4A3E

RNA Polymerase II initial transcribing complex with a 5nt DNA-RNA hybrid and soaked with AMPCPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

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This is version 1.5 of the entry. See complete history


Literature

Structural basis of initial RNA polymerase II transcription.

Cheung, A.C.Sainsbury, S.Cramer, P.

(2011) EMBO J 30: 4755-4763

  • DOI: https://doi.org/10.1038/emboj.2011.396
  • Primary Citation of Related Structures:  
    4A3B, 4A3C, 4A3D, 4A3E, 4A3F, 4A3G, 4A3I, 4A3J, 4A3K, 4A3L, 4A3M

  • PubMed Abstract: 

    During transcription initiation by RNA polymerase (Pol) II, a transient open promoter complex (OC) is converted to an initially transcribing complex (ITC) containing short RNAs, and to a stable elongation complex (EC). We report structures of a Pol II-DNA complex mimicking part of the OC, and of complexes representing minimal ITCs with 2, 4, 5, 6, and 7 nucleotide (nt) RNAs, with and without a non-hydrolyzable nucleoside triphosphate (NTP) in the insertion site +1. The partial OC structure reveals that Pol II positions the melted template strand opposite the active site. The ITC-mimicking structures show that two invariant lysine residues anchor the 3'-proximal phosphate of short RNAs. Short DNA-RNA hybrids adopt a tilted conformation that excludes the +1 template nt from the active site. NTP binding induces complete DNA translocation and the standard hybrid conformation. Conserved NTP contacts indicate a universal mechanism of NTP selection. The essential residue Q1078 in the closed trigger loop binds the NTP 2'-OH group, explaining how the trigger loop couples catalysis to NTP selection, suppressing dNTP binding and DNA synthesis.


  • Organizational Affiliation

    Gene Center and Department of Biochemistry, Center for Integrated Protein Science Munich (CIPSM), Ludwig-Maximilians-Universität München, Munich, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11,732Saccharomyces 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
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3318Saccharomyces cerevisiaeMutation(s): 0 
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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 RPABC 1215Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
RPB7, 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 RPABC 3146Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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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 RPABC 570Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11120Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 470Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains LengthOrganismImage
NON TEMPLATE DNA 5'-D(*TP*AP*AP*GP*TP*AP*CP*TP*TP*GP*AP *GP*CP*TP)-3'M [auth N]14Saccharomyces cerevisiae
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Entity ID: 14
MoleculeChains LengthOrganismImage
TRANSCRIPT RNA 5'-R(*CP*AP*GP*GP*AP)-3'N [auth P]5Saccharomyces cerevisiae
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Entity ID: 15
MoleculeChains LengthOrganismImage
TEMPLATE DNA 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*CP*TP*TP *TP*TP*TP*CP*CP*BRU*GP*GP*TP*CP*AP*TP*TP)-3'O [auth T]26Saccharomyces cerevisiae
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
APC
Query on APC

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Y [auth P]DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER
C11 H18 N5 O12 P3
CAWZRIXWFRFUQB-IOSLPCCCSA-N
ZN
Query on ZN

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 223.68α = 90
b = 394.17β = 90
c = 283.29γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-07
    Type: Initial release
  • Version 1.1: 2011-12-14
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Data collection
  • Version 1.3: 2019-02-20
    Changes: Data collection, Database references, Derived calculations, Experimental preparation, Source and taxonomy, Structure summary
  • Version 1.4: 2019-10-09
    Changes: Data collection, Other, Source and taxonomy
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Derived calculations