homo sapiensMutation(s): 0 
Gene Names: TAF11TAF2IPRO2134
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 13NA [auth Dm]124Homo sapiensMutation(s): 0 
Gene Names: TAF13TAF2KTAFII18
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIE subunit 1OA [auth EA]439Homo sapiensMutation(s): 0 
Gene Names: GTF2E1TF2E1
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaPA [auth EB]291Homo sapiensMutation(s): 0 
Gene Names: GTF2E2TF2E2
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 1QA [auth 1]548Homo sapiensMutation(s): 0 
Gene Names: GTF2H1BTF2
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 2RA [auth 2]395Homo sapiensMutation(s): 0 
Gene Names: GTF2H2BTF2P44
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 3SA [auth 3]308Homo sapiensMutation(s): 0 
Gene Names: GTF2H3
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription factor IIH subunit 4TA [auth 4]462Homo sapiensMutation(s): 0 
Gene Names: GTF2H4
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Entity ID: 41
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General transcription factor IIH subunit 5UA [auth 5]71Homo sapiensMutation(s): 0 
Gene Names: GTF2H5C6orf175TTDA
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetailsImage
General transcription and DNA repair factor IIH helicase subunit XPBVA [auth 6]782Homo sapiensMutation(s): 0 
Gene Names: ERCC3XPBXPBC
EC: 3.6.4.12
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Entity ID: 43
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General transcription and DNA repair factor IIH helicase subunit XPDWA [auth 7]760Homo sapiensMutation(s): 0 
Gene Names: ERCC2XPDXPDC
EC: 3.6.4.12
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 27XA [auth c]311Homo sapiensMutation(s): 0 
Gene Names: MED27CRSP34CRSP8
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 28YA [auth e]178Homo sapiensMutation(s): 0 
Gene Names: MED28EG1FKSG20
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 29ZA [auth b]200Homo sapiensMutation(s): 0 
Gene Names: MED29IXL
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Entity ID: 47
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Mediator of RNA polymerase II transcription subunit 30AB [auth l]178Homo sapiensMutation(s): 0 
Gene Names: MED30THRAP6TRAP25
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Entity ID: 48
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Mediator of RNA polymerase II transcription subunit 31BB [auth m]131Homo sapiensMutation(s): 0 
Gene Names: MED31SOH1CGI-125
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Entity ID: 49
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Mediator of RNA polymerase II transcription subunit 1CB [auth a]1581Homo sapiensMutation(s): 0 
Gene Names: 
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4DB [auth d]270Homo sapiensMutation(s): 0 
Gene Names: MED4ARC36DRIP36VDRIPHSPC126
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6EB [auth f]246Homo sapiensMutation(s): 0 
Gene Names: MED6ARC33
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7FB [auth g]233Homo sapiensMutation(s): 0 
Gene Names: MED7ARC34CRSP9
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetailsImage
Isoform 2 of Mediator of RNA polymerase II transcription subunit 8GB [auth h]268Homo sapiensMutation(s): 0 
Gene Names: MED8
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 9HB [auth i]146Homo sapiensMutation(s): 0 
Gene Names: MED9MED25
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 10IB [auth j]135Homo sapiensMutation(s): 0 
Gene Names: MED10L6TRG17TRG20
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11JB [auth k]117Homo sapiensMutation(s): 0 
Gene Names: MED11HSPC296
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 14KB [auth n]1454Homo sapiensMutation(s): 0 
Gene Names: MED14ARC150CRSP2CXorf4DRIP150EXLM1RGR1TRAP170
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 15LB [auth o]788Homo sapiensMutation(s): 0 
Gene Names: MED15ARC105CTG7APCQAPTIG1TNRC7
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17MB [auth q]651Homo sapiensMutation(s): 0 
Gene Names: MED17ARC77CRSP6DRIP77DRIP80TRAP80
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18NB [auth r]208Homo sapiensMutation(s): 0 
Gene Names: MED18
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Entity ID: 61
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Mediator of RNA polymerase II transcription subunit 19OB [auth s]244Homo sapiensMutation(s): 0 
Gene Names: MED19LCMR1
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20PB [auth t]212Homo sapiensMutation(s): 0 
Gene Names: MED20TRFP
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21QB [auth u]144Homo sapiensMutation(s): 0 
Gene Names: MED21SRB7SURB7
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22RB [auth v]200Homo sapiensMutation(s): 0 
Gene Names: MED22SURF5
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 26SB [auth z]600Homo sapiensMutation(s): 0 
Gene Names: MED26ARC70CRSP7
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 24TB [auth x]989Homo sapiensMutation(s): 0 
Gene Names: MED24ARC100CRSP4DRIP100KIAA0130THRAP4TRAP100
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 23UB [auth w]1368Homo sapiensMutation(s): 0 
Gene Names: MED23ARC130CRSP3DRIP130KIAA1216SUR2
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
Isoform 2 of Mediator of RNA polymerase II transcription subunit 16VB [auth p]841Homo sapiensMutation(s): 0 
Gene Names: MED16DRIP92THRAP5
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Entity ID: 69
MoleculeChainsLengthOrganismImage
DNA (69-MER)WB [auth X]69Homo sapiens
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Entity ID: 70
MoleculeChainsLengthOrganismImage
DNA(69-MER)XB [auth Y]69Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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PC [auth 7]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN

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AC [auth BA] , BC [auth PA] , CC [auth PA] , EC [auth PB] , FC [auth PC] , GC [auth PI] , HC [auth PI] , IC [auth PJ] , 
AC [auth BA], BC [auth PA], CC [auth PA], EC [auth PB], FC [auth PC], GC [auth PI], HC [auth PI], IC [auth PJ], JC [auth PL], KC [auth EA], LC [auth 2], MC [auth 2], NC [auth 2], OC [auth 3], YB [auth 0], ZB [auth 0]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
DC [auth PA]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.07 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references