PDBe 5xon

Electron Microscopy
3.83Å resolution

RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 18-mer (preferred)
Entry contents:
15 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (18 distinct):
DNA-directed RNA polymerase subunit Chain: A
DNA-directed RNA polymerase subunit beta Chain: B
RNA polymerase II third largest subunit B44, part of central core Chain: C
Molecule details ›
Chain: C
Length: 304 amino acids
Theoretical weight: 34.22 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R7L2 (Residues: 1-304; Coverage: 100%)
Gene name: PAS_chr4_0344
Sequence domains:
RNA polymerase II subunit B32 Chain: D
Molecule details ›
Chain: D
Length: 186 amino acids
Theoretical weight: 20.62 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R2U9 (Residues: 1-186; Coverage: 100%)
Gene name: PAS_chr2-2_0104
Sequence domains: RNA polymerase Rpb4
RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III Chain: E
Molecule details ›
Chain: E
Length: 214 amino acids
Theoretical weight: 24.96 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R3P8 (Residues: 1-214; Coverage: 100%)
Gene name: PAS_chr3_0157
Sequence domains:
RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III Chain: F
Molecule details ›
Chain: F
Length: 155 amino acids
Theoretical weight: 17.8 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R1V1 (Residues: 1-155; Coverage: 100%)
Gene name: PAS_chr2-2_0434
Sequence domains: RNA polymerase Rpb6
RNA polymerase II subunit Chain: G
Molecule details ›
Chain: G
Length: 171 amino acids
Theoretical weight: 18.8 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R9A1 (Residues: 1-171; Coverage: 100%)
Gene name: PAS_chr4_0906
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
Molecule details ›
Chain: H
Length: 145 amino acids
Theoretical weight: 16.25 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R273 (Residues: 1-145; Coverage: 100%)
Gene name: PAS_chr2-2_0309
Sequence domains: RNA polymerase Rpb8
DNA-directed RNA polymerase subunit Chain: I
Molecule details ›
Chain: I
Length: 115 amino acids
Theoretical weight: 13.61 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4QY79 (Residues: 9-113; Coverage: 93%)
Gene name: PAS_chr1-4_0359
Sequence domains:
RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III Chain: J
Molecule details ›
Chain: J
Length: 72 amino acids
Theoretical weight: 8.55 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R009 (Residues: 1-72; Coverage: 100%)
Gene name: PAS_chr2-1_0223
Sequence domains: RNA polymerases N / 8 kDa subunit
RNA polymerase II subunit B12.5 Chain: K
Molecule details ›
Chain: K
Length: 118 amino acids
Theoretical weight: 13.83 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R3Z5 (Residues: 1-118; Coverage: 100%)
Gene name: PAS_chr3_0244
Sequence domains: RNA polymerase Rpb3/Rpb11 dimerisation domain
RNA polymerase subunit, found in RNA polymerase complexes I, II, and III Chain: L
Molecule details ›
Chain: L
Length: 72 amino acids
Theoretical weight: 7.86 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4QWA8 (Residues: 1-69; Coverage: 95%)
Gene name: PAS_chr1-1_0166
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
General transcription elongation factor TFIIS Chain: U
Molecule details ›
Chain: U
Length: 190 amino acids
Theoretical weight: 21.69 KDa
Source organism: Komagataella phaffii GS115
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R2R6 (Residues: 99-285; Coverage: 66%)
Gene name: PAS_chr2-2_0135
Sequence domains:
Transcription elongation factor SPT4 Chain: V
Molecule details ›
Chain: V
Length: 108 amino acids
Theoretical weight: 12.04 KDa
Source organism: Komagataella phaffii GS115
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R0E6 (Residues: 8-114; Coverage: 94%)
Gene name: PAS_chr2-1_0350
Sequence domains: Spt4/RpoE2 zinc finger
Protein that forms a complex with Spt4p Chain: W
Molecule details ›
Chain: W
Length: 612 amino acids
Theoretical weight: 68.28 KDa
Source organism: Komagataella phaffii GS115
Expression system: Escherichia coli
UniProt:
  • Canonical: C4R370 (Residues: 206-815; Coverage: 67%)
Gene name: PAS_chr3_1136
Sequence domains:
DNA (48-MER) Chain: T
Molecule details ›
Chain: T
Length: 48 nucleotides
Theoretical weight: 14.66 KDa
DNA (48-MER) Chain: N
Molecule details ›
Chain: N
Length: 48 nucleotides
Theoretical weight: 14.92 KDa
RNA (30-MER) Chain: P
Molecule details ›
Chain: P
Length: 30 nucleotides
Theoretical weight: 9.49 KDa

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.83Å
Relevant EMDB volumes: EMD-6747
Expression system: Escherichia coli