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(-)Asym./Biol. Unit
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(-) Description

Title :  CRYSTAL STRUCTURE OF A UBX-EXD-DNA COMPLEX INCLUDING THE HEXAPEPTIDE AND UBDA MOTIFS
 
Authors :  N. Foos, M. J. Mate, M. Ortiz-Lombardia
Date :  10 Apr 14  (Deposition) - 18 Feb 15  (Release) - 18 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.36
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transcription, Hox, Pbc, Dna Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Foos, C. Maurel-Zaffran, M. J. Mate, R. Vincentelli, M. Hainaut, H. Berenger, J. Pradel, A. J. Saurin, M. Ortiz-Lombardia, Y. Graba
A Flexible Extension Of The Drosophila Ultrabithorax Homeodomain Defines A Novel Hox/Pbc Interaction Mode.
Structure V. 23 270 2015
PubMed-ID: 25651060  |  Reference-DOI: 10.1016/J.STR.2014.12.011

(-) Compounds

Molecule 1 - HOMEOTIC PROTEIN ULTRABITHORAX
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: UBXIVA PDEST14
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PLYSS
    Expression System Vector Type: PLASMID
    Fragment: HOMEODOMAIN WITH HX AND UBDA, RESIDUES 233-367
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
 
Molecule 2 - 5'-D(*GP*TP*CP*GP*CP*CP*AP*TP*AP*AP*AP*TP*CP*AP*CP)-3'
    Chains: C
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synthetic: YES
 
Molecule 3 - 5'-D(*AP*CP*GP*TP*GP*AP*TP*TP*TP*AP*TP*GP*GP*CP*GP)-3'
    Chains: D
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synthetic: YES
 
Molecule 4 - HOMEOBOX PROTEIN EXTRADENTICLE
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: EXD2 PETG20A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA PLYSS
    Fragment: HOMEODOMAIN RESIDUES 238-312
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: DPBX, HOMEOTIC PROTEIN EXTRADENTICLE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4CYC)

(-) Sites  (0, 0)

(no "Site" information available for 4CYC)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CYC)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CYC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CYC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CYC)

(-) Exons   (0, 0)

(no "Exon" information available for 4CYC)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:66
                                                                                                  
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 4cyc A -12 FYPWMARQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK  64
                                 ||  8        18        28        38        48        58      
                                -7|                                                           
                                  5                                                           


Chain B from PDB  Type:PROTEIN  Length:58
                                                                                          
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 4cyc B   3 RNFSKQASEILNEYFYSHLSNPYPSEEAKEELARKCGITVSQVSNWFGNKRIRYKKNI  60
                                    12        22        32        42        52        


Chain C from PDB  Type:DNA  Length:15
                                               
                 4cyc C   1 GTCGCCATAAATCAC  15
                                    10     


Chain D from PDB  Type:DNA  Length:15
                                               
                 4cyc D  16 ACGTGATTTATGGCG  30
                                    25
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4CYC)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CYC)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CYC)

(-) Gene Ontology  (48, 59)

Asymmetric/Biological Unit(hide GO term definitions)

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  UBX_DROME | P83949
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        EXD_DROME | P40427: 1b8i 2r5y 2r5z 4uus
        UBX_DROME | P83949: 1b8i 4uus 4uut

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4CYC)