› 5anc

Electron Microscopy
4.2Å resolution

Mechanism of eIF6 release from the nascent 60S ribosomal subunit

Released:
DOI: 10.2210/pdb5anc/pdb
PDB entry 5anc coloured by chain, front view.
PDB entry 5anc coloured by chain, side view.
PDB entry 5anc coloured by chain, top view.
Source organisms:
Primary publication:
Mechanism of eIF6 release from the nascent 60S ribosomal subunit.
Weis F, Giudice E, Churcher M, Jin L, Hilcenko C, Wong CC, Traynor D, Kay RR, Warren AJ
Nat Struct Mol Biol 22 914-9 (2015)
PMID: 26479198
Related structures: EMD-3147

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero undecamer (preferred)
PDBe Complex ID:
PDB-CPX-147100 (preferred)
Entry contents:
10 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (11 distinct):
Large ribosomal subunit protein uL3 Chain: A
Molecule details ›
Chain: A
Length: 398 amino acids
Theoretical weight: 45.16 KDa
Source organism: Dictyostelium discoideum
UniProt:
  • Canonical: P34113 (Residues: 1-398; Coverage: 100%)
Gene names: DDB_G0291862, rpl3
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL6 Chain: B
Molecule details ›
Chain: B
Length: 188 amino acids
Theoretical weight: 21.25 KDa
Source organism: Dictyostelium discoideum
UniProt:
  • Canonical: Q54XI5 (Residues: 1-188; Coverage: 100%)
Gene names: DDB_G0278959, rpl9
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein uL10 Chain: C
Molecule details ›
Chain: C
Length: 205 amino acids
Theoretical weight: 22.43 KDa
Source organism: Dictyostelium discoideum
UniProt:
  • Canonical: P22685 (Residues: 1-205; Coverage: 67%)
Gene names: DDB_G0286501, rplp0
Sequence domains:
Large ribosomal subunit protein uL11 Chain: D
Molecule details ›
Chain: D
Length: 166 amino acids
Theoretical weight: 17.81 KDa
Source organism: Dictyostelium discoideum
UniProt:
  • Canonical: Q54J50 (Residues: 1-166; Coverage: 100%)
Gene names: DDB_G0288295, rpl12
Sequence domains:
Large ribosomal subunit protein uL14 Chain: E
Molecule details ›
Chain: E
Length: 136 amino acids
Theoretical weight: 14.57 KDa
Source organism: Dictyostelium discoideum
UniProt:
  • Canonical: Q54G86 (Residues: 1-136; Coverage: 100%)
Gene names: DDB_G0290315, rpl23
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL16 Chain: F
Molecule details ›
Chain: F
Length: 217 amino acids
Theoretical weight: 24.59 KDa
Source organism: Dictyostelium discoideum
UniProt:
  • Canonical: Q54J69 (Residues: 1-217; Coverage: 100%)
Gene names: DDB_G0288273, rpl10, rpl10e
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein eL24 Chain: G
Molecule details ›
Chain: G
Length: 69 amino acids
Theoretical weight: 8.33 KDa
Source organism: Dictyostelium discoideum
UniProt:
  • Canonical: Q54VN6 (Residues: 1-69; Coverage: 54%)
Gene names: DDB_G0280229, rpl24
Sequence domains: Ribosomal protein L24e
Large ribosomal subunit protein eL40 Chain: H
Molecule details ›
Chain: H
Length: 52 amino acids
Theoretical weight: 6.17 KDa
Source organism: Dictyostelium discoideum
UniProt:
  • Canonical: P14794 (Residues: 77-128; Coverage: 41%)
Gene names: DDB_G0280755, ubqB
Sequence domains: Ribosomal L40e family
Ribosome maturation protein SBDS Chain: J
Molecule details ›
Chain: J
Length: 250 amino acids
Theoretical weight: 28.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9Y3A5 (Residues: 1-250; Coverage: 100%)
Gene names: CGI-97, SBDS
Sequence domains:
Elongation factor-like GTPase 1 Chain: K
Molecule details ›
Chain: K
Length: 1120 amino acids
Theoretical weight: 125.58 KDa
Source organism: Homo sapiens
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q7Z2Z2 (Residues: 1-1120; Coverage: 100%)
Gene names: EFL1, EFTUD1, FAM42A
Sequence domains:
26S RIBOSOMAL RNA Chain: N
Molecule details ›
Chain: N
Length: 3741 nucleotides
Theoretical weight: 1206 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.2Å
Relevant EMDB volumes: EMD-3147
Expression systems:
  • Escherichia coli BL21(DE3)
  • Saccharomyces cerevisiae

Quick links

Citations

38 review citations

Shwachman-Diamond Syndrome: Molecular Mechanisms and Current Perspectives.
Bezzerri et al. (2019)
37 more

6 mentions without citation

Mechanistic insight into eukaryotic 60S ribosomal subunit biogenesis by cryo-electron microscopy.
Greber BJ. (2016)
5 more