6DSZ

Crystal structure of DDB1 in complex with DET1- and DDB1-associated protein 1 (DDA1)

• PDB DOI: https://doi.org/10.2210/pdb6DSZ/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2018-06-14 Released: 2018-12-12 
• Deposition Author(s): Shabek, N., Zheng, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.09 Å
• R-Value Free: 0.307 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 

Literature

Structural insights into DDA1 function as a core component of the CRL4-DDB1 ubiquitin ligase.

Shabek, N., Ruble, J., Waston, C.J., Garbutt, K.C., Hinds, T.R., Li, T., Zheng, N.

(2018) Cell Discov 4: 67-67

• PubMed: 30564455 
• DOI: https://doi.org/10.1038/s41421-018-0064-8
• Primary Citation of Related Structures:  
  6DSZ

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Organizational Affiliation: 

1Department of Pharmacology, University of Washington, Box 357280, Seattle, WA 98195 USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: immunoprecipitation

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 258.67 kDa 
• Atom Count: 17,408 
• Modelled Residue Count: 2,217 
• Deposited Residue Count: 2,318 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	A, B	1,140	Homo sapiens	Mutation(s): 0  Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531  Go to UniProtKB:  Q16531
PHAROS:  Q16531 GTEx:  ENSG00000167986

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DET1- and DDB1-associated protein 1	C, D	19	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BW61 (Homo sapiens) Explore Q9BW61  Go to UniProtKB:  Q9BW61
PHAROS:  Q9BW61 GTEx:  ENSG00000130311

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.09 Å
• R-Value Free: 0.307 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.196	α = 90
b = 219.175	β = 89.98
c = 89.317	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Shabek, N., Zheng, N.

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2019-01-02
  Changes: Data collection, Database references
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description