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(-) Description

Title :  CRYSTAL STRUCTURE OF ARISTALESS AND CLAWLESS HOMEODOMAINS BOUND TO DNA
 
Authors :  K. Miyazono, K. Nagata, K. Saigo, T. Kojima, M. Tanokura
Date :  28 Feb 09  (Deposition) - 09 Mar 10  (Release) - 19 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Homeodomain, Protein-Dna Complex, Dna-Binding, Homeobox, Nucleus, Developmental Protein, Gene Regulation-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Miyazono, Y. Zhi, Y. Takamura, K. Nagata, K. Saigo, T. Kojima, M. Tanokura
Cooperative Dna-Binding And Sequence-Recognition Mechanism Of Aristaless And Clawless
Embo J. V. 29 1613 2010
PubMed-ID: 20389279  |  Reference-DOI: 10.1038/EMBOJ.2010.53

(-) Compounds

Molecule 1 - HOMEODOMAIN-CONTAINING PROTEIN
    ChainsA, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCLAWLESS HOMEOBOX, RESIDUES 170-261
    GeneC15, CG7937
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
 
Molecule 2 - HOMEOBOX PROTEIN ARISTALESS
    ChainsB, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentHOMEOBOX, RESIDUES 80-146
    GeneAL, CG3935
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
 
Molecule 3 - 5'-D(*GP*GP*CP*TP*TP*AP*AP*TP*TP*AP*AP*TP*TP*GP*CP*GP*G)- 3'
    ChainsC, G
    EngineeredYES
    SyntheticYES
 
Molecule 4 - 5'-D(*CP*CP*GP*CP*AP*AP*TP*TP*AP*AP*TP*TP*AP*AP*GP*CP*C)- 3'
    ChainsD, H
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)ABCD    
Biological Unit 2 (1x)    EFGH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3A01)

(-) Sites  (0, 0)

(no "Site" information available for 3A01)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3A01)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:186 -Lys A:187
2Arg E:189 -Thr E:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3A01)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_1PS00027 'Homeobox' domain signature.AL_DROME118-141
 
  2B:118-141
F:118-141
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_1PS00027 'Homeobox' domain signature.AL_DROME118-141
 
  1B:118-141
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_1PS00027 'Homeobox' domain signature.AL_DROME118-141
 
  1-
F:118-141

(-) Exons   (0, 0)

(no "Exon" information available for 3A01)

(-) Sequences/Alignments

Asymmetric 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    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
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:78
 aligned with Q9VD99_DROME | Q9VD99 from UniProtKB/TrEMBL  Length:307

    Alignment length:78
                                   179       189       199       209       219       229       239        
         Q9VD99_DROME   170 ARRIGHPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEE 247
               SCOP domains d3a01a_ A: automated matches                                                   SCOP domains
               CATH domains 3a01A00 A:170-247 Homeodomain-like                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......................hhhhhhhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 3a01 A 170 ARRIGHPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEE 247
                                   179       189       199       209       219       229       239        

Chain B from PDB  Type:PROTEIN  Length:57
 aligned with AL_DROME | Q06453 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:57
                                    95       105       115       125       135       
             AL_DROME    86 RRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 142
               SCOP domains d3a01b_ B: automated matches                              SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------HOMEOBOX_1              - PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 3a01 B  86 RRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRK 142
                                    95       105       115       125       135       

Chain C from PDB  Type:DNA  Length:17
                                                 
                 3a01 C   1 GGCTTAATTAATTGCGG  17
                                    10       

Chain D from PDB  Type:DNA  Length:17
                                                 
                 3a01 D   1 CCGCAATTAATTAAGCC  17
                                    10       

Chain E from PDB  Type:PROTEIN  Length:68
 aligned with Q9VD99_DROME | Q9VD99 from UniProtKB/TrEMBL  Length:307

    Alignment length:73
                                   184       194       204       214       224       234       244   
         Q9VD99_DROME   175 HPYQNRTPPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEE 247
               SCOP domains d3a01e_ E     : automated matches                                         SCOP domains
               CATH domains 3a01E00 E     :175-247 Homeodomain-like                                   CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...-----....hhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 3a01 E 175 HPYQNRTPP-----RTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEE 247
                                    |-    |  194       204       214       224       234       244   
                                  183   189                                                          

Chain F from PDB  Type:PROTEIN  Length:61
 aligned with AL_DROME | Q06453 from UniProtKB/Swiss-Prot  Length:408

    Alignment length:61
                                    95       105       115       125       135       145 
             AL_DROME    86 RRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 146
               SCOP domains d3a01f_ F: automated matches                                  SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------HOMEOBOX_1              ----- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 3a01 F  86 RRYRTTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEKV 146
                                    95       105       115       125       135       145 

Chain G from PDB  Type:DNA  Length:17
                                                 
                 3a01 G   1 GGCTTAATTAATTGCGG  17
                                    10       

Chain H from PDB  Type:DNA  Length:17
                                                 
                 3a01 H   1 CCGCAATTAATTAAGCC  17
                                    10       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3A01)

(-) Gene Ontology  (19, 31)

Asymmetric Unit(hide GO term definitions)
Chain A,E   (Q9VD99_DROME | Q9VD99)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0048800    antennal morphogenesis    The process in which the anatomical structures of the antenna are generated and organized.
    GO:0022416    chaeta development    The process whose specific outcome is the progression of a chaeta over time, from its formation to the mature structure. A chaeta is a sensory multicellular cuticular outgrowth of a specifically differentiated cell.
    GO:0035015    elongation of arista core    The increase in length of the aristal core. The arista is the terminal segment of the antenna and consists of a central core and a series of lateral extensions.
    GO:0007480    imaginal disc-derived leg morphogenesis    The process in which the anatomical structures of a leg derived from an imaginal disc are generated and organized. A leg is a limb on which an animal walks and stands. An example of this is found in Drosophila melanogaster.
    GO:0035218    leg disc development    Progression of the leg imaginal disc over time, from its initial formation through to its metamorphosis to form adult structures including the leg, coxa and ventral thoracic pleura.
    GO:0007501    mesodermal cell fate specification    The cell fate determination process in which a cell becomes capable of differentiating autonomously into a mesoderm cell in an environment that is neutral with respect to the developmental pathway; upon specification, the cell fate can be reversed.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045747    positive regulation of Notch signaling pathway    Any process that activates or increases the frequency, rate or extent of the Notch signaling pathway.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

Chain B,F   (AL_DROME | Q06453)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0048800    antennal morphogenesis    The process in which the anatomical structures of the antenna are generated and organized.
    GO:0022416    chaeta development    The process whose specific outcome is the progression of a chaeta over time, from its formation to the mature structure. A chaeta is a sensory multicellular cuticular outgrowth of a specifically differentiated cell.
    GO:0035015    elongation of arista core    The increase in length of the aristal core. The arista is the terminal segment of the antenna and consists of a central core and a series of lateral extensions.
    GO:0007480    imaginal disc-derived leg morphogenesis    The process in which the anatomical structures of a leg derived from an imaginal disc are generated and organized. A leg is a limb on which an animal walks and stands. An example of this is found in Drosophila melanogaster.
    GO:0035218    leg disc development    Progression of the leg imaginal disc over time, from its initial formation through to its metamorphosis to form adult structures including the leg, coxa and ventral thoracic pleura.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045747    positive regulation of Notch signaling pathway    Any process that activates or increases the frequency, rate or extent of the Notch signaling pathway.
    GO:0007449    proximal/distal pattern formation, imaginal disc    The establishment, maintenance and elaboration of the proximal/distal axis of the imaginal disc. Imaginal disks are masses of hypodermic cells, carried by the larvae of some insects after leaving the egg, from which masses the wings and legs of the adult are subsequently formed.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AL_DROME | Q064533a02 3lnq

(-) Related Entries Specified in the PDB File

3a02 ARISTALESS HOMEODOMAIN
3a03 HOX11L1 HOMEODOMAIN