› 6gml

Electron Microscopy
3.2Å resolution

Structure of paused transcription complex Pol II-DSIF-NELF

Released:
DOI: 10.2210/pdb6gml/pdb
PDB entry 6gml coloured by chain, front view.
PDB entry 6gml coloured by chain, side view.
PDB entry 6gml coloured by chain, top view.
Source organisms:
Primary publication:
Structure of paused transcription complex Pol II-DSIF-NELF.
Vos SM, Farnung L, Urlaub H, Cramer P
Nature 560 601-606 (2018)
PMID: 30135580
Related structures: EMD-0038

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 21-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-236763 (preferred)
Entry contents:
18 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (21 distinct):
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: I3LJR4 (Residues: 1-526, 527-1298, 1299-1968; 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:
Structure domains:
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:
Structure 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
Structure domains: Eukaryotic RPB6 RNA polymerase subunit
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
Structure domains: Nucleic acid-binding proteins
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:
Uncharacterized protein Chain: J
Molecule details ›
Chain: J
Length: 67 amino acids
Theoretical weight: 7.66 KDa
Source organism: Sus scrofa
Structure domains: Homeodomain-like
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein Chain: K
Molecule details ›
Chain: K
Length: 117 amino acids
Theoretical weight: 13.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RKE4 (Residues: 1-117; Coverage: 100%)
Gene name: POLR2J
Sequence domains:
Structure domains: RNA polymerase, RBP11-like subunit
DNA-directed RNA polymerases I, II, and III subunit RPABC4 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
Structure domains: RNA polymerase ii, chain L
Negative elongation factor A Chain: U
Molecule details ›
Chain: U
Length: 528 amino acids
Theoretical weight: 57.34 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9H3P2 (Residues: 1-528; Coverage: 100%)
Gene names: NELFA, P/OKcl.15, WHSC2
Negative elongation factor B Chain: V
Molecule details ›
Chain: V
Length: 577 amino acids
Theoretical weight: 64.58 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8WX92 (Residues: 42-580; Coverage: 93%)
Gene names: COBRA1, KIAA1182, NELFB
Sequence domains: Cofactor of BRCA1 (COBRA1)
Negative elongation factor C/D Chain: W
Molecule details ›
Chain: W
Length: 584 amino acids
Theoretical weight: 64.65 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8IXH7 (Residues: 10-590; Coverage: 99%)
Gene names: HSPC130, NELFCD, NELFD, TH1, TH1L
Sequence domains: TH1 protein
Negative elongation factor E Chain: X
Molecule details ›
Chain: X
Length: 404 amino acids
Theoretical weight: 45.36 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
Transcription elongation factor SPT4 Chain: Y
Molecule details ›
Chain: Y
Length: 121 amino acids
Theoretical weight: 13.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P63272 (Residues: 1-117; Coverage: 100%)
Gene names: SPT4H, SUPT4H, SUPT4H1
Sequence domains: Spt4/RpoE2 zinc finger
Structure domains: Herpes Virus-1
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 BL21(DE3)
UniProt:
  • Canonical: O00267 (Residues: 1-1087; Coverage: 100%)
Gene names: SPT5, SPT5H, SUPT5H
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: A0A287ADR4 (Residues: 43-184; Coverage: 77%)
Gene name: POLR2D
Sequence domains: RNA polymerase Rpb4
Structure domains: Growth Hormone; Chain: A;
RNA polymerase II subunit G Chain: G
Molecule details ›
Chain: G
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Sus scrofa
Structure domains:
Non-template DNA Chain: N
Molecule details ›
Chain: N
Length: 48 nucleotides
Theoretical weight: 14.71 KDa
Template DNA Chain: T
Molecule details ›
Chain: T
Length: 48 nucleotides
Theoretical weight: 14.91 KDa
TAR RNA Chain: P
Molecule details ›
Chain: P
Length: 46 nucleotides
Theoretical weight: 14.75 KDa
Sequence domains: Trans-activation response element (TAR)

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.2Å
Relevant EMDB volumes: EMD-0038
Expression systems:
  • Trichoplusia ni
  • Escherichia coli BL21(DE3)

Quick links

Citations

40 review citations

Organization and regulation of gene transcription.
Cramer P. (2019)
39 more

13 mentions without citation

Structure and mechanism of the RNA polymerase II transcription machinery.
Schier et al. (2020)
12 more