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Complete RNA Polymerase II elongation complex with substrate analogue GMPCPP

X-ray diffraction
4.5Å resolution
PDB entry 1y77 coloured by chain, front view.
PDB entry 1y77 coloured by chain, side view.
PDB entry 1y77 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Assembly composition:
hetero pentadecamer (preferred)
Entry contents: 12 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA-directed RNA polymerase II complex and RNA and DNA
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Multimeric state: hetero pentadecamer
Accessible surface area: 164818.35 Å2
Buried surface area: 71683.49 Å2
Dissociation area: 1,383.9 Å2
Dissociation energy (ΔGdiss): 5.6 kcal/mol
Dissociation entropy (TΔSdiss): 14.99 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-114840

Macromolecules

DNA-directed RNA polymerase II subunit RPB1
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
Pfam:
InterPro:
SCOP: RNA polymerase
DNA-directed RNA polymerase II subunit RPB1 in PDB entry 1y77, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB1 in PDB entry 1y77, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB1 in PDB entry 1y77, assembly 1, top view.
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DNA-directed RNA polymerase II subunit RPB2
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
Pfam:
InterPro:
SCOP: RNA polymerase
DNA-directed RNA polymerase II subunit RPB2 in PDB entry 1y77, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB2 in PDB entry 1y77, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB2 in PDB entry 1y77, assembly 1, top view.
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DNA-directed RNA polymerase II subunit RPB3
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
Pfam:
InterPro:
SCOP: RNA polymerase
DNA-directed RNA polymerase II subunit RPB3 in PDB entry 1y77, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB3 in PDB entry 1y77, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB3 in PDB entry 1y77, assembly 1, top view.
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DNA-directed RNA polymerase II subunit RPB4
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
Pfam: RNA polymerase Rpb4
InterPro:
SCOP: RNA polymerase
DNA-directed RNA polymerase II subunit RPB4 in PDB entry 1y77, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB4 in PDB entry 1y77, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB4 in PDB entry 1y77, 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
UniProt:
  • Canonical: P20434 (Residues: 1-215; Coverage: 100%)
Gene names: RPA7, RPB5, RPC9, YBR1204, YBR154C
Pfam:
InterPro:
SCOP: RNA polymerase
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 1y77, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 1y77, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC1 in PDB entry 1y77, 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
UniProt:
  • Canonical: P20435 (Residues: 1-155; Coverage: 100%)
Gene names: P9677.8, RPB6, RPO26, YPR187W
Pfam: RNA polymerase Rpb6
InterPro:
SCOP: RNA polymerase
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 1y77, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 1y77, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC2 in PDB entry 1y77, assembly 1, top view.
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DNA-directed RNA polymerase II subunit RPB7
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
Pfam:
InterPro:
SCOP: RNA polymerase
DNA-directed RNA polymerase II subunit RPB7 in PDB entry 1y77, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB7 in PDB entry 1y77, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB7 in PDB entry 1y77, 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
UniProt:
  • Canonical: P20436 (Residues: 1-146; Coverage: 100%)
Gene names: RPB8, YOR224C, YOR50-14
Pfam: RNA polymerase Rpb8
InterPro:
SCOP: RNA polymerase
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 1y77, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 1y77, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 1y77, assembly 1, top view.
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DNA-directed RNA polymerase II subunit RPB9
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
Pfam:
InterPro:
SCOP: RNA polymerase
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 1y77, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 1y77, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 1y77, 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
UniProt:
  • Canonical: P22139 (Residues: 1-70; Coverage: 100%)
Gene names: RPB10, YOR210W
Pfam: RNA polymerases N / 8 kDa subunit
InterPro:
SCOP: RNA polymerase
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 1y77, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 1y77, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 1y77, assembly 1, top view.
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DNA-directed RNA polymerase II subunit RPB11
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
Pfam:
InterPro:
SCOP: RNA polymerase
DNA-directed RNA polymerase II subunit RPB11 in PDB entry 1y77, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB11 in PDB entry 1y77, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB11 in PDB entry 1y77, 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
UniProt:
  • Canonical: P40422 (Residues: 1-70; Coverage: 100%)
Gene names: RPB12, RPC10, YHR143BW, YHR143W-A
Pfam: DNA directed RNA polymerase, 7 kDa subunit
InterPro:
SCOP: RNA polymerase
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 1y77, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 1y77, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC4 in PDB entry 1y77, assembly 1, top view.
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DNA chain T
Name: 5'-D(P*AP*GP*TP*AP*CP*TP*TP*AP*CP*T*CP*GP*CP*CP*TP*GP*GP*TP*CP*TP*G)-3'
Representative chains: T
Length: 19 nucleotides
Theoretical weight: 5.81 KDa
5'-D(P*AP*GP*TP*AP*CP*TP*TP*AP*CP*T*CP*GP*CP*CP*TP*GP*GP*TP*CP*TP*G)-3' in PDB entry 1y77, assembly 1, front view.
5'-D(P*AP*GP*TP*AP*CP*TP*TP*AP*CP*T*CP*GP*CP*CP*TP*GP*GP*TP*CP*TP*G)-3' in PDB entry 1y77, assembly 1, side view.
5'-D(P*AP*GP*TP*AP*CP*TP*TP*AP*CP*T*CP*GP*CP*CP*TP*GP*GP*TP*CP*TP*G)-3' in PDB entry 1y77, assembly 1, top view.
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DNA chain N
Name: 5'-D(*AP*AP*GP*TP*AP*CP*T)-3'
Representative chains: N
Length: 7 nucleotides
Theoretical weight: 2.12 KDa
5'-D(*AP*AP*GP*TP*AP*CP*T)-3' in PDB entry 1y77, assembly 1, front view.
5'-D(*AP*AP*GP*TP*AP*CP*T)-3' in PDB entry 1y77, assembly 1, side view.
5'-D(*AP*AP*GP*TP*AP*CP*T)-3' in PDB entry 1y77, assembly 1, top view.
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RNA chain P
Name: 5'-R(*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3'
Representative chains: P
Length: 10 nucleotides
Theoretical weight: 3.22 KDa
5'-R(*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3' in PDB entry 1y77, assembly 1, front view.
5'-R(*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3' in PDB entry 1y77, assembly 1, side view.
5'-R(*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3' in PDB entry 1y77, assembly 1, top view.
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