2NVQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1016/j.cell.2006.11.023
  • Structures With Same Primary Citation

  • 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 formi ...

    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: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II 45 kDa polypeptide
C
318Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P16370

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
E
215Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20434

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
F
155Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20435

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
H
146Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20436

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit 9
I
122Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P27999

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
L
70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40422

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I/II/III subunit 10
J
70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22139

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II 13.6 kDa polypeptide
K
120Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38902

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II largest subunit
A
1733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04050

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II 140 kDa polypeptide
B
1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08518
Entity ID: 1
MoleculeChainsLengthOrganism
5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3'R10synthetic construct

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Entity ID: 2
MoleculeChainsLengthOrganism
28-MER DNA template strandT28synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3'N14synthetic construct
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DUT
Query on DUT

Download CCD File 
T
DEOXYURIDINE-5'-TRIPHOSPHATE
C9 H15 N2 O14 P3
AHCYMLUZIRLXAA-SHYZEUOFSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A, B, C, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 170.646α = 90
b = 222.76β = 101.31
c = 195.281γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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: 2015-05-27
    Changes: Derived calculations