› 8uhd

Electron Microscopy
2.8Å resolution

Structure of paused transcription complex Pol II-DSIF-NELF - post-translocated

Released:
DOI: 10.2210/pdb8uhd/pdb
PDB entry 8uhd coloured by chain, front view.
PDB entry 8uhd coloured by chain, side view.
PDB entry 8uhd 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-42270

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero 21-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-281124 (preferred)
Entry contents:
18 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (21 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
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
Negative elongation factor C/D Chain: W
Negative elongation factor B Chain: V
DNA-directed RNA polymerase subunit Chain: A
DNA-directed RNA polymerase subunit beta Chain: B
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein Chain: C
RNA polymerase Rpb4/RPC9 core domain-containing protein Chain: D
DNA-directed RNA polymerase II subunit E Chain: E
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
DNA-directed RNA polymerase subunit Chain: G
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
DNA-directed RNA polymerase II subunit RPB9 Chain: I
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein Chain: K
RNA polymerase II, I and III subunit K Chain: L
Negative elongation factor A Chain: U
Transcription elongation factor SPT4 Chain: Y
Non-template DNA Chain: N
Template DNA Chain: T
RNA Chain: P

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 2.8Å
Relevant EMDB volumes: EMD-42270
Expression systems:
  • Trichoplusia ni
  • Escherichia coli
  • Not provided

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