4A0C

Structure of the CAND1-CUL4B-RBX1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Molecular Basis of Crl4(Ddb2/Csa) Ubiquitin Ligase Architecture, Targeting, and Activation

Scrima, A.Fischer, E.S.Iwai, S.Gut, H.Thoma, N.H.

(2011) Cell 147: 1024

  • DOI: 10.1016/j.cell.2011.10.035
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The DDB1-CUL4-RBX1 (CRL4) ubiquitin ligase family regulates a diverse set of cellular pathways through dedicated substrate receptors (DCAFs). The DCAF DDB2 detects UV-induced pyrimidine dimers in the genome and facilitates nucleotide excision repair. ...

    The DDB1-CUL4-RBX1 (CRL4) ubiquitin ligase family regulates a diverse set of cellular pathways through dedicated substrate receptors (DCAFs). The DCAF DDB2 detects UV-induced pyrimidine dimers in the genome and facilitates nucleotide excision repair. We provide the molecular basis for DDB2 receptor-mediated cyclobutane pyrimidine dimer recognition in chromatin. The structures of the fully assembled DDB1-DDB2-CUL4A/B-RBX1 (CRL4(DDB2)) ligases reveal that the mobility of the ligase arm creates a defined ubiquitination zone around the damage, which precludes direct ligase activation by DNA lesions. Instead, the COP9 signalosome (CSN) mediates the CRL4(DDB2) inhibition in a CSN5 independent, nonenzymatic, fashion. In turn, CSN inhibition is relieved upon DNA damage binding to the DDB2 module within CSN-CRL4(DDB2). The Cockayne syndrome A DCAF complex crystal structure shows that CRL4(DCAF(WD40)) ligases share common architectural features. Our data support a general mechanism of ligase activation, which is induced by CSN displacement from CRL4(DCAF) on substrate binding to the DCAF.


    Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CULLIN-ASSOCIATED NEDD8-DISSOCIATED PROTEIN 1
A, B
1253Homo sapiensMutation(s): 0 
Gene Names: CAND1 (KIAA0829, TIP120, TIP120A)
Find proteins for Q86VP6 (Homo sapiens)
Go to Gene View: CAND1
Go to UniProtKB:  Q86VP6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CULLIN-4B
C, E
741Homo sapiensMutation(s): 0 
Gene Names: CUL4B (KIAA0695)
Find proteins for Q13620 (Homo sapiens)
Go to Gene View: CUL4B
Go to UniProtKB:  Q13620
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
E3 UBIQUITIN-PROTEIN LIGASE RBX1
D, F
98Mus musculusMutation(s): 0 
Gene Names: Rbx1
EC: 2.3.2.27, 2.3.2.32
Find proteins for P62878 (Mus musculus)
Go to UniProtKB:  P62878
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D, F
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.238 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 77.090α = 90.00
b = 152.360β = 89.37
c = 263.010γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2011-12-07
    Type: Database references
  • Version 1.2: 2017-08-23
    Type: Data collection