7EMF

Human Mediator (deletion of MED1-IDR) in a Tail-extended conformation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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 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
Mediator of RNA polymerase II transcription subunit 1A1581Homo sapiensMutation(s): 0 
Gene Names: 
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GTEx:  ENSG00000125686 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Unknown Chain (poly A)B20Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4C [auth D]270Homo sapiensMutation(s): 0 
Gene Names: MED4, ARC36, DRIP36, VDRIP, HSPC126
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GTEx:  ENSG00000136146 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6D [auth F]246Homo sapiensMutation(s): 0 
Gene Names: MED6, ARC33
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GTEx:  ENSG00000133997 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7E [auth G]233Homo sapiensMutation(s): 0 
Gene Names: MED7, ARC34, CRSP9
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GTEx:  ENSG00000155868 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Isoform 2 of Mediator of RNA polymerase II transcription subunit 8F [auth H]268Homo sapiensMutation(s): 0 
Gene Names: MED8
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GTEx:  ENSG00000159479 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 9G [auth I]146Homo sapiensMutation(s): 0 
Gene Names: MED9, MED25
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GTEx:  ENSG00000141026 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 10H [auth J]135Homo sapiensMutation(s): 0 
Gene Names: MED10, L6, TRG17, TRG20
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Entity ID: 9
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Mediator of RNA polymerase II transcription subunit 11I [auth K]117Homo sapiensMutation(s): 0 
Gene Names: MED11, HSPC296
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GTEx:  ENSG00000161920 
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Entity ID: 10
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Mediator of RNA polymerase II transcription subunit 14J [auth N]1454Homo sapiensMutation(s): 0 
Gene Names: MED14, ARC150, CRSP2, CXorf4, DRIP150, EXLM1, RGR1, TRAP170
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GTEx:  ENSG00000180182 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 15K [auth O]788Homo sapiensMutation(s): 0 
Gene Names: MED15, ARC105, CTG7A, PCQAP, TIG1, TNRC7
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Entity ID: 12
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Isoform 2 of Mediator of RNA polymerase II transcription subunit 16L [auth P]841Homo sapiensMutation(s): 0 
Gene Names: MED16, DRIP92, THRAP5
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GTEx:  ENSG00000175221 
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Entity ID: 13
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Mediator of RNA polymerase II transcription subunit 17M [auth Q]651Homo sapiensMutation(s): 0 
Gene Names: MED17, ARC77, CRSP6, DRIP77, DRIP80, TRAP80
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Entity ID: 14
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Mediator of RNA polymerase II transcription subunit 18N [auth R]208Homo sapiensMutation(s): 0 
Gene Names: MED18
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GTEx:  ENSG00000130772 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 19O [auth S]244Homo sapiensMutation(s): 0 
Gene Names: MED19, LCMR1
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GTEx:  ENSG00000156603 
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Entity ID: 16
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Mediator of RNA polymerase II transcription subunit 20P [auth T]212Homo sapiensMutation(s): 0 
Gene Names: MED20, TRFP
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GTEx:  ENSG00000124641 
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Entity ID: 17
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Mediator of RNA polymerase II transcription subunit 21Q [auth U]144Homo sapiensMutation(s): 0 
Gene Names: MED21, SRB7, SURB7
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GTEx:  ENSG00000152944 
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Entity ID: 18
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Mediator of RNA polymerase II transcription subunit 22R [auth V]200Homo sapiensMutation(s): 0 
Gene Names: MED22, SURF5
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GTEx:  ENSG00000148297 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 23S [auth W]1368Homo sapiensMutation(s): 0 
Gene Names: MED23, ARC130, CRSP3, DRIP130, KIAA1216, SUR2
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GTEx:  ENSG00000112282 
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Entity ID: 20
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Mediator of RNA polymerase II transcription subunit 24T [auth X]989Homo sapiensMutation(s): 0 
Gene Names: MED24, ARC100, CRSP4, DRIP100, KIAA0130, THRAP4, TRAP100
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GTEx:  ENSG00000008838 
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Entity ID: 21
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Mediator of RNA polymerase II transcription subunit 25U [auth Y]747Homo sapiensMutation(s): 0 
Gene Names: MED25, ACID1, ARC92, PTOV2, TCBAP0758
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GTEx:  ENSG00000104973 
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Entity ID: 22
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Mediator of RNA polymerase II transcription subunit 26V [auth Z]600Homo sapiensMutation(s): 0 
Gene Names: MED26, ARC70, CRSP7
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GTEx:  ENSG00000105085 
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Entity ID: 23
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Mediator of RNA polymerase II transcription subunit 27W [auth 0]311Homo sapiensMutation(s): 0 
Gene Names: MED27, CRSP34, CRSP8
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Entity ID: 24
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Mediator of RNA polymerase II transcription subunit 28X [auth 1]178Homo sapiensMutation(s): 0 
Gene Names: MED28, EG1, FKSG20
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Entity ID: 25
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Mediator of RNA polymerase II transcription subunit 29Y [auth 2]200Homo sapiensMutation(s): 0 
Gene Names: MED29, IXL
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GTEx:  ENSG00000063322 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 30Z [auth 3]178Homo sapiensMutation(s): 0 
Gene Names: MED30, THRAP6, TRAP25
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Entity ID: 27
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Mediator of RNA polymerase II transcription subunit 31AA [auth 4]131Homo sapiensMutation(s): 0 
Gene Names: MED31, SOH1, CGI-125
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
BA [auth P],
CA [auth 0]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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: 2021-05-05
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references
  • Version 1.2: 2021-06-16
    Changes: Database references