5SVA

Mediator-RNA Polymerase II Pre-Initiation Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15.3 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

Structure of a Complete Mediator-RNA Polymerase II Pre-Initiation Complex.

Robinson, P.J.Trnka, M.J.Bushnell, D.A.Davis, R.E.Mattei, P.J.Burlingame, A.L.Kornberg, R.D.

(2016) Cell 166: 1411-1422.e16

  • DOI: 10.1016/j.cell.2016.08.050
  • Primary Citation of Related Structures:  
    5SVA

  • PubMed Abstract: 
  • A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structure reveals two components of functional significance, absent from previous structures, a protein kinase complex and the Mediator-activator interaction region ...

    A complete, 52-protein, 2.5 million dalton, Mediator-RNA polymerase II pre-initiation complex (Med-PIC) was assembled and analyzed by cryo-electron microscopy and by chemical cross-linking and mass spectrometry. The resulting complete Med-PIC structure reveals two components of functional significance, absent from previous structures, a protein kinase complex and the Mediator-activator interaction region. It thereby shows how the kinase and its target, the C-terminal domain of the polymerase, control Med-PIC interaction and transcription.


    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: kornberg@stanford.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1A1733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2B1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3C318Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4D221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1E215Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2F155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7G171Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9I122Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
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DNA-directed RNA polymerases I, II, and III subunit RPABC5J70Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11K120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
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DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6M295Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 8N223Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11O115Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17P687Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18Q307Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
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Mediator of RNA polymerase II transcription subunit 20R210Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
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Mediator of RNA polymerase II transcription subunit 22S121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
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Mediator of RNA polymerase II transcription subunit 4T284Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7U222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 9V149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21W140Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31X127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
DNA repair helicase RAD3Y778Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 26
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DNA repair helicase RAD25Z843Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 27
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RNA polymerase II transcription factor B subunit 2AA [auth a]513Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
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RNA polymerase II transcription factor B subunit 5BA [auth b]72Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIBCA [auth c]345Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SUA7YPR086WP9513.4
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA large subunitDA [auth d]286Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TOA1YOR194C
UniProt
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2EA [auth e]122Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TOA2YKL058W
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIF subunit alphaFA [auth f]735Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIF subunit betaGA [auth g]400Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit alphaHA [auth h]482Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TFA1YKL028W
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaIA [auth i]328Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TFA2YKR062W
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Entity ID: 36
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TATA-box-binding proteinJA [auth j]240Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPT15BTF1TBP1YER148W
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Entity ID: 37
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DNA-directed RNA polymerase II subunit RPB1KA [auth k]25Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 40
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Transcription initiation factor TFIID subunit 14NA [auth n]244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChainsLengthOrganismImage
108bp HIS4 Promoter Non-template Strand (-92/+16)LA [auth l]108Saccharomyces cerevisiae
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Entity ID: 39
MoleculeChainsLengthOrganismImage
108bp HIS4 Promoter Template Strand (+16/-92)MA [auth m]108Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15.3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI21144
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM49985
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM36659
National Science Foundation (NSF, United States)United States1231306
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM103481

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence