› 8jaq

Electron Microscopy
3.26Å resolution

Structure of CRL2APPBP2 bound with RxxGP degron (tetramer)

Released:
DOI: 10.2210/pdb8jaq/pdb
PDB entry 8jaq coloured by chain, front view.
PDB entry 8jaq coloured by chain, side view.
PDB entry 8jaq coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular basis for C-degron recognition by CRL2APPBP2 ubiquitin ligase.
Zhao S, Olmayev-Yaakobov D, Ru W, Li S, Chen X, Zhang J, Yao X, Koren I, Zhang K, Xu C
Proc Natl Acad Sci U S A 120 e2308870120 (2023)
PMID: 37844242
Related structures: EMD-36131

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
S-[NEDD8-protein]-yl-[E2 NEDD8-conjugating enzyme]-L-cysteine + [cullin]-L-lysine = [E2 NEDD8-conjugating enzyme]-L-cysteine + N(6)-[NEDD8-protein]-yl-[cullin]-L-lysine
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 22-mer (preferred)
PDBe Complex ID:
PDB-CPX-274094 (preferred)
Entry contents:
6 distinct polypeptide molecules
Macromolecules (6 distinct):
Amyloid protein-binding protein 2 Chains: A, B, J, K
Molecule details ›
Chains: A, B, J, K
Length: 578 amino acids
Theoretical weight: 66.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q92624 (Residues: 1-578; Coverage: 99%)
Gene names: APPBP2, KIAA0228, PAT1
Sequence domains:
Cullin-2 Chains: E, I, L, U
Molecule details ›
Chains: E, I, L, U
Length: 745 amino acids
Theoretical weight: 87.07 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13617 (Residues: 2-745; Coverage: 100%)
Gene name: CUL2
Sequence domains:
Elongin-B Chains: C, G, M, Q
Molecule details ›
Chains: C, G, M, Q
Length: 118 amino acids
Theoretical weight: 13.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15370 (Residues: 1-118; Coverage: 100%)
Gene names: ELOB, TCEB2
Sequence domains: Ubiquitin family
Elongin-C Chains: D, H, N, T
Molecule details ›
Chains: D, H, N, T
Length: 96 amino acids
Theoretical weight: 10.84 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15369 (Residues: 17-112; Coverage: 86%)
Gene names: ELOC, TCEB1
Sequence domains: Skp1 family, tetramerisation domain
XP_211896 C-degron Chains: F, O, P, S
Molecule details ›
Chains: F, O, P, S
Length: 16 amino acids
Theoretical weight: 1.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
E3 ubiquitin-protein ligase RBX1 Chains: R, V
Molecule details ›
Chains: R, V
Length: 108 amino acids
Theoretical weight: 12.29 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62877 (Residues: 1-108; Coverage: 100%)
Gene names: RBX1, RNF75, ROC1
Sequence domains: RING-H2 zinc finger domain

Ligands and Environments

1 bound ligand:
Ligand ZN 8 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.26Å
Relevant EMDB volumes: EMD-36131
Expression system: Escherichia coli

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