ISDA

Deposition Date 2011-09-08

Release Date 2011-11-30

Last Version Date 2023-12-20

Entry Detail

PDB ID:

4A08

Keywords:

DNA-BINDING PROTEIN/DNA

Title:

Structure of hsDDB1-drDDB2 bound to a 13 bp CPD-duplex (purine at D-1 position) at 3.0 A resolution (CPD 1)

Biological Source:

Source Organism:

HOMO SAPIENS (Taxon ID: 9606)
DANIO RERIO (Taxon ID: 7955)
synthetic construct (Taxon ID: 32630)

Host Organism:

TRICHOPLUSIA NI

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.00 Å

R-Value Free:

0.29

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA DAMAGE-BINDING PROTEIN 1
Gene (Uniprot):DDB1
Mutations:YES
Chain IDs:A
Chain Length:1159
Number of Molecules:1
Biological Source:HOMO SAPIENS

UniProt ID:Q16531 Pfam ID:PF10433, PF03178

Protein Blast

Polymer Type:polypeptide(L)
Molecule:DNA DAMAGE-BINDING PROTEIN 2
Gene (Uniprot):ddb2
Chain IDs:B
Chain Length:382
Number of Molecules:1
Biological Source:DANIO RERIO

UniProt ID:Q2YDS1 Pfam ID:PF00400

Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*AP*CP*GP*CP*GP*AP*(TTD)P*GP*CP*GP*CP*CP*C)-3'
Chain IDs:C (auth: G)
Chain Length:13
Number of Molecules:1
Biological Source:synthetic construct

Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*TP*GP*GP*GP*CP*GP*CP*CP*CP*TP*CP*GP*CP*G)-3'
Chain IDs:D (auth: H)
Chain Length:14
Number of Molecules:1
Biological Source:synthetic construct

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
TTD	C	DT	CIS-SYN CYCLOBUTANE THYMINE DIMER

Ligand Molecules

MES

Primary Citation

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.Show

Cell(Cambridge,Mass.) 147 1024 ? (2011)

PMID: 22118460 DOI: 10.1016/J.CELL.2011.10.035

Abstact

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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Primary Citation of related structures