Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 280.34 kDa 
• Atom Count: 17885 
• Residue Count: 2224 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

4A0K

STRUCTURE OF DDB1-DDB2-CUL4A-RBX1 BOUND TO A 12 BP ABASIC SITE CONTAINING DNA-DUPLEX

• DOI: 10.2210/pdb4A0K/pdb
• NDB: NA1436

• Classification: LIGASE/DNA-BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, Mus musculus, Danio rerio, synthetic construct
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2011-09-09 Released: 2011-12-14 
• Deposition Author(s): Fischer, E.S., Scrima, A., Gut, H., Thoma, N.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 5.93 Å
• R-Value Free: 0.270 
• R-Value Work: 0.269 
• R-Value Observed: 0.269 

Literature

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

Fischer, E.S., Scrima, A., Bohm, K., Matsumoto, S., Lingaraju, G.M., Faty, M., Yasuda, T., Cavadini, S., Wakasugi, M., Hanaoka, F., Iwai, S., Gut, H., Sugasawa, K., Thoma, N.H.

(2011) Cell 147: 1024

• PubMed: 22118460 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CULLIN-4A	A	742	Homo sapiens	Mutation(s): 0  Gene Names: CUL4A
Find proteins for Q13619 (Homo sapiens) Explore Q13619  Go to UniProtKB:  Q13619
NIH Common Fund Data Resources
PHAROS:  Q13619 GTEx:  ENSG00000139842

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 UBIQUITIN-PROTEIN LIGASE RBX1	B	117	Mus musculus	Mutation(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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA DAMAGE-BINDING PROTEIN 1	C	1159	Homo sapiens	Mutation(s): 0  Gene Names: DDB1, XAP1
Find proteins for Q16531 (Homo sapiens) Explore Q16531  Go to UniProtKB:  Q16531
NIH Common Fund Data Resources
PHAROS:  Q16531 GTEx:  ENSG00000167986

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA DAMAGE-BINDING PROTEIN 2	D	382	Danio rerio	Mutation(s): 2  Gene Names: ddb2, si:dkey-45f10.3
Find proteins for Q2YDS1 (Danio rerio) Explore Q2YDS1  Go to UniProtKB:  Q2YDS1

Entity ID: 5
Molecule	Chains	Length	Organism	Image
12 BP THF CONTAINING DNA	E	12	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
12 BP DNA	F	12	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 5.93 Å
• R-Value Free: 0.270 
• R-Value Work: 0.269 
• R-Value Observed: 0.269 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 210.65	α = 90
b = 78.02	β = 108.5
c = 276.62	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-09-09 
• Released Date: 2011-12-14 
Deposition Author(s): Fischer, E.S., Scrima, A., Gut, H., Thoma, N.H.

Revision History 

• Version 1.0: 2011-12-14
  Type: Initial release
  
• Version 1.1: 2019-04-03
  Changes: Data collection, Derived calculations, Other, Source and taxonomy