8ZZ3 | pdb_00008zz3

Molecular architecture of the yeast Mediator complex

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.


Integrative Structure Snapshot

  • Multi-Scale: Yes 
  • Multi-State: No 
  • Ordered-State: No 
  • Deposited Models: 
  • Representative Model: 

This is version 1.0 of the entry. See complete history

Literature

Molecular architecture of the yeast Mediator complex

Robinson, P.J.Trnka, M.J.Pellarin, R.Greenberg, C.H.Bushnell, D.A.Davis, R.Burlingame, A.L.Sali, A.Kornberg, R.D.

(2015) Elife 4: e08719

  • DOI: https://doi.org/10.7554/eLife.08719
  • Primary Citation Related Structures: 
    8ZZ3

  • PubMed Abstract: 

    The 21-subunit Mediator complex transduces regulatory information from enhancers to promoters, and performs an essential role in the initiation of transcription in all eukaryotes. Structural information on two-thirds of the complex has been limited to coarse subunit mapping onto 2-D images from electron micrographs. We have performed chemical cross-linking and mass spectrometry, and combined the results with information from X-ray crystallography, homology modeling, and cryo-electron microscopy by an integrative modeling approach to determine a 3-D model of the entire Mediator complex. The approach is validated by the use of X-ray crystal structures as internal controls and by consistency with previous results from electron microscopy and yeast two-hybrid screens. The model shows the locations and orientations of all Mediator subunits, as well as subunit interfaces and some secondary structural elements. Segments of 20-40 amino acid residues are placed with an average precision of 20 Å. The model reveals roles of individual subunits in the organization of the complex.


  • Organizational Affiliation
    • Department of Structural Biology, Stanford University School of Medicine, Stanford, United States.

Macromolecule Content 

  • Total Structure Weight: 1,174.82 kDa 
  • Modeled Residue Count: 8,968 
  • Deposited Residue Count: 8,968 
  • Unique protein chains: 21

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
med6295Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MED6
UniProt
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
med8223Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MED8
UniProt
Find proteins for P38304 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
med11115Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MED11
UniProt
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
med17687Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SRB4
UniProt
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
med18307Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SRB5
UniProt
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
med20210Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SRB2
UniProt
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
med22121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SRB6
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
med4284Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MED4
UniProt
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
med7222Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MED7
UniProt
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
med9149Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CSE2
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
med31127Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SOH1
UniProt
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
med21140Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SRB7
UniProt
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
med10157Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NUT2
UniProt
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
med1566Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MED1
UniProt
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
med141,082Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RGR1
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
med19220Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ROX3
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
med2436Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: MED2
UniProt
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
med3401Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: PGD1
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
med51,146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NUT1
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Entity ID: 20
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med151,094Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: GAL11
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Find proteins for P19659 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
med16986Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SIN4
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Find proteins for P32259 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Experimental Data & Validation

Integrative Structure Snapshot

  • Multi-Scale: Yes 
  • Multi-State: No 
  • Ordered-State: No 
  • Deposited Models: 
  • Representative Model: 

Structure Validation

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View Summary Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-31
    Type: Initial release