› 8rbx

Electron Microscopy
4.1Å resolution

Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex

Released:
DOI: 10.2210/pdb8rbx/pdb
PDB entry 8rbx coloured by chain, front view.
PDB entry 8rbx coloured by chain, side view.
PDB entry 8rbx coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of Integrator-dependent RNA polymerase II termination.
Fianu I, Ochmann M, Walshe JL, Dybkov O, Cruz JN, Urlaub H, Cramer P
OpenAccess logo Nature (2024)
PMID: 38570683
Related structures: EMD-19038

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
[a protein]-serine/threonine phosphate + H(2)O = [a protein]-serine/threonine + phosphate
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 46-mer (preferred)
PDBe Complex ID:
PDB-CPX-244946 (preferred)
Entry contents:
38 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (41 distinct):
UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK Chain: 1
Molecule details ›
Chain: 1
Length: 8 amino acids
Theoretical weight: 699 Da
Source organism: Sus scrofa
DNA-directed RNA polymerase subunit Chains: A, Y
Molecule details ›
Chains: A, Y
Length: 1970 amino acids
Theoretical weight: 217.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A7M4DUC2 (Residues: 1-1984; Coverage: 99%)
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: 275 amino acids
Theoretical weight: 31.44 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LCH3 (Residues: 1-275; Coverage: 100%)
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: A0A287ADR4 (Residues: 43-184; Coverage: 77%)
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: A0A8D1KNW4 (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: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VKG7 (Residues: 1-172; Coverage: 100%)
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: A0A4X1VYD0 (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: 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
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
Histone H3.3C Chains: M, S
Molecule details ›
Chains: M, S
Length: 135 amino acids
Theoretical weight: 15.35 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6NXT2 (Residues: 1-135; Coverage: 100%)
Gene names: H3-5, H3F3C
Sequence domains: Core histone H2A/H2B/H3/H4
Histone H4 Chains: O, U
Molecule details ›
Chains: O, U
Length: 103 amino acids
Theoretical weight: 11.39 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62805 (Residues: 1-103; Coverage: 100%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4
Sequence domains: Centromere kinetochore component CENP-T histone fold
Histone H2A type 1 Chains: Q, V
Molecule details ›
Chains: Q, V
Length: 130 amino acids
Theoretical weight: 14.09 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P02262 (Residues: 1-130; Coverage: 100%)
Sequence domains:
Histone H2B type 1-J Chains: R, W
Molecule details ›
Chains: R, W
Length: 126 amino acids
Theoretical weight: 13.98 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P06899 (Residues: 1-126; Coverage: 100%)
Gene names: H2BC11, H2BFR, HIST1H2BJ
Sequence domains: Core histone H2A/H2B/H3/H4
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:
Integrator complex subunit 1 Chain: a
Molecule details ›
Chain: a
Length: 2192 amino acids
Theoretical weight: 244.78 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8N201 (Residues: 1-2190; Coverage: 100%)
Gene names: INTS1, KIAA1440, UNQ1821/PRO3434
Sequence domains:
Integrator complex subunit 2 Chain: b
Molecule details ›
Chain: b
Length: 1204 amino acids
Theoretical weight: 134.45 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9H0H0 (Residues: 1-1204; Coverage: 100%)
Gene names: INTS2, KIAA1287
Sequence domains: Integrator complex subunit 2
Integrator complex subunit 4 Chain: d
Molecule details ›
Chain: d
Length: 963 amino acids
Theoretical weight: 108.31 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q96HW7 (Residues: 1-963; Coverage: 100%)
Gene names: INTS4, MSTP093
Sequence domains:
Integrator complex subunit 5 Chain: e
Molecule details ›
Chain: e
Length: 1021 amino acids
Theoretical weight: 108.32 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q6P9B9 (Residues: 1-1019; Coverage: 100%)
Gene names: INTS5, KIAA1698
Sequence domains:
Integrator complex subunit 6 Chain: f
Molecule details ›
Chain: f
Length: 889 amino acids
Theoretical weight: 100.73 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9UL03 (Residues: 1-887; Coverage: 100%)
Gene names: DBI1, DDX26, DDX26A, INTS6
Sequence domains:
Integrator complex subunit 7 Chain: g
Molecule details ›
Chain: g
Length: 964 amino acids
Theoretical weight: 107.15 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9NVH2 (Residues: 1-962; Coverage: 100%)
Gene names: C1orf73, INTS7
Sequence domains: Integrator complex subunit 7, C-terminal domain
Integrator complex subunit 8 Chain: h
Molecule details ›
Chain: h
Length: 995 amino acids
Theoretical weight: 113.22 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q75QN2 (Residues: 1-995; Coverage: 100%)
Gene names: C8orf52, INTS8
Integrator complex subunit 9 Chain: i
Molecule details ›
Chain: i
Length: 658 amino acids
Theoretical weight: 73.89 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9NV88 (Residues: 1-658; Coverage: 100%)
Gene names: INTS9, RC74
Sequence domains:
Integrator complex subunit 10 Chain: j
Molecule details ›
Chain: j
Length: 710 amino acids
Theoretical weight: 82.34 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9NVR2 (Residues: 1-710; Coverage: 100%)
Gene names: C8orf35, INTS10
Sequence domains: Integrator subunit 10
Integrator complex subunit 11 Chain: k
Molecule details ›
Chain: k
Length: 602 amino acids
Theoretical weight: 67.96 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q5TA45 (Residues: 1-600; Coverage: 100%)
Gene names: CPSF3L, INTS11, RC68
Sequence domains:
Integrator complex subunit 13 Chain: m
Molecule details ›
Chain: m
Length: 706 amino acids
Theoretical weight: 80.35 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9NVM9 (Residues: 1-706; Coverage: 100%)
Gene names: ASUN, C12orf11, GCT1, INTS13
Sequence domains: Cell cycle and development regulator Mat89Bb
Integrator complex subunit 14 Chain: n
Molecule details ›
Chain: n
Length: 518 amino acids
Theoretical weight: 57.53 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q96SY0 (Residues: 1-518; Coverage: 100%)
Gene names: C15orf44, INTS14, VWA9
Sequence domains:
Integrator complex subunit 15 Chain: o
Molecule details ›
Chain: o
Length: 451 amino acids
Theoretical weight: 50.3 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q96N11 (Residues: 1-449; Coverage: 100%)
Gene names: C7orf26, INTS15
Sequence domains: Integrator complex subunit 15
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform Chain: p
Molecule details ›
Chain: p
Length: 591 amino acids
Theoretical weight: 65.58 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P30153 (Residues: 1-589; Coverage: 100%)
Gene name: PPP2R1A
Sequence domains: HEAT repeat
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform Chain: q
Molecule details ›
Chain: q
Length: 311 amino acids
Theoretical weight: 35.84 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P67775 (Residues: 1-309; Coverage: 100%)
Gene name: PPP2CA
Sequence domains: Calcineurin-like phosphoesterase
DSS1 Chain: r
Molecule details ›
Chain: r
Length: 28 amino acids
Theoretical weight: 3.56 KDa
Source organism: Trichoplusia ni
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: 613 amino acids
Theoretical weight: 68.59 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8WX92 (Residues: 1-580; Coverage: 100%)
Gene names: COBRA1, KIAA1182, NELFB
Sequence domains: Cofactor of BRCA1 (COBRA1)
Negative elongation factor C/D Chain: w
Molecule details ›
Chain: w
Length: 583 amino acids
Theoretical weight: 65.75 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
UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK Chain: x
Molecule details ›
Chain: x
Length: 22 amino acids
Theoretical weight: 1.89 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
non-template DNA Chain: N
Molecule details ›
Chain: N
Length: 148 nucleotides
Theoretical weight: 45.94 KDa
Template DNA Chain: T
Molecule details ›
Chain: T
Length: 185 nucleotides
Theoretical weight: 56.76 KDa
RNA Chain: P
Molecule details ›
Chain: P
Length: 17 nucleotides
Theoretical weight: 5.55 KDa

Ligands and Environments

3 bound ligands:
Ligand ZN 10 x ZN
Ligand MG 1 x MG
Ligand MN 2 x MN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.1Å
Relevant EMDB volumes: EMD-19038
Expression systems:
  • Escherichia coli
  • Trichoplusia ni

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