3S1R

RNA Polymerase II Initiation Complex with a 5-nt 3'-deoxy RNA soaked with GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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Ligand Structure Quality Assessment 


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

  • 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 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
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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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 polymerases I, II, and III subunit RPABC1D [auth E]215Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2E [auth F]155Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3F [auth H]146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9G [auth I]122Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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UniProt GroupP27999
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5H [auth J]70Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11I [auth K]120Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4J [auth L]70Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains LengthOrganismImage
RNA (5'-R(*AP*GP*AP*GP*G*)-3')K [auth R]5N/A
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Entity ID: 12
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*AP*CP*CP*GP*AP*TP*AP*AP*GP*CP*AP*GP*AP*CP*GP*AP*TP*CP*CP*TP*CP*TP*CP*GP*AP*TP*G)-3')L [auth T]29N/A
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

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V [auth R]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ZN
Query on ZN

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M [auth A]
N [auth A]
P [auth B]
Q [auth C]
R [auth I]
M [auth A],
N [auth A],
P [auth B],
Q [auth C],
R [auth I],
S [auth I],
T [auth J],
U [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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O [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.67α = 90
b = 221.32β = 98.31
c = 193.21γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
XSCALEdata processing
PDB_EXTRACTdata extraction
XSCALEdata scaling
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-10
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations