6DSZ | pdb_00006dsz

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free:
0.307 (Depositor), 0.310 (DCC)
R-Value Work:
0.247 (Depositor), 0.249 (DCC)
R-Value Observed:
0.250 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6DSZ

This is version 1.3 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41421-018-0064-8
Primary Citation Related Structures:
6DSZ

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16531
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9BW61
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.09 Å
R-Value Free: 0.307 (Depositor), 0.310 (DCC)
R-Value Work: 0.247 (Depositor), 0.249 (DCC)
R-Value Observed: 0.250 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2018-12-12

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.3: 2024-11-06
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.