› 9bvt

X-ray diffraction
3.4Å resolution

RNA Pol II - High Mn(+2) concentration

Released:
DOI: 10.2210/pdb9bvt/pdb
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PDB entry 9bvt coloured by chain, front view.
PDB entry 9bvt coloured by chain, side view.
PDB entry 9bvt coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser.
Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G
Proc Natl Acad Sci U S A 121 e2318527121 (2024)
PMID: 39190355

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetradecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-281336 (preferred)
Entry contents:
12 distinct polypeptide molecules
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (14 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:
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:
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
DNA (5'-D(P*AP*CP*GP*TP*CP*CP*CP*TP*CP*TP*CP*GP*A)-3') Chain: W
RNA (5'-R(*AP*UP*CP*GP*AP*GP*AP*GP*GP*A)-3') Chain: X

Ligands and Environments

3 bound ligands:
Ligand ZN 8 x ZN
Ligand MN 2 x MN
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRL BEAMLINE BL12-1
Spacegroup: C2221
Unit cell:
a: 221.19Å b: 393.97Å c: 283.28Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.22 0.249

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Citations

1 citations in other articles

Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser.
Lin et al. (2024)

PDB-REDO

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