› 2yu9

X-ray diffraction
3.4Å resolution

RNA polymerase II elongation complex in 150 mm MG+2 with UTP

Released:
DOI: 10.2210/pdb2yu9/pdb
Model geometry
Fit model/data
PDB entry 2yu9 coloured by chain, front view.
PDB entry 2yu9 coloured by chain, side view.
PDB entry 2yu9 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis.
Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD
Cell 127 941-54 (2006)
PMID: 17129781

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero tridecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115954 (preferred)
Entry contents:
10 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (13 distinct):
DNA-directed RNA polymerase II subunit RPB1 Chain: A
Molecule details ›
Chain: A
Length: 1733 amino acids
Theoretical weight: 191.82 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04050 (Residues: 1-1733; Coverage: 100%)
Gene names: D2150, RPB1, RPB220, RPO21, SUA8, YDL140C
Sequence domains:
Structure domains:
DNA-directed RNA polymerase II subunit RPB2 Chain: B
Molecule details ›
Chain: B
Length: 1224 amino acids
Theoretical weight: 138.94 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P08518 (Residues: 1-1224; Coverage: 100%)
Gene names: RPB150, RPB2, RPO22, YOR151C
Sequence domains:
Structure domains:
DNA-directed RNA polymerase II subunit RPB3 Chain: C
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chain: E
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
DNA-directed RNA polymerase II subunit RPB9 Chain: I
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
DNA-directed RNA polymerase II subunit RPB11 Chain: K
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: L
28-MER DNA template strand Chain: T
5'-D(*CP*TP*GP*CP*TP*TP*AP*TP*CP*GP*GP*TP*AP*G)-3' Chain: N
5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3' Chain: R

Ligands and Environments

3 bound ligands:
Ligand ZN 8 x ZN
Ligand MG 2 x MG
Ligand UTP 1 x UTP
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: C2
Unit cell:
a: 170.61Å b: 222.729Å c: 196.16Å
α: 90° β: 101.87° γ: 90°
R-values:
R R work R free
0.285 0.283 0.344

Quick links

Citations

57 review citations

Looping back to leap forward: transcription enters a new era.
Levine et al. (2014)
56 more

6 mentions without citation

Dynamics: the missing link between structure and function of the viral RNA-dependent RNA polymerase?
Cameron et al. (2009)
5 more