PDBe 2nn6

X-ray diffraction
3.35Å resolution

Structure of the human RNA exosome composed of Rrp41, Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, and Rrp40

Released:
Source organism: Homo sapiens
Primary publication:
Reconstitution, activities, and structure of the eukaryotic RNA exosome.
Cell 127 1223-37 (2006)
PMID: 17174896

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero nonamer (preferred)
Entry contents:
9 distinct polypeptide molecules
Macromolecules (9 distinct):
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
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component RRP4 Chain: H
Molecule details ›
Chain: H
Length: 308 amino acids
Theoretical weight: 34.59 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13868 (Residues: 1-293; Coverage: 100%)
Gene names: EXOSC2, RRP4
Sequence domains:
Exosome complex component RRP40 Chain: G
Molecule details ›
Chain: G
Length: 289 amino acids
Theoretical weight: 31.23 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: KH domain
Structure domains: Nucleic acid-binding proteins
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: 2-245; Coverage: 100%)
Gene names: EXOSC4, RRP41, SKI6
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component RRP42 Chain: E
Molecule details ›
Chain: E
Length: 305 amino acids
Theoretical weight: 33.48 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 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 CSL4 Chain: I
Molecule details ›
Chain: I
Length: 209 amino acids
Theoretical weight: 23.1 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 RRP45 Chain: A
Molecule details ›
Chain: A
Length: 358 amino acids
Theoretical weight: 39.41 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q06265 (Residues: 1-302; Coverage: 69%)
Gene names: EXOSC9, PMSCL1
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P432
Unit cell:
a: 307.8Å b: 307.8Å c: 307.8Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.291 0.291 0.344
Expression system: Escherichia coli