6ttu

Electron Microscopy
3.7Å resolution

Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2

Released:

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
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
PDBe Complex ID:
PDB-CPX-124769 (preferred)
Entry contents:
8 distinct polypeptide molecules
Macromolecules (8 distinct):
F-box/WD repeat-containing protein 1A Chain: T
Molecule details ›
Chain: T
Length: 605 amino acids
Theoretical weight: 68.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9Y297 (Residues: 1-605; Coverage: 100%)
Gene names: BTRC, BTRCP, FBW1A, FBXW1A
Sequence domains:
S-phase kinase-associated protein 1 Chain: S
Molecule details ›
Chain: S
Length: 163 amino acids
Theoretical weight: 18.68 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P63208 (Residues: 1-163; Coverage: 100%)
Gene names: EMC19, OCP2, SKP1, SKP1A, TCEB1L
Sequence domains:
Cullin-1 Chain: C
Molecule details ›
Chain: C
Length: 776 amino acids
Theoretical weight: 89.8 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13616 (Residues: 1-776; Coverage: 100%)
Gene name: CUL1
Sequence domains:
NEDD8 Chain: N
Molecule details ›
Chain: N
Length: 77 amino acids
Theoretical weight: 8.66 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q15843 (Residues: 1-76; Coverage: 94%)
Gene name: NEDD8
Sequence domains: Ubiquitin family
RING-type domain-containing protein Chain: R
Molecule details ›
Chain: R
Length: 108 amino acids
Theoretical weight: 12.33 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: H2QLR9 (Residues: 1-108; Coverage: 100%)
Gene name: RBX1
Sequence domains: RING-H2 zinc finger domain
Ubiquitin-conjugating enzyme E2 D2 Chain: D
Molecule details ›
Chain: D
Length: 147 amino acids
Theoretical weight: 16.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
Ubiquitin Chain: U
Molecule details ›
Chain: U
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
NF-kappa-B inhibitor alpha Chain: I
Molecule details ›
Chain: I
Length: 30 amino acids
Theoretical weight: 3.78 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P25963 (Residues: 21-41; Coverage: 7%)
Gene names: IKBA, MAD3, NFKBI, NFKBIA

Ligands and Environments

1 bound ligand:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
Resolution: 3.7Å
Relevant EMDB volumes: EMD-10585
Expression systems:
  • Escherichia coli
  • Trichoplusia ni
  • Not provided