5FMF

the P-lobe of RNA polymerase II pre-initiation complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of an RNA Polymerase II Pre-Initiation Complex

Murakami, K.Tsai, K.Kalisman, N.Bushnell, D.A.Asturias, F.J.Kornberg, R.D.

(2015) Proc Natl Acad Sci U S A 112: 13543

  • DOI: 10.1073/pnas.1518255112
  • Primary Citation of Related Structures:  
    5FMF

  • PubMed Abstract: 
  • The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the mass were fitted into the electron density map in a manner consistent with protein-protein cross-links previously identified by mass spectrometry ...

    The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the mass were fitted into the electron density map in a manner consistent with protein-protein cross-links previously identified by mass spectrometry. The resulting model of the PIC confirmed the main conclusions from previous cryo-EM at lower resolution, including the association of promoter DNA only with general transcription factors and not with the polymerase. Electron density due to DNA was identifiable by the grooves of the double helix and exhibited sharp bends at points downstream of the TATA box, with an important consequence: The DNA at the downstream end coincides with the DNA in a transcribing polymerase. The structure of the PIC is therefore conducive to promoter melting, start-site scanning, and the initiation of transcription.


    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305; kornberg@stanford.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA REPAIR HELICASE RAD25, SSL2A [auth 1]492Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 2
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TRANSCRIPTION ELONGATION FACTOR S-II, DST1B [auth 2]174Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1C [auth A]1733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 4
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DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2D [auth B]1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3E [auth C]266Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RNA POLYMERASE II PRE-INITIATION COMPLEX, RPB4F [auth D]178Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1, RPB5G [auth E]214Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2, RPB6H [auth F]84Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
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DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7I [auth G]171Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3, RPB8J [auth H]146Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
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DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9K [auth I]119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5, RPB10L [auth J]65Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
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DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11M [auth K]115Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
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DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4, RPB12N [auth L]46Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
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RNA POLYMERASE II PRE-INITIATION COMPLEX, TOA1O [auth M]116Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
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TRANSCRIPTION INITIATION FACTOR IIA SUBUNIT 2, TOA2Q [auth O]122Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
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TRANSCRIPTION INITIATION FACTOR IIB, SUA7R [auth P]345Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
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TATA-BOX-BINDING PROTEIN, TBPS [auth Q]180Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
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TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT ALPHA, TFA1T [auth R]160Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
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TRANSCRIPTION INITIATION FACTOR IIE SUBUNIT BETA, TFA2U [auth S]123Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
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RNA POLYMERASE II PRE-INITIATION COMPLEX, TFG1W [auth U]150Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
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TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT BETA, TFG2X [auth V]174Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 25
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RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 2, TFB2Y [auth W]62Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
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RNA POLYMERASE II TRANSCRIPTION FACTOR B SUBUNIT 5, TFB5Z [auth X]63Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
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DNA REPAIR HELICASE RAD3AA [auth Y]778Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.12
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Entity ID: 16
MoleculeChainsLengthOrganismImage
NON-TEMPLATE STRAND DNAP [auth N]72Saccharomyces cerevisiae
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Entity ID: 22
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TEMPLATE STRAND DNAV [auth T]72Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 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: 2015-11-25
    Type: Initial release
  • Version 1.1: 2017-07-12
    Changes: Structure summary