4A0C

Structure of the CAND1-CUL4B-RBX1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.3 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:  
    4A0A, 4A0B, 4A08, 4A09, 4A0K, 4A0L, 4A11, 4A0C

  • 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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CULLIN-ASSOCIATED NEDD8-DISSOCIATED PROTEIN 1AB1253Homo sapiensMutation(s): 1 
Gene Names: CAND1KIAA0829TIP120TIP120A
Find proteins for Q86VP6 (Homo sapiens)
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Go to UniProtKB:  Q86VP6
NIH Common Fund Data Resources
PHAROS  Q86VP6
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CULLIN-4BCE741Homo sapiensMutation(s): 0 
Gene Names: CUL4BKIAA0695
Find proteins for Q13620 (Homo sapiens)
Explore Q13620 
Go to UniProtKB:  Q13620
NIH Common Fund Data Resources
PHAROS  Q13620
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
E3 UBIQUITIN-PROTEIN LIGASE RBX1DF98Mus musculusMutation(s): 0 
Gene Names: Rbx1
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt), 2.3.2.32 (UniProt)
Find proteins for P62878 (Mus musculus)
Explore P62878 
Go to UniProtKB:  P62878
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.319 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.242 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.09α = 90
b = 152.36β = 89.37
c = 263.01γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-30
    Type: Initial release
  • Version 1.1: 2011-12-07
    Changes: Database references
  • Version 1.2: 2017-08-23
    Changes: Data collection
  • Version 1.3: 2019-04-03
    Changes: Data collection, Source and taxonomy