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
  • Structures With Same Primary Citation

  • 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 structu ...

    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 LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB1A1733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB7G171Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB9I122Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5J70Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB11K120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 6M295Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 11O115Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 17P687Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 18Q307Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 20R210Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 22S121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 4T284Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 7U222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 9V149Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 21W140Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 31X127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
DNA repair helicase RAD3Y778Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
DNA repair helicase RAD25Z843Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
Find proteins for Q00578 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II transcription factor B subunit 2a513Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q02939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase II transcription factor B subunit 5b72Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q3E7C1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIA large subunitd286Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TOA1YOR194C
Find proteins for P32773 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIA subunit 2e122Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TOA2YKL058W
Find proteins for P32774 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIF subunit alphaf735Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P41895 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIF subunit betag400Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIE subunit alphah482Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TFA1YKL028W
Find proteins for P36100 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB1k25Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor TFIID subunit 14n244Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P35189 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Mediator of RNA polymerase II transcription subunit 8N223Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P38304 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB2B1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIBc345Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SUA7YPR086WP9513.4
Find proteins for P29055 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB3C318Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Transcription initiation factor IIE subunit betai328Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: TFA2YKR062W
Find proteins for P36145 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
TATA-box-binding proteinj240Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: SPT15BTF1TBP1YER148W
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB4D221Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC1E215Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2F155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChainsLengthOrganism
108bp HIS4 Promoter Non-template Strand (-92/+16)l108Saccharomyces cerevisiae

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Entity ID: 39
MoleculeChainsLengthOrganism
108bp HIS4 Promoter Template Strand (+16/-92)m108Saccharomyces cerevisiae
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B, C, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



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 

  • 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