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Yeast RNA polymerase III elongation complex

Electron Microscopy
4.5Å resolution
PDB entry 6cnf coloured by chain, front view.
PDB entry 6cnf coloured by chain, side view.
PDB entry 6cnf coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Assembly composition:
hetero 21-mer (preferred)
Entry contents: 19 distinct polypeptide molecules
2 distinct DNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA-directed RNA polymerase III complex and DNA
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Multimeric state: hetero 21-mer
Accessible surface area: 263501.54 Å2
Buried surface area: 115676.68 Å2
Dissociation area: 1,604.59 Å2
Dissociation energy (ΔGdiss): 10 kcal/mol
Dissociation entropy (TΔSdiss): 10.65 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-119673

Macromolecules

DNA-directed RNA polymerase III subunit RPC1
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
Pfam:
InterPro:
DNA-directed RNA polymerase III subunit RPC1 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC1 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC1 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC2
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
Pfam:
InterPro:
DNA-directed RNA polymerase III subunit RPC2 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC2 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC2 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerases I and III subunit RPAC1
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
Pfam:
InterPro:
DNA-directed RNA polymerases I and III subunit RPAC1 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerases I and III subunit RPAC1 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerases I and III subunit RPAC1 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC9
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
Pfam: RNA polymerase Rpb4
InterPro:
DNA-directed RNA polymerase III subunit RPC9 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC9 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC9 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC1
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
Pfam:
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC2
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
Pfam: RNA polymerase Rpb6
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC8
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
Pfam:
InterPro:
DNA-directed RNA polymerase III subunit RPC8 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC8 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC8 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC3
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
Pfam: RNA polymerase Rpb8
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC10
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
Pfam:
InterPro:
DNA-directed RNA polymerase III subunit RPC10 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC10 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC10 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC5
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
Pfam: RNA polymerases N / 8 kDa subunit
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerases I and III subunit RPAC2
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
Pfam: RNA polymerase Rpb3/Rpb11 dimerisation domain
InterPro:
DNA-directed RNA polymerases I and III subunit RPAC2 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerases I and III subunit RPAC2 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerases I and III subunit RPAC2 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC4
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
Pfam: DNA directed RNA polymerase, 7 kDa subunit
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC5
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
Pfam: RPC5 protein
InterPro: DNA-directed RNA polymerase III subunit Rpc5
DNA-directed RNA polymerase III subunit RPC5 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC5 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC5 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC4
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
Pfam: RNA polymerase III RPC4
InterPro: DNA-directed RNA polymerase III subunit RPC4
DNA-directed RNA polymerase III subunit RPC4 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC4 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC4 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC3
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
Pfam:
InterPro:
DNA-directed RNA polymerase III subunit RPC3 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC3 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC3 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC6
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
Pfam: RNA polymerase Rpc34 subunit
InterPro:
DNA-directed RNA polymerase III subunit RPC6 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC6 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC6 in PDB entry 6cnf, assembly 1, top view.
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DNA-directed RNA polymerase III subunit RPC7
Chain: Q
Length: 251 amino acids
Theoretical weight: 27.3 KDa
Source organism: Saccharomyces cerevisiae S288C
UniProt:
  • Canonical: P17890 (Residues: 1-251; Coverage: 100%)
Gene names: ACP2, N1769, RPC31, RPC8, YNL151C
Pfam: DNA-directed RNA polymerase III subunit Rpc31
InterPro: DNA-directed RNA polymerase III, subunit Rpc31
DNA-directed RNA polymerase III subunit RPC7 in PDB entry 6cnf, assembly 1, front view.
DNA-directed RNA polymerase III subunit RPC7 in PDB entry 6cnf, assembly 1, side view.
DNA-directed RNA polymerase III subunit RPC7 in PDB entry 6cnf, assembly 1, top view.
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TATA-box-binding protein; Transcription factor IIIB 70 kDa subunit
Chain: R
Length: 736 amino acids
Theoretical weight: 82.1 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P29056 (Residues: 1-382, 438-596; Coverage: 91%)
  • Canonical: P13393 (Residues: 61-240; Coverage: 75%)
    • nullnull
Gene names: BRF1, BTF1, PCF4, SPT15, TBP1, TDS4, YER148W, YGR246C
Pfam:
InterPro:
TATA-box-binding protein in PDB entry 6cnf, assembly 1, front view.
TATA-box-binding protein in PDB entry 6cnf, assembly 1, side view.
TATA-box-binding protein in PDB entry 6cnf, assembly 1, top view.
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Transcription factor TFIIIB component B''
Chain: S
Length: 594 amino acids
Theoretical weight: 66.25 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P46678 (Residues: 1-594; Coverage: 100%)
Gene names: BDP1, N2682, TFC5, YNL039W
Pfam: Myb-like DNA-binding domain
InterPro:
Transcription factor TFIIIB component B'' in PDB entry 6cnf, assembly 1, front view.
Transcription factor TFIIIB component B'' in PDB entry 6cnf, assembly 1, side view.
Transcription factor TFIIIB component B'' in PDB entry 6cnf, assembly 1, top view.
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DNA chain X
Name: DNA (79-MER)
Representative chains: X
Length: 79 nucleotides
Theoretical weight: 24.39 KDa
DNA (79-MER) in PDB entry 6cnf, assembly 1, front view.
DNA (79-MER) in PDB entry 6cnf, assembly 1, side view.
DNA (79-MER) in PDB entry 6cnf, assembly 1, top view.
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DNA chain Y
Name: DNA (79-MER)
Representative chains: Y
Length: 79 nucleotides
Theoretical weight: 24.3 KDa
DNA (79-MER) in PDB entry 6cnf, assembly 1, front view.
DNA (79-MER) in PDB entry 6cnf, assembly 1, side view.
DNA (79-MER) in PDB entry 6cnf, assembly 1, top view.
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