› 6f40

Electron Microscopy
3.7Å resolution

RNA Polymerase III open complex

Released:
DOI: 10.2210/pdb6f40/pdb
PDB entry 6f40 coloured by chain, front view.
PDB entry 6f40 coloured by chain, side view.
PDB entry 6f40 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Molecular mechanism of promoter opening by RNA polymerase III.
Vorländer MK, Khatter H, Wetzel R, Hagen WJH, Müller CW
Nature 553 295-300 (2018)
PMID: 29345638
Related structures: EMD-4180

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 22-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119872 (preferred)
Entry contents:
20 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (22 distinct):
DNA-directed RNA polymerase III subunit RPC1 Chain: A
Molecule details ›
Chain: A
Length: 1460 amino acids
Theoretical weight: 162.52 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P04051 (Residues: 1-1460; Coverage: 100%)
Gene names: O3254, RPC1, RPC160, RPO31, YOR116C, YOR3254C
Sequence domains:
DNA-directed RNA polymerase III subunit RPC2 Chain: B
Molecule details ›
Chain: B
Length: 1149 amino acids
Theoretical weight: 129.63 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P22276 (Residues: 1-1149; Coverage: 100%)
Gene names: RET1, RPC128, RPC2, YOR207C
Sequence domains:
DNA-directed RNA polymerases I and III subunit RPAC1 Chain: C
Molecule details ›
Chain: C
Length: 335 amino acids
Theoretical weight: 37.73 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P07703 (Residues: 1-335; Coverage: 100%)
Gene names: P8283.18, RPC40, RPC5, YPR110C
Sequence domains:
Structure domains:
DNA-directed RNA polymerase III subunit RPC9 Chain: D
Molecule details ›
Chain: D
Length: 161 amino acids
Theoretical weight: 18.62 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P47076 (Residues: 1-161; Coverage: 100%)
Gene names: J1349, RPC17, YJL011C
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 S288C
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 S288C
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 III subunit RPC8 Chain: G
Molecule details ›
Chain: G
Length: 212 amino acids
Theoretical weight: 24.35 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P35718 (Residues: 1-212; Coverage: 100%)
Gene names: RPC25, UNF1, YKL1, YKL144C
Sequence domains:
Structure domains: RNA polymerase Rpb7-like, N-terminal domain
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 S288C
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 III subunit RPC10 Chain: I
Molecule details ›
Chain: I
Length: 110 amino acids
Theoretical weight: 12.53 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: Q04307 (Residues: 1-110; Coverage: 100%)
Gene names: RPC11, YD9609.01C, YDR045C
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 S288C
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 polymerases I and III subunit RPAC2 Chain: K
Molecule details ›
Chain: K
Length: 142 amino acids
Theoretical weight: 16.17 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P28000 (Residues: 1-142; Coverage: 100%)
Gene names: N1937, RPC19, YNL113W
Sequence domains:
Structure domains: RNA polymerase, RBP11-like subunit
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 S288C
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 polymerase III subunit RPC5 Chain: M
Molecule details ›
Chain: M
Length: 282 amino acids
Theoretical weight: 32.18 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P36121 (Residues: 1-282; Coverage: 100%)
Gene names: RPC37, YKR025W
Sequence domains: RPC5 protein
DNA-directed RNA polymerase III subunit RPC4 Chain: N
Molecule details ›
Chain: N
Length: 422 amino acids
Theoretical weight: 46.75 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P25441 (Residues: 1-422; Coverage: 100%)
Gene names: D1557, RPC4, RPC53, YDL150W
Sequence domains: RNA polymerase III RPC4
DNA-directed RNA polymerase III subunit RPC3 Chain: O
Molecule details ›
Chain: O
Length: 654 amino acids
Theoretical weight: 74.11 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32349 (Residues: 1-654; Coverage: 100%)
Gene names: P9677.11, RPC3, RPC82, YPR190C
Sequence domains:
DNA-directed RNA polymerase III subunit RPC6 Chain: P
Molecule details ›
Chain: P
Length: 317 amino acids
Theoretical weight: 36.17 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P32910 (Residues: 1-317; Coverage: 100%)
Gene names: N2031, RPC34, YNR003C
Sequence domains: RNA polymerase Rpc34 subunit
DNA-directed RNA polymerase III subunit RPC7 Chain: Q
Molecule details ›
Chain: Q
Length: 251 amino acids
Theoretical weight: 27.75 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P17890 (Residues: 1-251; Coverage: 100%)
Gene names: ACP2, N1769, RPC31, RPC8, YNL151C
Sequence domains: DNA-directed RNA polymerase III subunit Rpc31
TATA-box-binding protein Chain: U
Molecule details ›
Chain: U
Length: 240 amino acids
Theoretical weight: 27.04 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P13393 (Residues: 1-240; Coverage: 100%)
Gene names: BTF1, SPT15, TBP1, YER148W
Sequence domains: Transcription factor TFIID (or TATA-binding protein, TBP)
Structure domains: TATA-Binding Protein
Transcription factor IIIB 70 kDa subunit Chain: V
Molecule details ›
Chain: V
Length: 596 amino acids
Theoretical weight: 67.01 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P29056 (Residues: 1-596; Coverage: 100%)
Gene names: BRF1, PCF4, TDS4, YGR246C
Sequence domains:
Transcription factor TFIIIB component B'' Chain: W
Molecule details ›
Chain: W
Length: 594 amino acids
Theoretical weight: 67.8 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P46678 (Residues: 1-594; Coverage: 100%)
Gene names: BDP1, N2682, TFC5, YNL039W
Sequence domains: Myb-like DNA-binding domain
Non-Template DNA Chain: X
Molecule details ›
Chain: X
Length: 81 nucleotides
Theoretical weight: 24.89 KDa
Template DNA Chain: Y
Molecule details ›
Chain: Y
Length: 81 nucleotides
Theoretical weight: 25.07 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 7 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-4180
Expression system: Escherichia coli

Quick links

Citations

15 review citations

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

6 mentions without citation

The cryo-EM resolution revolution and transcription complexes.
Hanske et al. (2018)
5 more