› 5x51

X-ray diffraction
7Å resolution

RNA Polymerase II from Komagataella Pastoris (Type-3 crystal)

Released:
DOI: 10.2210/pdb5x51/pdb
PDB entry 5x51 coloured by chain, front view.
PDB entry 5x51 coloured by chain, side view.
PDB entry 5x51 coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of RNA polymerase II from Komagataella pastoris.
Ehara H, Umehara T, Sekine SI, Yokoyama S
Biochem Biophys Res Commun 487 230-235 (2017)
PMID: 28412353

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 dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-111378 (preferred)
Entry contents:
12 distinct polypeptide molecules
Macromolecules (12 distinct):
DNA-directed RNA polymerase subunit Chains: A, M
Molecule details ›
Chains: A, M
Length: 1743 amino acids
Theoretical weight: 194.11 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R4Y0 (Residues: 1-1743; Coverage: 100%)
Gene name: PAS_chr3_0568
Sequence domains:
DNA-directed RNA polymerase subunit beta Chains: B, N
Molecule details ›
Chains: B, N
Length: 1227 amino acids
Theoretical weight: 139.75 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4QZQ7 (Residues: 1-1227; Coverage: 100%)
Gene name: PAS_chr2-1_0125
Sequence domains:
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein Chains: C, O
Molecule details ›
Chains: C, O
Length: 304 amino acids
Theoretical weight: 34.22 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R7L2 (Residues: 1-304; Coverage: 100%)
Gene name: PAS_chr4_0344
Sequence domains:
RNA polymerase Rpb4/RPC9 core domain-containing protein Chains: D, P
Molecule details ›
Chains: D, P
Length: 186 amino acids
Theoretical weight: 20.62 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R2U9 (Residues: 1-186; Coverage: 100%)
Gene name: PAS_chr2-2_0104
Sequence domains: RNA polymerase Rpb4
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chains: E, Q
Molecule details ›
Chains: E, Q
Length: 214 amino acids
Theoretical weight: 24.96 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R3P8 (Residues: 1-214; Coverage: 100%)
Gene name: PAS_chr3_0157
Sequence domains:
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III Chains: F, R
Molecule details ›
Chains: F, R
Length: 155 amino acids
Theoretical weight: 17.8 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R1V1 (Residues: 1-155; Coverage: 100%)
Gene name: PAS_chr2-2_0434
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerase subunit Chains: G, S
Molecule details ›
Chains: G, S
Length: 171 amino acids
Theoretical weight: 18.8 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R9A1 (Residues: 1-171; Coverage: 100%)
Gene name: PAS_chr4_0906
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chains: H, T
Molecule details ›
Chains: H, T
Length: 145 amino acids
Theoretical weight: 16.25 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R273 (Residues: 1-145; Coverage: 100%)
Gene name: PAS_chr2-2_0309
Sequence domains: RNA polymerase Rpb8
DNA-directed RNA polymerase subunit Chains: I, U
Molecule details ›
Chains: I, U
Length: 115 amino acids
Theoretical weight: 13.61 KDa
Source organism: Komagataella phaffii CBS 7435
UniProt:
  • Canonical: F2QPE6 (Residues: 1-115; Coverage: 100%)
Gene names: PP7435_Chr1-1144, RPB9
Sequence domains:
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III Chains: J, V
Molecule details ›
Chains: J, V
Length: 72 amino acids
Theoretical weight: 8.55 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R009 (Residues: 1-72; Coverage: 100%)
Gene name: PAS_chr2-1_0223
Sequence domains: RNA polymerases N / 8 kDa subunit
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein Chains: K, W
Molecule details ›
Chains: K, W
Length: 118 amino acids
Theoretical weight: 13.83 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R3Z5 (Residues: 1-118; Coverage: 100%)
Gene name: PAS_chr3_0244
Sequence domains:
RNA polymerase subunit, found in RNA polymerase complexes I, II, and III Chains: L, X
Molecule details ›
Chains: L, X
Length: 73 amino acids
Theoretical weight: 7.97 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4QWA8 (Residues: 1-73; Coverage: 100%)
Gene name: PAS_chr1-1_0166
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit

Ligands and Environments

1 bound ligand:
Ligand ZN 16 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21
Unit cell:
a: 148.77Å b: 158.05Å c: 254.96Å
α: 90° β: 92.54° γ: 90°
R-values:
R R work R free
0.337 0.338 0.335

Quick links

Citations

1 review citation

Distinct Mechanisms of Transcription Initiation by RNA Polymerases I and II.
Engel et al. (2018)
2 other articles