› 8ui0

Electron Microscopy
2.7Å resolution

Structure of poised transcription complex Pol II-DSIF-NELF - pre-translocated

Released:
DOI: 10.2210/pdb8ui0/pdb
PDB entry 8ui0 coloured by chain, front view.
PDB entry 8ui0 coloured by chain, side view.
PDB entry 8ui0 coloured by chain, top view.
Source organisms:
Primary publication:
Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing.
Su BG, Vos SM
Mol Cell (2024)
PMID: 38401543
Related structures: EMD-42285

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero icosamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-269374 (preferred)
Entry contents:
17 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (20 distinct):
Negative elongation factor E Chain: X
Molecule details ›
Chain: X
Length: 380 amino acids
Theoretical weight: 43.32 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P18615 (Residues: 1-380; Coverage: 100%)
Gene names: NELFE, RD, RDBP
Sequence domains: RNA recognition motif
Negative elongation factor B Chain: V
Molecule details ›
Chain: V
Length: 554 amino acids
Theoretical weight: 63.23 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8WX92 (Residues: 1-554; Coverage: 96%)
Gene names: COBRA1, KIAA1182, NELFB
Sequence domains: Cofactor of BRCA1 (COBRA1)
Negative elongation factor C/D Chain: W
Molecule details ›
Chain: W
Length: 590 amino acids
Theoretical weight: 66.32 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8IXH7 (Residues: 1-590; Coverage: 100%)
Gene names: HSPC130, NELFCD, NELFD, TH1, TH1L
Sequence domains: TH1 protein
DNA-directed RNA polymerase subunit Chain: A
Molecule details ›
Chain: A
Length: 1970 amino acids
Theoretical weight: 217.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1DPV6 (Residues: 1-1970; Coverage: 100%)
Gene name: POLR2A
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: B
Molecule details ›
Chain: B
Length: 1174 amino acids
Theoretical weight: 134.04 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGP4 (Residues: 127-1300; Coverage: 90%)
Gene name: POLR2B
Sequence domains:
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 271 amino acids
Theoretical weight: 31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LCH3 (Residues: 1-271; Coverage: 99%)
Gene name: POLR2C
Sequence domains:
RNA polymerase Rpb4/RPC9 core domain-containing protein Chain: D
Molecule details ›
Chain: D
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VM56 (Residues: 1-142; Coverage: 100%)
Gene name: POLR2D
Sequence domains: RNA polymerase Rpb4
DNA-directed RNA polymerase II subunit E Chain: E
Molecule details ›
Chain: E
Length: 210 amino acids
Theoretical weight: 24.64 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LSI7 (Residues: 1-210; Coverage: 100%)
Gene name: POLR2E
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
Molecule details ›
Chain: F
Length: 127 amino acids
Theoretical weight: 14.48 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VEK9 (Residues: 1-127; Coverage: 100%)
Gene name: POLR2F
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerase subunit Chain: G
Molecule details ›
Chain: G
Length: 171 amino acids
Theoretical weight: 19.23 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VKG7 (Residues: 1-171; Coverage: 99%)
Gene name: POLR2G
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
Molecule details ›
Chain: H
Length: 150 amino acids
Theoretical weight: 17.16 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LCB2 (Residues: 1-150; Coverage: 100%)
Gene name: POLR2H
Sequence domains: RNA polymerase Rpb8
DNA-directed RNA polymerase II subunit RPB9 Chain: I
Molecule details ›
Chain: I
Length: 125 amino acids
Theoretical weight: 14.54 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P60899 (Residues: 1-125; Coverage: 100%)
Gene name: POLR2I
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
Molecule details ›
Chain: J
Length: 67 amino acids
Theoretical weight: 7.66 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8W4F9W9 (Residues: 1-67; Coverage: 100%)
Gene name: POLR2L
Sequence domains: RNA polymerases N / 8 kDa subunit
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein Chain: K
Molecule details ›
Chain: K
Length: 115 amino acids
Theoretical weight: 13.07 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RKE4 (Residues: 1-115; Coverage: 98%)
Gene name: POLR2J
Sequence domains: RNA polymerase Rpb3/Rpb11 dimerisation domain
RNA polymerase II, I and III subunit K Chain: L
Molecule details ›
Chain: L
Length: 58 amino acids
Theoretical weight: 7.02 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TRS6 (Residues: 1-58; Coverage: 100%)
Gene name: POLR2K
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Negative elongation factor A Chain: U
Molecule details ›
Chain: U
Length: 527 amino acids
Theoretical weight: 55.69 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9H3P2 (Residues: 1-528; Coverage: 100%)
  • Best match: Q9H3P2-7 (Residues: 1-265)
Gene names: NELFA, P/OKcl.15, WHSC2
Transcription elongation factor SPT5 Chain: Z
Molecule details ›
Chain: Z
Length: 1087 amino acids
Theoretical weight: 121.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O00267 (Residues: 1-1087; Coverage: 100%)
Gene names: SPT5, SPT5H, SUPT5H
Sequence domains:
DNA Chain: N
Molecule details ›
Chain: N
Length: 50 nucleotides
Theoretical weight: 15.41 KDa
DNA (38-MER) Chain: T
Molecule details ›
Chain: T
Length: 38 nucleotides
Theoretical weight: 11.73 KDa
RNA Chain: P
Molecule details ›
Chain: P
Length: 16 nucleotides
Theoretical weight: 5.08 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.7Å
Relevant EMDB volumes: EMD-42285
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

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