5SVA | pdb_00005sva

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 1.3 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: https://doi.org/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. 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.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB21,224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3318Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4221Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1215Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7171Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9122Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC570Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC470Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 6295Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 8223Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 11115Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 17687Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 18307Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 20210Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 22121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 4284Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 7222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 9149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 21140Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Mediator of RNA polymerase II transcription subunit 31127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair helicase RAD3778Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12 (PDB Primary Data), 5.6.2.3 (UniProt)
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
DNA repair helicase RAD25843Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II transcription factor B subunit 2AA [auth a]513Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II transcription factor B subunit 5BA [auth b]72Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIBCA [auth c]345Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SUA7, YPR086W, P9513.4
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA large subunitDA [auth d]286Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TOA1, YOR194C
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIA subunit 2EA [auth e]122Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TOA2, YKL058W
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIF subunit alphaFA [auth f]735Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence 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
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit alphaHA [auth h]482Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TFA1, YKL028W
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor IIE subunit betaIA [auth i]328Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TFA2, YKR062W
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
TATA-box-binding proteinJA [auth j]240Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPT15, BTF1, TBP1, YER148W
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
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
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 14NA [auth n]244Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChains LengthOrganismImage
108bp HIS4 Promoter Non-template Strand (-92/+16)LA [auth l]108Saccharomyces cerevisiae
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Entity ID: 39
MoleculeChains LengthOrganismImage
108bp HIS4 Promoter Template Strand (+16/-92)MA [auth m]108Saccharomyces cerevisiae
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
OA [auth A]
PA [auth A]
RA [auth B]
SA [auth C]
TA [auth I]
OA [auth A],
PA [auth A],
RA [auth B],
SA [auth C],
TA [auth I],
UA [auth I],
VA [auth J],
WA [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
QA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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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View more in-depth experimental data
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
  • Version 1.3: 2024-11-20
    Changes: Data collection, Database references, Structure summary