4A0L Ligase Dna-Binding Protein Dna date Sep 09, 2011
title Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic Site Containing Dna-Duplex
authors E.S.Fischer, A.Scrima, H.Gut, N.H.Thoma
compound source
Molecule: Dna Damage-Binding Protein 1
Chain: A, C
Synonym: Ddb P127 Subunit, Dna Damage-Binding Protein A, Dd Damage-Specific Dna-Binding Protein 1, Hbv X-Associated Pr Xap-1, Uv-Damaged Dna-Binding Factor, Uv-Damaged Dna-Bindi Protein 1, Uv-Ddb 1, Xpe-Binding Factor, Xpe-Bf, Xeroderma Pigmentosum Group E-Complementing Protein, Xpce;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_strain: Cabbage Looper
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac Derived

Molecule: Dna Damage-Binding Protein 2
Chain: B, 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_strain: Cabbage Looper
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac Derived

Molecule: Cullin-4b
Chain: E, H
Fragment: Residues 193-913
Synonym: Cullin Homolog 4b, Cul-4b
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_strain: Cabbage Looper
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac Derived

Molecule: E3 Ubiquitin-Protein Ligase Rbx1
Chain: F, I
Fragment: Residues 12-108
Synonym: Ring Finger Protein 75, Ring-Box Protein 1, Rbx1
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Expression_system: Trichoplusia Ni
Expression_system_taxid: 7111
Expression_system_strain: Cabbage Looper
Expression_system_cell_line: High Five
Expression_system_vector_type: Baculovirus
Expression_system_plasmid: Pfastbac Derived

Molecule: 12 Bp Thf Containing Dna Duplex
Chain: R, T

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 12 Bp Dna Duplex
Chain: S, U

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 21 1
R_factor 0.3178 R_Free 0.3199
crystal
cell
length a length b length c angle alpha angle beta angle gamma
130.800 155.840 255.390 90.00 94.17 90.00
method X-Ray Diffractionresolution 7.40 Å
ligand 3DR enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, C


F, I


H, E


Primary referenceThe 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] (1577 Kb) [Save to disk]
  • Biological Unit Coordinates (4a0l.pdb1.gz) 788 Kb
  • Biological Unit Coordinates (4a0l.pdb2.gz) 789 Kb
  • LPC: Ligand-Protein Contacts for 4A0L
  • CSU: Contacts of Structural Units for 4A0L
  • Structure Factors (111 Kb)
  • Retrieve 4A0L in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4A0L from S2C, [Save to disk]
  • Re-refined 4a0l structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4A0L 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 4A0L
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4A0L, from MSDmotif at EBI
  • Fold representative 4a0l from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4a0l_F] [4a0l_A] [4a0l_E] [4a0l_U] [4a0l_T] [4a0l_S] [4a0l] [4a0l_H] [4a0l_C] [4a0l_B] [4a0l_I] [4a0l_D] [4a0l_R]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 4A0L with the sequences similar proteins can be viewed for 4A0L's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 4A0L
  • Community annotation for 4A0L at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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