7ENJ

Human Mediator (deletion of MED1-IDR) in a Tail-bent conformation (MED-B)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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: https://doi.org/10.1126/science.abg0635
  • Primary Citation of Related Structures:  
    7EMF, 7ENA, 7ENC, 7ENJ

  • PubMed Abstract: 

    The 1.3-megadalton 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 the 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 megadaltons) 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; this suggests a CTD-gating mechanism favorable for phosphorylation. The TFIID-based PIC architecture modulates Mediator organization and TFIIH stabilization, underscoring the importance of TFIID in orchestrating PIC-Mediator assembly.


  • Organizational Affiliation

    Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11,581Homo sapiensMutation(s): 0 
Gene Names: MED1
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GTEx:  ENSG00000125686 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown Chain20Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4C [auth D]270Homo sapiensMutation(s): 0 
Gene Names: MED4
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GTEx:  ENSG00000136146 
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UniProt GroupQ9NPJ6
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6D [auth F]246Homo sapiensMutation(s): 0 
Gene Names: MED6
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GTEx:  ENSG00000133997 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7E [auth G]233Homo sapiensMutation(s): 0 
Gene Names: MED7
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GTEx:  ENSG00000155868 
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Entity ID: 6
MoleculeChains Sequence 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
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 9G [auth I]146Homo sapiensMutation(s): 0 
Gene Names: MED9
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GTEx:  ENSG00000141026 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 10H [auth J]135Homo sapiensMutation(s): 0 
Gene Names: MED10
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GTEx:  ENSG00000133398 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11I [auth K]117Homo sapiensMutation(s): 0 
Gene Names: MED11
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GTEx:  ENSG00000161920 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 14J [auth N]1,454Homo sapiensMutation(s): 0 
Gene Names: MED14
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GTEx:  ENSG00000180182 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 15K [auth O]788Homo sapiensMutation(s): 0 
Gene Names: MED15
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GTEx:  ENSG00000099917 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 16L [auth P]877Homo sapiensMutation(s): 0 
Gene Names: MED16DRIP92THRAP5
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GTEx:  ENSG00000175221 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17M [auth Q]651Homo sapiensMutation(s): 0 
Gene Names: MED17
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GTEx:  ENSG00000042429 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
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
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 19O [auth S]244Homo sapiensMutation(s): 0 
Gene Names: MED19
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GTEx:  ENSG00000156603 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20P [auth T]212Homo sapiensMutation(s): 0 
Gene Names: MED20
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GTEx:  ENSG00000124641 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21Q [auth U]144Homo sapiensMutation(s): 0 
Gene Names: MED21
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GTEx:  ENSG00000152944 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22R [auth V]200Homo sapiensMutation(s): 0 
Gene Names: MED22
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GTEx:  ENSG00000148297 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 23S [auth W]1,368Homo sapiensMutation(s): 0 
Gene Names: MED23
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GTEx:  ENSG00000112282 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 24T [auth X]989Homo sapiensMutation(s): 0 
Gene Names: MED24
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Find proteins for O75448 (Homo sapiens)
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GTEx:  ENSG00000008838 
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UniProt GroupO75448
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 26U [auth Z]600Homo sapiensMutation(s): 0 
Gene Names: MED26
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GTEx:  ENSG00000105085 
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UniProt GroupO95402
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 27V [auth 0]311Homo sapiensMutation(s): 0 
Gene Names: MED27
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GTEx:  ENSG00000160563 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 28W [auth 1]178Homo sapiensMutation(s): 0 
Gene Names: MED28
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GTEx:  ENSG00000118579 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 29X [auth 2]200Homo sapiensMutation(s): 0 
Gene Names: MED29
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GTEx:  ENSG00000063322 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 30Y [auth 3]178Homo sapiensMutation(s): 0 
Gene Names: MED30
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GTEx:  ENSG00000164758 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31Z [auth 4]131Homo sapiensMutation(s): 0 
Gene Names: MED31
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GTEx:  ENSG00000108590 
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth 0]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 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: 2021-05-19
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references
  • Version 1.2: 2024-06-05
    Changes: Data collection, Database references