5okz

X-ray diffraction
3.2Å resolution

Crystal Strucrure of the Mpp6 Exosome complex

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero decamer (preferred)
PDBe Complex ID:
PDB-CPX-150441 (preferred)
Entry contents:
10 distinct polypeptide molecules
Macromolecules (10 distinct):
Exosome complex component CSL4 Chains: I, S, c, m
Molecule details ›
Chains: I, S, c, m
Length: 295 amino acids
Theoretical weight: 31.91 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P53859 (Residues: 1-292; Coverage: 100%)
Gene names: CSL4, N1154, SKI4, YNL232W
Sequence domains:
Exosome complex component RRP45 Chains: A, K, U, e
Molecule details ›
Chains: A, K, U, e
Length: 305 amino acids
Theoretical weight: 34 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q05636 (Residues: 1-305; Coverage: 100%)
Gene names: D9954.1, RRP45, YDR280W
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component SKI6 Chains: B, L, V, f
Molecule details ›
Chains: B, L, V, f
Length: 249 amino acids
Theoretical weight: 27.89 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P46948 (Residues: 1-246; Coverage: 100%)
Gene names: ECM20, G7587, RRP41, SKI6, YGR195W
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component RRP43 Chains: C, M, W, g
Molecule details ›
Chains: C, M, W, g
Length: 394 amino acids
Theoretical weight: 44.09 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P25359 (Residues: 1-394; Coverage: 100%)
Gene names: RRP43, YCR035C, YCR35C, YCR522
Sequence domains: 3' exoribonuclease family, domain 1
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component RRP46 Chains: D, N, X, h
Molecule details ›
Chains: D, N, X, h
Length: 226 amino acids
Theoretical weight: 24.66 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P53256 (Residues: 1-223; Coverage: 100%)
Gene names: RRP46, YGR095C
Sequence domains:
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component RRP42 Chains: E, O, Y, i
Molecule details ›
Chains: E, O, Y, i
Length: 268 amino acids
Theoretical weight: 29.39 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q12277 (Residues: 1-265; Coverage: 100%)
Gene names: RRP42, YDL111C
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component MTR3 Chains: F, P, Z, j
Molecule details ›
Chains: F, P, Z, j
Length: 250 amino acids
Theoretical weight: 27.57 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P48240 (Residues: 1-250; Coverage: 100%)
Gene names: G6676, MTR3, YGR158C
Sequence domains: 3' exoribonuclease family, domain 1
Structure domains: GHMP Kinase, N-terminal domain
Exosome complex component RRP40 Chains: G, Q, a, k
Molecule details ›
Chains: G, Q, a, k
Length: 244 amino acids
Theoretical weight: 26.94 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q08285 (Residues: 1-240; Coverage: 100%)
Gene names: RRP40, YOL142W
Sequence domains:
Structure domains:
Exosome complex component RRP4 Chains: H, R, b, l
Molecule details ›
Chains: H, R, b, l
Length: 316 amino acids
Theoretical weight: 34.6 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P38792 (Residues: 50-359; Coverage: 86%)
Gene names: RRP4, YHR069C
Sequence domains:
Structure domains: OB fold (Dihydrolipoamide Acetyltransferase, E2P)
M-phase phosphoprotein 6 homolog Chains: J, T, d, n
Molecule details ›
Chains: J, T, d, n
Length: 190 amino acids
Theoretical weight: 21.54 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P53725 (Residues: 1-186; Coverage: 100%)
Gene names: MPP6, N3230, YNR024W
Sequence domains: M-phase phosphoprotein 6

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21
Unit cell:
a: 161.779Å b: 237.43Å c: 201.895Å
α: 90° β: 110.37° γ: 90°
R-values:
R R work R free
0.224 0.223 0.262
Expression system: Escherichia coli BL21(DE3)