› 4a3c

X-ray diffraction
3.5Å resolution

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

Released:
DOI: 10.2210/pdb4a3c/pdb
Model geometry
Fit model/data
PDB entry 4a3c coloured by chain, front view.
PDB entry 4a3c coloured by chain, side view.
PDB entry 4a3c coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis of initial RNA polymerase II transcription.
Cheung AC, Sainsbury S, Cramer P
OpenAccess logo EMBO J 30 4755-63 (2011)
PMID: 22056778

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-117188 (preferred)
Entry contents:
12 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (15 distinct):
DNA-directed RNA polymerase II subunit RPB1 Chain: A
Molecule details ›
Chain: A
Length: 1732 amino acids
Theoretical weight: 191.66 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04050 (Residues: 1-1732; Coverage: 100%)
Gene names: D2150, RPB1, RPB220, RPO21, SUA8, YDL140C
Sequence 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 polymerase II subunit RPB4 Chain: D
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 polymerase II subunit RPB7 Chain: G
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
NON TEMPLATE DNA Chain: N
TEMPLATE DNA Chain: T
TRANSCRIPT RNA, 5'-R(*CP*AP*GP*GP*AP)-3' Chain: P

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand MG 1 x MG
1 modified residue:
Ligand BRU 1 x BRU

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE ID29
Spacegroup: C2221
Unit cell:
a: 221.41Å b: 393.12Å c: 282.51Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.158 0.158 0.184

Quick links

Citations

17 review citations

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

3 mentions without citation

Basic mechanisms of RNA polymerase II activity and alteration of gene expression in Saccharomyces cerevisiae.
Kaplan CD. (2013)
2 more

PDB-REDO

The sliders below show the change in model quality between original PDB entry and the PDB-REDO entry

Model Geometry
 
 
Data not available
DNA/RNA Geometry
 
 
Data not available
Fit model/data
 
 
Data not available
PDB-REDO