› 7ycx

Electron Microscopy
4.18Å resolution

The structure of INTAC-PEC complex

Released:
DOI: 10.2210/pdb7ycx/pdb
PDB entry 7ycx coloured by chain, front view.
PDB entry 7ycx coloured by chain, side view.
PDB entry 7ycx coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of INTAC-regulated transcription.
Zheng H, Jin Q, Wang X, Qi Y, Liu W, Ren Y, Zhao D, Xavier Chen F, Cheng J, Chen X, Xu Y
OpenAccess logo Protein Cell (2023)
PMID: 36869814
Related structures: EMD-33741

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero 34-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-243606 (preferred)
Entry contents:
31 distinct polypeptide molecules
2 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (34 distinct):
Integrator complex subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 2190 amino acids
Theoretical weight: 244.57 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
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: Homo sapiens
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: Homo sapiens
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: 1019 amino acids
Theoretical weight: 108.12 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
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: 887 amino acids
Theoretical weight: 100.53 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
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: 962 amino acids
Theoretical weight: 106.95 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
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: Homo sapiens
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: Homo sapiens
UniProt:
  • Canonical: Q9NV88 (Residues: 1-658; Coverage: 100%)
Gene names: INTS9, RC74
Sequence domains:
Integrator complex subunit 11 Chain: K
Molecule details ›
Chain: K
Length: 600 amino acids
Theoretical weight: 67.76 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q5TA45 (Residues: 1-600; Coverage: 100%)
Gene names: CPSF3L, INTS11, RC68
Sequence domains:
Unknown2 Chain: M
Molecule details ›
Chain: M
Length: 17 amino acids
Theoretical weight: 1.46 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform Chain: P
Molecule details ›
Chain: P
Length: 589 amino acids
Theoretical weight: 65.38 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
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: 309 amino acids
Theoretical weight: 35.64 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P67775 (Residues: 1-309; Coverage: 100%)
Gene name: PPP2CA
Sequence domains: Calcineurin-like phosphoesterase
Unknown Chain: U
Molecule details ›
Chain: U
Length: 27 amino acids
Theoretical weight: 2.32 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
DNA-directed RNA polymerase II subunit RPB1 Chain: 1
Molecule details ›
Chain: 1
Length: 1970 amino acids
Theoretical weight: 217.22 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P24928 (Residues: 1-1970; Coverage: 100%)
  • Best match: P24928-2 (Residues: 1-557)
Gene names: POLR2, POLR2A
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: 2
Molecule details ›
Chain: 2
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: 3
Molecule details ›
Chain: 3
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:
DNA-directed RNA polymerase II subunit E Chain: 4
Molecule details ›
Chain: 4
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: 5
Molecule details ›
Chain: 5
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 polymerases I, II, and III subunit RPABC3 Chain: 6
Molecule details ›
Chain: 6
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: 7
Molecule details ›
Chain: 7
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: 8
Molecule details ›
Chain: 8
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: 9
Molecule details ›
Chain: 9
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: a
Molecule details ›
Chain: a
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: e
Molecule details ›
Chain: e
Length: 528 amino acids
Theoretical weight: 57.34 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q9H3P2 (Residues: 1-528; Coverage: 100%)
Gene names: NELFA, P/OKcl.15, WHSC2
Negative elongation factor B Chain: f
Molecule details ›
Chain: f
Length: 580 amino acids
Theoretical weight: 65.78 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
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: g
Molecule details ›
Chain: g
Length: 590 amino acids
Theoretical weight: 66.32 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: Q8IXH7 (Residues: 1-590; Coverage: 100%)
Gene names: HSPC130, NELFCD, NELFD, TH1, TH1L
Sequence domains: TH1 protein
Negative elongation factor E Chain: h
Molecule details ›
Chain: h
Length: 380 amino acids
Theoretical weight: 43.32 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P18615 (Residues: 1-380; Coverage: 100%)
Gene names: NELFE, RD, RDBP
Sequence domains: RNA recognition motif
Transcription elongation factor SPT4 Chain: i
Molecule details ›
Chain: i
Length: 121 amino acids
Theoretical weight: 13.51 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P63272 (Residues: 1-117; Coverage: 100%)
Gene names: SPT4H, SUPT4H, SUPT4H1
Sequence domains: Spt4/RpoE2 zinc finger
Transcription elongation factor SPT5 Chain: j
Molecule details ›
Chain: j
Length: 1087 amino acids
Theoretical weight: 121.15 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O00267 (Residues: 1-1087; Coverage: 100%)
Gene names: SPT5, SPT5H, SUPT5H
Sequence domains:
DNA-directed RNA polymerase subunit Chain: k
Molecule details ›
Chain: k
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:
RNA polymerase Rpb4/RPC9 core domain-containing protein Chain: l
Molecule details ›
Chain: l
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
non-template DNA Chain: b
Molecule details ›
Chain: b
Length: 48 nucleotides
Theoretical weight: 14.93 KDa
template DNA Chain: d
Molecule details ›
Chain: d
Length: 48 nucleotides
Theoretical weight: 14.66 KDa
RNA Chain: c
Molecule details ›
Chain: c
Length: 23 nucleotides
Theoretical weight: 7.43 KDa

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 4.18Å
Relevant EMDB volumes: EMD-33741
Expression system: Homo sapiens

Quick links

Citations

1 review citation

3'-End Processing of Eukaryotic mRNA: Machinery, Regulation, and Impact on Gene Expression.
Boreikaitė et al. (2023)
3 other articles