4A0K	Ligase Dna-Binding Protein Dna	date	Sep 09, 2011
title	Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic Si Containing Dna-Duplex
authors	E.S.Fischer, A.Scrima, H.Gut, N.H.Thoma
compound		source
Molecule: Cullin-4a Chain: A Fragment: Residues 38-759 Synonym: Cullin Homolog 4a, Cul-4a Engineered: Yes		Organism_scientific: Homo Sapiens Organism_taxid: 9606 Expression_system: Trichoplusia Ni Expression_system_common: Cabbage Looper Expression_system_taxid: 7111 Expression_system_cell_line: High Five Expression_system_vector_type: Baculovirus Expression_system_plasmid: Pfastbac Derived
Molecule: E3 Ubiquitin-Protein Ligase Rbx1 Chain: B Fragment: Residues 12-108 Synonym: Ring Finger Protein 75, Ring-Box Protein 1, Rbx1 Ec: 6.3.2.- Engineered: Yes		Organism_scientific: Mus Musculus Organism_common: House Mouse Organism_taxid: 10090 Expression_system: Trichoplusia Ni Expression_system_common: Cabbage Looper Expression_system_taxid: 7111 Expression_system_cell_line: High Five Expression_system_vector_type: Baculovirus Expression_system_plasmid: Pfastbac Derived
Molecule: Dna Damage-Binding Protein 1 Chain: C Synonym: Ddb P127 Subunit, Dna Damage-Binding Protein A, Dd Damage-Specific Dna-Binding Protein 1, Hbv X-Associated Pro Xap-1, Uv-Damaged Dna-Binding Factor, Uv-Damaged Dna-Bindin 1, Uv-Ddb 1, Xpe-Binding Factor, Xpe-Bf, Xeroderma Pigmento E-Complementing Protein, Xpce; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_taxid: 9606 Expression_system: Trichoplusia Ni Expression_system_taxid: 7111 Expression_system_cell_line: High Five Expression_system_vector_type: Baculovirus Expression_system_plasmid: Pfastbac Derived
Molecule: Dna Damage-Binding Protein 2 Chain: D Fragment: Residues 60-423 Synonym: Damage-Specific Dna-Binding Protein 2 Engineered: Yes Other_details: Variant With Gln At Position 180 And Arg At 214 (Similar To Pdb Entry 3ei2);		Organism_scientific: Danio Rerio Organism_common: Zebrafish Organism_taxid: 7955 Expression_system: Trichoplusia Ni Expression_system_taxid: 7111 Expression_system_cell_line: High Five Expression_system_vector_type: Baculovirus Expression_system_plasmid: Pfastbac Derived
Molecule: 12 Bp Thf Containing Dna Chain: E Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: 12 Bp Dna Chain: F Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
symmetry	Space Group: C 1 2 1	R_factor 0.269 R_Free 0.270
crystal cell	length a length b length c angle alpha angle beta angle gamma 210.650 78.020 276.620 90.00 108.50 90.00
method	X-Ray Diffraction	resolution	5.93 Å
ligand	3DR	enzyme	Ligase E.C.6.3.2 BRENDA
Gene Ontology	Chain Function Process Component A B C D
Primary reference	The Molecular Basis of CRL4(DDB2/CSA) Ubiquitin Ligase Architecture, Targeting, and Activation., Fischer ES, Scrima A, Bohm K, Matsumoto S, Lingaraju GM, Faty M, Yasuda T, Cavadini S, Wakasugi M, Hanaoka F, Iwai S, Gut H, Sugasawa K, Thoma NH, Cell. 2011 Nov 23;147(5):1024-39. PMID:22118460

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (772 Kb) [Save to disk] Biological Unit Coordinates (4a0k.pdb1.gz) 763 Kb LPC: Ligand-Protein Contacts for 4A0K CSU: Contacts of Structural Units for 4A0K Structure Factors (93 Kb) Retrieve 4A0K in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 4A0K from S2C, [Save to disk] Re-refined 4a0k structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 4A0K in 3D

Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 4A0K

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 4A0K, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [4a0k_C] [4a0k_F] [4a0k_D] [4a0k_E] [4a0k_A] [4a0k_B] [4a0k] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 4A0K: [CULLIN] [Cullin_Nedd8] [RING] [WD40 ] by SMART

Other resources with information on 4A0K

Community annotation for 4A0K at PDBWiki (http://pdbwiki.org)

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