3S2D

RNA Polymerase II Initiation Complex with a 5-nt RNA containing a 5Br-U


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Initiation complex structure and promoter proofreading.

Liu, X.Bushnell, D.A.Silva, D.A.Huang, X.Kornberg, R.D.

(2011) Science 333: 633-637

  • DOI: 10.1126/science.1206629
  • Primary Citation of Related Structures:  
    3S1M, 3S1N, 3S14, 3S15, 3S16, 3S17, 3S2D, 3S2H, 3S1Q, 3S1R

  • PubMed Abstract: 
  • The initiation of transcription by RNA polymerase II is a multistage process. X-ray crystal structures of transcription complexes containing short RNAs reveal three structural states: one with 2- and 3-nucleotide RNAs, in which only the 3'-end of the ...

    The initiation of transcription by RNA polymerase II is a multistage process. X-ray crystal structures of transcription complexes containing short RNAs reveal three structural states: one with 2- and 3-nucleotide RNAs, in which only the 3'-end of the RNA is detectable; a second state with 4- and 5-nucleotide RNAs, with an RNA-DNA hybrid in a grossly distorted conformation; and a third state with RNAs of 6 nucleotides and longer, essentially the same as a stable elongating complex. The transition from the first to the second state correlates with a markedly reduced frequency of abortive initiation. The transition from the second to the third state correlates with partial "bubble collapse" and promoter escape. Polymerase structure is permissive for abortive initiation, thereby setting a lower limit on polymerase-promoter complex lifetime and allowing the dissociation of nonspecific complexes. Abortive initiation may be viewed as promoter proofreading, and the structural transitions as checkpoints for promoter control.


    Organizational Affiliation

    Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1A1733Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO21RPB1RPB220SUA8YDL140CD2150
EC: 2.7.7.6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB2B1224Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB2RPB150RPO22YOR151C
EC: 2.7.7.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3C318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB3YIL021W
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1E215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB5RPA7RPC9YBR154CYBR1204
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2F155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26RPB6YPR187WP9677.8
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8YOR224CYOR50-14
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9I122Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB9YGL070C
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5J70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB10YOR210W
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11K120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB11YOL005C
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10RPB12YHR143W-AYHR143BW
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  • Reference Sequence
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  • Entity ID: 11
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*AP*GP*GP*(5BU)P*G)-3')R5N/A
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    Entity ID: 12
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*TP*AP*CP*CP*GP*AP*TP*AP*AP*GP*CP*AP*GP*AP*CP*GP*AP*TP*CP*AP*CP*CP*TP*CP*GP*AP*TP*G)-3')T29N/A
    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: X-RAY DIFFRACTION
    • Resolution: 3.20 Å
    • R-Value Free: 0.231 
    • R-Value Work: 0.183 
    • R-Value Observed: 0.185 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 158.286α = 90
    b = 220.768β = 97.69
    c = 192.241γ = 90
    Software Package:
    Software NamePurpose
    BUSTER-TNTrefinement
    DENZOdata reduction
    SCALEPACKdata scaling
    PDB_EXTRACTdata extraction
    BUSTERrefinement

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2011-08-10
      Type: Initial release
    • Version 1.1: 2017-11-08
      Changes: Refinement description