PDBe 3k7a

X-ray diffraction
3.8Å resolution

Crystal Structure of an RNA polymerase II-TFIIB complex

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 11-mer (preferred)
Entry contents:
11 distinct polypeptide molecules
Macromolecules (11 distinct):
Transcription initiation factor IIB Chain: M
Molecule details ›
Chain: M
Length: 345 amino acids
Theoretical weight: 38.26 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P29055 (Residues: 1-345; Coverage: 100%)
Gene names: P9513.4, SUA7, YPR086W
Sequence domains:
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
Expression system: 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 RPB3 Chain: C
Molecule details ›
Chain: C
Length: 318 amino acids
Theoretical weight: 35.33 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P16370 (Residues: 1-318; Coverage: 100%)
Gene names: RPB3, YIL021W
Sequence domains:
Structure domains:
DNA-directed RNA polymerase II subunit RPB9 Chain: I
Molecule details ›
Chain: I
Length: 122 amino acids
Theoretical weight: 14.31 KDa
Source organism: Saccharomyces cerevisiae
Expression system: 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 polymerase II subunit RPB11 Chain: K
Molecule details ›
Chain: K
Length: 120 amino acids
Theoretical weight: 13.63 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38902 (Residues: 1-120; Coverage: 100%)
Gene names: RPB11, YOL005C
Sequence domains: RNA polymerase Rpb3/Rpb11 dimerisation domain
Structure domains: Gyrase A; domain 2
DNA-directed RNA polymerases I, II, and III subunit RPABC1 Chain: E
Molecule details ›
Chain: E
Length: 215 amino acids
Theoretical weight: 25.12 KDa
Source organism: Saccharomyces cerevisiae
Expression system: 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 Chain: F
Molecule details ›
Chain: F
Length: 155 amino acids
Theoretical weight: 17.93 KDa
Source organism: Saccharomyces cerevisiae
Expression system: 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 polymerases I, II, and III subunit RPABC3 Chain: H
Molecule details ›
Chain: H
Length: 146 amino acids
Theoretical weight: 16.53 KDa
Source organism: Saccharomyces cerevisiae
Expression system: 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 polymerases I, II, and III subunit RPABC4 Chain: L
Molecule details ›
Chain: L
Length: 70 amino acids
Theoretical weight: 7.73 KDa
Source organism: Saccharomyces cerevisiae
Expression system: 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
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
Molecule details ›
Chain: J
Length: 70 amino acids
Theoretical weight: 8.29 KDa
Source organism: Saccharomyces cerevisiae
Expression system: 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

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: I222
Unit cell:
a: 204.15Å b: 216.21Å c: 420.98Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.268 0.263 0.313
Expression systems:
  • Escherichia coli
  • Saccharomyces cerevisiae