2HYE: Crystal Structure Of The Ddb1-cul4a-rbx1-sv5v Complex

Protein ubiquitination is a common form of post-translational modification that regulates a broad spectrum of protein substrates in diverse cellular pathways. Through a three-enzyme (E1-E2-E3) cascade, the attachment of ubiquitin to proteins is catalysed by the E3 ubiquitin ligase, which is best represented by the superfamily of the cullin-RING complexes. Conserved from yeast to human, the DDB1-CUL4-ROC1 complex is a recently identified cullin-RING ubiquitin ligase, which regulates DNA repair, DNA replication and transcription, and can also be subverted by pathogenic viruses to benefit viral infection. Lacking a canonical SKP1-like cullin adaptor and a defined substrate recruitment module, how the DDB1-CUL4-ROC1 E3 apparatus is assembled for ubiquitinating various substrates remains unclear. Here we present crystallographic analyses of the virally hijacked form of the human DDB1-CUL4A-ROC1 machinery, which show that DDB1 uses one beta-propeller domain for cullin scaffold binding and a variably attached separate double-beta-propeller fold for substrate presentation. Through tandem-affinity purification of human DDB1 and CUL4A complexes followed by mass spectrometry analysis, we then identify a novel family of WD40-repeat proteins, which directly bind to the double-propeller fold of DDB1 and serve as the substrate-recruiting module of the E3. Together, our structural and proteomic results reveal the structural mechanisms and molecular logic underlying the assembly and versatility of a new family of cullin-RING E3 complexes.
PDB ID: 2HYEDownload
MMDB ID: 41721
PDB Deposition Date: 2006/8/5
Updated in MMDB: 2007/11
Experimental Method:
x-ray diffraction
Resolution: 3.1  Å
Source Organism:
Mammalian rubulavirus 5
Similar Structures:
Biological Unit for 2HYE: tetrameric; determined by author
Molecular Components in 2HYE
Label Count Molecule
Proteins (4 molecules)
DNA Damage-binding Protein 1(Gene symbol: DDB1)
Molecule annotation
Nonstructural Protein V(Gene symbol: V/P)
Molecule annotation
Cullin-4a(Gene symbol: CUL4A)
Molecule annotation
Ring-box Protein 1(Gene symbol: RBX1)
Molecule annotation
Chemicals (5 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB