› 6sxo

Electron Microscopy
3.3Å resolution

Cryo-EM structure of the human Ebp1-ribosome complex

Released:
DOI: 10.2210/pdb6sxo/pdb
PDB entry 6sxo coloured by chain, front view.
PDB entry 6sxo coloured by chain, side view.
PDB entry 6sxo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments.
Wild K, Aleksi�� M, Lapouge K, Juaire KD, Flemming D, Pfeffer S, Sinning I
Nat Commun 11 776 (2020)
PMID: 32034140
Related structures: EMD-10344

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
PDBe Complex ID:
PDB-CPX-154861 (preferred)
Entry contents:
6 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (8 distinct):
Proliferation-associated protein 2G4 Chain: A
Molecule details ›
Chain: A
Length: 394 amino acids
Theoretical weight: 43.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UQ80 (Residues: 1-394; Coverage: 100%)
Gene names: EBP1, PA2G4
Sequence domains: Metallopeptidase family M24
Large ribosomal subunit protein uL29 Chain: Lh
Molecule details ›
Chain: Lh
Length: 123 amino acids
Theoretical weight: 14.59 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P42766 (Residues: 1-123; Coverage: 100%)
Gene name: RPL35
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein eL38 Chain: Lk
Molecule details ›
Chain: Lk
Length: 70 amino acids
Theoretical weight: 8.24 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P63173 (Residues: 1-70; Coverage: 100%)
Gene name: RPL38
Sequence domains: Ribosomal L38e protein family
Large ribosomal subunit protein eL19 Chain: LR
Molecule details ›
Chain: LR
Length: 196 amino acids
Theoretical weight: 23.54 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P84098 (Residues: 1-196; Coverage: 100%)
Gene name: RPL19
Sequence domains: Ribosomal protein L19e
Large ribosomal subunit protein uL23 Chain: LX
Molecule details ›
Chain: LX
Length: 156 amino acids
Theoretical weight: 17.74 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62750 (Residues: 1-156; Coverage: 100%)
Gene name: RPL23A
Sequence domains:
Large ribosomal subunit protein uL24 Chain: LY
Molecule details ›
Chain: LY
Length: 145 amino acids
Theoretical weight: 17.3 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P61254 (Residues: 1-145; Coverage: 100%)
Gene name: RPL26
Sequence domains:
28S ribosomal RNA including ES27L-B (2839-3265) Chain: L5
Molecule details ›
Chain: L5
Length: 5070 nucleotides
Theoretical weight: 1640.22 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5.8S ribosomal RNA Chain: L8
Molecule details ›
Chain: L8
Length: 157 nucleotides
Theoretical weight: 50.45 KDa
Sequence domains: 5.8S ribosomal RNA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.3Å
Relevant EMDB volumes: EMD-10344
Expression system: Escherichia coli

Quick links

Citations

3 review citations

The roles of multifunctional protein ErbB3 binding protein 1 (EBP1) isoforms from development to disease.
Hwang et al. (2020)
2 more

7 mentions without citation

A structural view of PA2G4 isoforms with opposing functions in cancer.
Stevenson et al. (2020)
6 more