› 5xog

X-ray diffraction
3Å resolution

RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1

Released:
DOI: 10.2210/pdb5xog/pdb
PDB entry 5xog coloured by chain, front view.
PDB entry 5xog coloured by chain, side view.
PDB entry 5xog coloured by chain, top view.
Source organisms:
Primary publication:
Structure of the complete elongation complex of RNA polymerase II with basal factors.
Ehara H, Yokoyama T, Shigematsu H, Yokoyama S, Shirouzu M, Sekine SI
Science 357 921-924 (2017)
PMID: 28775211

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 heptadecamer (preferred)
PDBe Complex ID:
PDB-CPX-103262 (preferred)
Entry contents:
14 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (17 distinct):
DNA-directed RNA polymerase subunit Chain: A
Molecule details ›
Chain: A
Length: 1743 amino acids
Theoretical weight: 194.11 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4R4Y0 (Residues: 1-1743; Coverage: 100%)
Gene name: PAS_chr3_0568
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: B
Molecule details ›
Chain: B
Length: 1227 amino acids
Theoretical weight: 139.75 KDa
Source organism: Komagataella phaffii GS115
UniProt:
  • Canonical: C4QZQ7 (Residues: 1-1227; Coverage: 100%)
Gene name: PAS_chr2-1_0125
Sequence domains:
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein 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:
Structure domains:
RNA polymerase Rpb4/RPC9 core domain-containing protein 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
Structure domains: Growth Hormone; Chain: A;
DNA-directed RNA polymerases I, II, and III subunit RPABC1 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:
Structure 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
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
DNA-directed RNA polymerase 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:
Structure 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
Structure domains: Nucleic acid-binding proteins
DNA-directed RNA polymerase subunit Chain: I
Molecule details ›
Chain: I
Length: 115 amino acids
Theoretical weight: 13.61 KDa
Source organism: Komagataella phaffii CBS 7435
UniProt:
  • Canonical: F2QPE6 (Residues: 1-115; Coverage: 100%)
Gene names: PP7435_Chr1-1144, RPB9
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
Structure domains: Homeodomain-like
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein 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:
Structure domains: RNA polymerase, RBP11-like subunit
RNA polymerase subunit ABC10-alpha Chain: L
Molecule details ›
Chain: L
Length: 72 amino acids
Theoretical weight: 7.86 KDa
Source organism: Komagataella phaffii CBS 7435
UniProt:
  • Canonical: F2QMI1 (Residues: 1-72; Coverage: 100%)
Gene names: PP7435_Chr1-0476, RPC10
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Structure domains: RNA polymerase ii, chain L
Transcription elongation factor 1 homolog Chain: M
Molecule details ›
Chain: M
Length: 85 amino acids
Theoretical weight: 9.41 KDa
Source organism: Komagataella pastoris
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A1B2JER8 (Residues: 1-82; Coverage: 75%)
Gene names: ATY40_BA7504229, ELF1
Sequence domains: Transcription elongation factor Elf1 like
Structure domains: N-terminal domain of TfIIb
Transcription elongation factor SPT5 Chain: W
Molecule details ›
Chain: W
Length: 83 amino acids
Theoretical weight: 9.2 KDa
Source organism: Komagataella phaffii CBS 7435
Expression system: Escherichia coli
UniProt:
  • Canonical: F2QUC3 (Residues: 736-815; Coverage: 9%)
Gene names: PP7435_Chr3-0027, SPT5
Sequence domains: KOW motif
DNA (39-MER) Chain: T
Molecule details ›
Chain: T
Length: 39 nucleotides
Theoretical weight: 11.91 KDa
DNA (30-MER) Chain: N
Molecule details ›
Chain: N
Length: 30 nucleotides
Theoretical weight: 9.32 KDa
RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') Chain: P
Molecule details ›
Chain: P
Length: 17 nucleotides
Theoretical weight: 5.38 KDa

Ligands and Environments

3 bound ligands:
Ligand ZN 9 x ZN
Ligand MG 1 x MG
Ligand APC 1 x APC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 155.25Å b: 159.91Å c: 268.93Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.195 0.225
Expression system: Escherichia coli

Quick links

Citations

28 review citations

Eukaryotic core promoters and the functional basis of transcription initiation.
Haberle et al. (2018)
27 more

7 mentions without citation

SARS-CoV-2 (COVID-19) structural and evolutionary dynamicome: Insights into functional evolution and human genomics.
Gupta et al. (2020)
6 more