2NVT

RNA Polymerase II Elongation Complex in 150 mM Mg+2 with GMPCPP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history. 


Literature

Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis

Wang, D., Bushnell, D.A., Westover, K.D., Kaplan, C.D., Kornberg, R.D.

(2006) Cell 127: 941-954

  • DOI: https://doi.org/10.1016/j.cell.2006.11.023
  • Primary Citation of Related Structures:  
    2E2H, 2E2I, 2E2J, 2NVQ, 2NVT, 2NVX, 2NVY, 2NVZ, 2YU9

  • PubMed Abstract: 

    New structures of RNA polymerase II (pol II) transcribing complexes reveal a likely key to transcription. The trigger loop swings beneath a correct nucleoside triphosphate (NTP) in the nucleotide addition site, closing off the active center and forming an extensive network of interactions with the NTP base, sugar, phosphates, and additional pol II residues. A histidine side chain in the trigger loop, precisely positioned by these interactions, may literally "trigger" phosphodiester bond formation. Recognition and catalysis are thus coupled, ensuring the fidelity of transcription.

    • Organizational Affiliation: 

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


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II largest subunitD [auth A]1,733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II 140 kDa polypeptideE [auth B]1,224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II 45 kDa polypeptideF [auth C]318Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptideG [auth E]215Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III 23 kDa polypeptideH [auth F]155Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptideI [auth H]146Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit 9J [auth I]122Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I/II/III subunit 10K [auth J]70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II 13.6 kDa polypeptideL [auth K]120Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptideM [auth L]70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-R(*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3'A [auth R]10N/A
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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(P*CP*AP*AP*GP*TP*AP*CP*TP*TP*AP*CP*GP*CP*CP*TP*GP*GP*TP*CP*TP*T)-3'B [auth T]21N/A
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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*GP*TP*AP*CP*TP*TP*G)-3'C [auth N]7N/A
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G2P
Query on G2P
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N [auth T]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
GXTIEXDFEKYVGY-KQYNXXCUSA-N
ZN
Query on ZN
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O [auth A]
P [auth A]
S [auth B]
T [auth C]
U [auth I]
O [auth A],
P [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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Q [auth A],
R [auth A]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.36 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.872α = 90
b = 222.824β = 102.39
c = 195.802γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-12
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Structure summary