› 9d1i

X-ray diffraction
2Å resolution

Structure of Ubiquitin bound to KLHDC3-EloB/C

Released:
DOI: 10.2210/pdb9d1i/pdb
Model geometry
Fit model/data
PDB entry 9d1i coloured by chain, front view.
PDB entry 9d1i coloured by chain, side view.
PDB entry 9d1i coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis for C-degron selectivity across KLHDCX family E3 ubiquitin ligases.
Scott DC, Chittori S, Purser N, King MT, Maiwald SA, Churion K, Nourse A, Lee C, Paulo JA, Miller DJ, Elledge SJ, Harper JW, Kleiger G, Schulman BA
Nat Commun 15 9899 (2024)
PMID: 39548056

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-281507 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Kelch domain-containing protein 3 Chain: A
Molecule details ›
Chain: A
Length: 383 amino acids
Theoretical weight: 43.25 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9BQ90 (Residues: 1-382; Coverage: 100%)
Gene names: KLHDC3, PEAS
Sequence domains:
Elongin-B Chain: B
Molecule details ›
Chain: B
Length: 104 amino acids
Theoretical weight: 11.75 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q15370 (Residues: 1-104; Coverage: 88%)
Gene names: ELOB, TCEB2
Sequence domains: Ubiquitin family
Elongin-C Chain: C
Ubiquitin Chain: D

Ligands and Environments

1 bound ligand:
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 24-ID-E
Spacegroup: C2221
Unit cell:
a: 114.709Å b: 121.44Å c: 153.142Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.168 0.167 0.189
Expression systems:
  • Trichoplusia ni
  • Escherichia coli

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