› 6d6q

Electron Microscopy
3.45Å resolution

Human nuclear exosome-MTR4 RNA complex - overall reconstruction

Released:
DOI: 10.2210/pdb6d6q/pdb
PDB entry 6d6q coloured by chain, front view.
PDB entry 6d6q coloured by chain, side view.
PDB entry 6d6q coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex.
Weick EM, Puno MR, Januszyk K, Zinder JC, DiMattia MA, Lima CD
Cell 173 1663-1677.e21 (2018)
PMID: 29906447
Related structures: EMD-7808

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentadecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113214 (preferred)
Entry contents:
13 distinct polypeptide molecules
1 distinct RNA molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (15 distinct):
Exosome complex component RRP45 Chain: A
Molecule details ›
Chain: A
Length: 473 amino acids
Theoretical weight: 52.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q06265 (Residues: 1-385, 386-439; Coverage: 100%)
Gene names: EXOSC9, PMSCL1
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component RRP41 Chain: B
Molecule details ›
Chain: B
Length: 249 amino acids
Theoretical weight: 26.83 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NPD3 (Residues: 1-245; Coverage: 100%)
Gene names: EXOSC4, RRP41, SKI6
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component RRP43 Chain: C
Molecule details ›
Chain: C
Length: 278 amino acids
Theoretical weight: 30.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96B26 (Residues: 1-276; Coverage: 100%)
Gene names: EXOSC8, OIP2, RRP43
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component RRP46 Chain: D
Molecule details ›
Chain: D
Length: 237 amino acids
Theoretical weight: 25.48 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NQT4 (Residues: 1-235; Coverage: 100%)
Gene names: CML28, EXOSC5, RRP46
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component RRP42 Chain: E
Molecule details ›
Chain: E
Length: 293 amino acids
Theoretical weight: 32.07 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15024 (Residues: 1-291; Coverage: 100%)
Gene names: EXOSC7, KIAA0116, RRP42
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component MTR3 Chain: F
Molecule details ›
Chain: F
Length: 272 amino acids
Theoretical weight: 28.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5RKV6 (Residues: 1-272; Coverage: 100%)
Gene names: EXOSC6, MTR3
Sequence domains: 3' exoribonuclease family, domain 1
Exosome complex component RRP40 Chain: G
Molecule details ›
Chain: G
Length: 277 amino acids
Theoretical weight: 29.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NQT5 (Residues: 1-275; Coverage: 100%)
Gene names: CGI-102, EXOSC3, RRP40
Sequence domains:
Structure domains:
Exosome complex component RRP4 Chain: H
Molecule details ›
Chain: H
Length: 296 amino acids
Theoretical weight: 33.18 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13868 (Residues: 1-293; Coverage: 100%)
Gene names: EXOSC2, RRP4
Sequence domains:
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Exosome complex component CSL4 Chain: I
Molecule details ›
Chain: I
Length: 197 amino acids
Theoretical weight: 21.69 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y3B2 (Residues: 1-195; Coverage: 100%)
Gene names: CGI-108, CSL4, EXOSC1
Sequence domains:
Exosome complex component 10 Chain: J
Molecule details ›
Chain: J
Length: 761 amino acids
Theoretical weight: 86.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q01780 (Residues: 1-648, 705-804; Coverage: 85%)
Gene names: EXOSC10, PMSCL, PMSCL2, RRP6
Sequence domains:
Exosome complex exonuclease RRP44 Chain: K
Molecule details ›
Chain: K
Length: 960 amino acids
Theoretical weight: 109.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y2L1 (Residues: 1-958; Coverage: 100%)
Gene names: DIS3, KIAA1008, RRP44
Sequence domains:
M-phase phosphoprotein 6 Chain: L
Molecule details ›
Chain: L
Length: 162 amino acids
Theoretical weight: 19.27 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99547 (Residues: 1-160; Coverage: 100%)
Gene names: MPHOSPH6, MPP6
Sequence domains: M-phase phosphoprotein 6
Exosome RNA helicase MTR4 Chain: M
Molecule details ›
Chain: M
Length: 1045 amino acids
Theoretical weight: 118.22 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P42285 (Residues: 1-1042; Coverage: 100%)
Gene names: DOB1, KIAA0052, MTR4, MTREX, SKIV2L2
Sequence domains:
RNA (5'-R(*AP*GP*CP*AP*CP*CP*GP*UP*AP*AP*AP*GP*AP*CP*GP*C)-3') Chain: N
Molecule details ›
Chain: N
Length: 16 nucleotides
Theoretical weight: 5.14 KDa
DNA/RNA (62-MER) Chain: O
Molecule details ›
Chain: O
Length: 62 nucleotides
Theoretical weight: 19.49 KDa

Ligands and Environments

3 bound ligands:
Ligand MG 1 x MG
Ligand ZN 1 x ZN
Ligand ANP 1 x ANP
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.45Å
Relevant EMDB volumes: EMD-7808
Expression system: Escherichia coli

Quick links

Citations

19 review citations

Regulation of long non-coding RNAs and genome dynamics by the RNA surveillance machinery.
Nair et al. (2020)
18 more

10 mentions without citation

Post-transcriptional control of cellular differentiation by the RNA exosome complex.
Fraga de Andrade et al. (2020)
9 more