PDBe 6gml

Electron Microscopy
3.2Å resolution

Structure of paused transcription complex Pol II-DSIF-NELF

Released:
Source organisms:
Primary publication:
Structure of paused transcription complex Pol II-DSIF-NELF.
Nature 560 601-606 (2018)
PMID: 30135580
Related structures: EMD-0038

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 21-mer (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: 1-525, 526-1294, 1295-1959; 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: 78-1251; Coverage: 94%)
Gene name: POLR2B
Sequence domains:
RNA polymerase II subunit C 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 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:
RNA polymerase II subunit F Chain: F
Molecule details ›
Chain: F
Length: 127 amino acids
Theoretical weight: 14.48 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1SKN8 (Residues: 1-127; Coverage: 100%)
Gene name: POLR2F
Sequence domains: RNA polymerase Rpb6
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:
Uncharacterized protein Chain: J
Molecule details ›
Chain: J
Length: 67 amino acids
Theoretical weight: 7.66 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287B432 (Residues: 1-67; Coverage: 100%)
Gene name: POLR2L
Sequence domains: RNA polymerases N / 8 kDa subunit
Uncharacterized 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: RNA polymerase Rpb3/Rpb11 dimerisation domain
RNA polymerase II subunit K Chain: L
Molecule details ›
Chain: L
Length: 58 amino acids
Theoretical weight: 7.02 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LN51 (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: 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%)
  • Best match: Q8IXH7-4 (Residues: 1-581)
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. (a.k.a. RRM, RBD, or RNP domain)
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
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 II subunit D Chain: D
Molecule details ›
Chain: D
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287ADR4 (Residues: 1-142; Coverage: 100%)
Gene name: POLR2D
Sequence domains: RNA polymerase Rpb4
RNA polymerase II subunit G Chain: G
Molecule details ›
Chain: G
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LJZ9 (Residues: 1-172; Coverage: 100%)
Gene name: POLR2G
Sequence 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:

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)