› 5fyw

Electron Microscopy
4.35Å resolution

Transcription initiation complex structures elucidate DNA opening (OC)

Released:
DOI: 10.2210/pdb5fyw/pdb
PDB entry 5fyw coloured by chain, front view.
PDB entry 5fyw coloured by chain, side view.
PDB entry 5fyw coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Transcription initiation complex structures elucidate DNA opening.
Plaschka C, Hantsche M, Dienemann C, Burzinski C, Plitzko J, Cramer P
Nature 533 353-8 (2016)
PMID: 27193681
Related structures: EMD-3378

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 22-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118693 (preferred)
Entry contents:
20 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (22 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
Molecule details ›
Chain: C
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:
DNA-directed RNA polymerase II subunit RPB4 Chain: D
Molecule details ›
Chain: D
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
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
UniProt:
  • Canonical: P20434 (Residues: 1-215; Coverage: 100%)
Gene names: RPA7, RPB5, RPC9, YBR1204, YBR154C
Sequence 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
UniProt:
  • Canonical: P20435 (Residues: 1-155; Coverage: 100%)
Gene names: P9677.8, RPB6, RPO26, YPR187W
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerase II subunit RPB7 Chain: G
Molecule details ›
Chain: G
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:
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
UniProt:
  • Canonical: P20436 (Residues: 1-146; Coverage: 100%)
Gene names: RPB8, YOR224C, YOR50-14
Sequence domains: RNA polymerase Rpb8
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
UniProt:
  • Canonical: P27999 (Residues: 1-122; Coverage: 100%)
Gene names: RPB9, YGL070C
Sequence domains:
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
UniProt:
  • Canonical: P22139 (Residues: 1-70; Coverage: 100%)
Gene names: RPB10, YOR210W
Sequence domains: RNA polymerases N / 8 kDa subunit
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
UniProt:
  • Canonical: P38902 (Residues: 1-120; Coverage: 100%)
Gene names: RPB11, YOL005C
Sequence domains:
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
UniProt:
  • Canonical: P40422 (Residues: 1-70; Coverage: 100%)
Gene names: RPB12, RPC10, YHR143BW, YHR143W-A
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
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 BL21(DE3)
UniProt:
  • Canonical: P29055 (Residues: 1-345; Coverage: 100%)
Gene names: P9513.4, SUA7, YPR086W
Sequence domains:
TATA-box-binding protein Chain: O
Molecule details ›
Chain: O
Length: 240 amino acids
Theoretical weight: 27.04 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P13393 (Residues: 1-240; Coverage: 100%)
Gene names: BTF1, SPT15, TBP1, YER148W
Sequence domains: Transcription factor TFIID (or TATA-binding protein, TBP)
Transcription initiation factor IIF subunit alpha Chain: Q
Molecule details ›
Chain: Q
Length: 735 amino acids
Theoretical weight: 82.32 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P41895 (Residues: 1-735; Coverage: 100%)
Gene names: G7526, SSU71, TFG1, YGR186W
Sequence domains: Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
Transcription initiation factor IIF subunit beta Chain: R
Molecule details ›
Chain: R
Length: 400 amino acids
Theoretical weight: 46.68 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P41896 (Residues: 1-400; Coverage: 100%)
Gene names: TFG2, YGR005C
Sequence domains:
Transcription initiation factor IIA large subunit Chain: U
Molecule details ›
Chain: U
Length: 286 amino acids
Theoretical weight: 32.23 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P32773 (Residues: 1-286; Coverage: 100%)
Gene names: TOA1, YOR194C
Sequence domains: Transcription factor IIA, alpha/beta subunit
Transcription initiation factor IIA subunit 2 Chain: V
Molecule details ›
Chain: V
Length: 122 amino acids
Theoretical weight: 13.47 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P32774 (Residues: 1-122; Coverage: 100%)
Gene names: TOA2, YKL058W
Sequence domains:
Transcription initiation factor IIE subunit alpha Chain: W
Molecule details ›
Chain: W
Length: 482 amino acids
Theoretical weight: 54.8 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P36100 (Residues: 1-482; Coverage: 100%)
Gene names: TFA1, YKL028W
Sequence domains: TFIIE alpha subunit
Transcription initiation factor IIE subunit beta Chain: X
Molecule details ›
Chain: X
Length: 328 amino acids
Theoretical weight: 37.05 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P36145 (Residues: 1-328; Coverage: 100%)
Gene names: TFA2, YKR062W
Sequence domains:
NONTEMPLATE DNA Chain: N
Molecule details ›
Chain: N
Length: 72 nucleotides
Theoretical weight: 22.42 KDa
NONTEMPLATE DNA Chain: T
Molecule details ›
Chain: T
Length: 72 nucleotides
Theoretical weight: 22.14 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 10 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.35Å
Relevant EMDB volumes: EMD-3378
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

41 review citations

Organization and regulation of gene transcription.
Cramer P. (2019)
40 more

15 mentions without citation

Structural Insights into the Eukaryotic Transcription Initiation Machinery.
Nogales et al. (2017)
14 more