› 3hou

X-ray diffraction
3.2Å resolution

Complete RNA polymerase II elongation complex I with a T-U mismatch

Released:
DOI: 10.2210/pdb3hou/pdb
PDB entry 3hou coloured by chain, front view.
PDB entry 3hou coloured by chain, side view.
PDB entry 3hou coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA.
Sydow JF, Brueckner F, Cheung AC, Damsma GE, Dengl S, Lehmann E, Vassylyev D, Cramer P
Mol Cell 34 710-21 (2009)
PMID: 19560423

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-116366 (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 Chains: A, M
Molecule details ›
Chains: A, M
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:
DNA-directed RNA polymerase II subunit RPB2 Chains: B, N
Molecule details ›
Chains: B, N
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 Chains: C, O
Molecule details ›
Chains: C, O
Length: 318 amino acids
Theoretical weight: 35.33 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P16370 (Residues: 1-318; Coverage: 100%)
Gene names: RPB3, YIL021W
Sequence domains:
Structure domains:
DNA-directed RNA polymerase II subunit RPB4 Chains: D, P
Molecule details ›
Chains: D, P
Length: 221 amino acids
Theoretical weight: 25.45 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20433 (Residues: 1-221; Coverage: 100%)
Gene names: J0654, RPB4, YJL140W
Sequence domains: RNA polymerase Rpb4
Structure domains: Growth Hormone; Chain: A;
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chains: E, Q
Molecule details ›
Chains: E, Q
Length: 215 amino acids
Theoretical weight: 25.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20434 (Residues: 1-215; Coverage: 100%)
Gene names: RPA7, RPB5, RPC9, YBR1204, YBR154C
Sequence domains:
Structure domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chains: F, R
Molecule details ›
Chains: F, R
Length: 155 amino acids
Theoretical weight: 17.93 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20435 (Residues: 1-155; Coverage: 100%)
Gene names: P9677.8, RPB6, RPO26, YPR187W
Sequence domains: RNA polymerase Rpb6
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
DNA-directed RNA polymerase II subunit RPB7 Chains: G, S
Molecule details ›
Chains: G, S
Length: 171 amino acids
Theoretical weight: 19.08 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P34087 (Residues: 1-171; Coverage: 100%)
Gene names: D9509.22, RPB7, YDR404C
Sequence domains:
Structure domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chains: H, T
Molecule details ›
Chains: H, T
Length: 146 amino acids
Theoretical weight: 16.53 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P20436 (Residues: 1-146; Coverage: 100%)
Gene names: RPB8, YOR224C, YOR50-14
Sequence domains: RNA polymerase Rpb8
Structure domains: Nucleic acid-binding proteins
DNA-directed RNA polymerase II subunit RPB9 Chains: I, U
Molecule details ›
Chains: I, U
Length: 122 amino acids
Theoretical weight: 14.31 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P27999 (Residues: 1-122; Coverage: 100%)
Gene names: RPB9, YGL070C
Sequence domains:
Structure domains: N-terminal domain of TfIIb
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chains: J, V
Molecule details ›
Chains: J, V
Length: 70 amino acids
Theoretical weight: 8.29 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P22139 (Residues: 1-70; Coverage: 100%)
Gene names: RPB10, YOR210W
Sequence domains: RNA polymerases N / 8 kDa subunit
Structure domains: Homeodomain-like
DNA-directed RNA polymerase II subunit RPB11 Chains: K, W
Molecule details ›
Chains: K, W
Length: 120 amino acids
Theoretical weight: 13.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38902 (Residues: 1-120; Coverage: 100%)
Gene names: RPB11, YOL005C
Sequence domains:
Structure domains: RNA polymerase, RBP11-like subunit
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chains: L, X
Molecule details ›
Chains: L, X
Length: 70 amino acids
Theoretical weight: 7.73 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P40422 (Residues: 1-70; Coverage: 100%)
Gene names: RPB12, RPC10, YHR143BW, YHR143W-A
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Structure domains: RNA polymerase ii, chain L
5'-D(*AP*GP*CP*TP*CP*A*AP*GP*TP*AP*GP*TP*TP*AP*TP*GP*CP*CP*(BRU)P*GP*GP*TP*CP*AP*TP*T)-3' Chains: 1, 4
Molecule details ›
Chains: 1, 4
Length: 26 nucleotides
Theoretical weight: 8.06 KDa
5'-D(*A*AP*CP*TP*AP*CP*TP*TP*GP*AP*GP*CP*T)-3' Chains: 2, 5
Molecule details ›
Chains: 2, 5
Length: 13 nucleotides
Theoretical weight: 3.95 KDa
5'-R(*UP*GP*CP*AP*UP*U*UP*CP*GP*AP*CP*CP*AP*GP*GP*CP*U)-3' Chains: 3, 6
Molecule details ›
Chains: 3, 6
Length: 17 nucleotides
Theoretical weight: 5.38 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 16 x ZN
1 modified residue:
Ligand BRU 2 x BRU

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: C2
Unit cell:
a: 394.264Å b: 221.614Å c: 283.446Å
α: 90° β: 90.9° γ: 90°
R-values:
R R work R free
0.233 0.233 0.252

Quick links

Citations

24 review citations

Transcript Elongation by RNA Polymerase II.
Selth et al. (2010)
23 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