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(-) Description

Title :  STRUCTURE OF A HOMEODOMAIN IN COMPLEX WITH DNA
 
Authors :  G. Birrane, J. A. A. Ladias, A. Soni
Date :  24 Mar 08  (Deposition) - 17 Feb 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C  (2x)
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Dna-Binding Protein, Dna, Transcription Regulation, Transcription Regulator-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Birrane, A. Soni, J. A. Ladias
Structural Basis For Dna Recognition By The Human Pax3 Homeodomain.
Biochemistry V. 48 1148 2009
PubMed-ID: 19199574  |  Reference-DOI: 10.1021/BI802052Y

(-) Compounds

Molecule 1 - PAIRED BOX PROTEIN PAX-3
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-6H
    Expression System StrainC41
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentHOMEODOMAIN (UNP RESIDUES 219-278)
    GenePAX3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHUP2
 
Molecule 2 - 5'-D(*DAP*DCP*DAP*DTP*DAP*DAP*DP*DCP*DGP*DAP*DTP*DTP*DAP*DC )-3'
    ChainsB
    EngineeredYES
    SyntheticYES
 
Molecule 3 - 5'-D(*DTP*DGP*DTP*DAP*DAP*DTP*DCP*DGP*DAP*DTP*DTP*DAP*DTP*D G)-3'
    ChainsC
    EngineeredYES
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit (2x)ABC
Biological Unit 1 (2x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:4BINDING SITE FOR RESIDUE EDO A 61

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CMY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

Asymmetric Unit (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_003804F238SPAX3_HUMANDisease (WS1)  ---AF20S
2UniProtVAR_003805V265FPAX3_HUMANDisease (WS1)  ---AV47F
3UniProtVAR_017536W266CPAX3_HUMANDisease (WS1)  ---AW48C
4UniProtVAR_013619R270CPAX3_HUMANDisease (WS3)  ---AR52C
5UniProtVAR_017537R271CPAX3_HUMANDisease (WS1)  ---AR53C
6UniProtVAR_003806R271GPAX3_HUMANDisease (WS1)  ---AR53G
7UniProtVAR_017538R271HPAX3_HUMANDisease (WS1)774528745AR53H
8UniProtVAR_017539R273KPAX3_HUMANUnclassified  ---AR55K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_003804F238SPAX3_HUMANDisease (WS1)  ---AF20S
2UniProtVAR_003805V265FPAX3_HUMANDisease (WS1)  ---AV47F
3UniProtVAR_017536W266CPAX3_HUMANDisease (WS1)  ---AW48C
4UniProtVAR_013619R270CPAX3_HUMANDisease (WS3)  ---AR52C
5UniProtVAR_017537R271CPAX3_HUMANDisease (WS1)  ---AR53C
6UniProtVAR_003806R271GPAX3_HUMANDisease (WS1)  ---AR53G
7UniProtVAR_017538R271HPAX3_HUMANDisease (WS1)774528745AR53H
8UniProtVAR_017539R273KPAX3_HUMANUnclassified  ---AR55K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_2PS50071 'Homeobox' domain profile.PAX3_HUMAN217-277  1A:1-59
2HOMEOBOX_1PS00027 'Homeobox' domain signature.PAX3_HUMAN252-275  1A:34-57
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_2PS50071 'Homeobox' domain profile.PAX3_HUMAN217-277  1A:1-59
2HOMEOBOX_1PS00027 'Homeobox' domain signature.PAX3_HUMAN252-275  1A:34-57

(-) Exons   (0, 0)

(no "Exon" information available for 3CMY)

(-) 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:60
 aligned with PAX3_HUMAN | P23760 from UniProtKB/Swiss-Prot  Length:479

    Alignment length:74
                                   213       223       233       243       253       263       273    
           PAX3_HUMAN   204 GSDIDSEPDLPLKRKQRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ 277
               SCOP domains d              3cmya_ A: automated matches                                 SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--------------........hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
             SAPs(SNPs) (1) ----------------------------------S--------------------------FC---CC-K---- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------G------ SAPs(SNPs) (2)
             SAPs(SNPs) (3) -------------------------------------------------------------------H------ SAPs(SNPs) (3)
                PROSITE (1) -------------HOMEOBOX_2  PDB: A:1-59 UniProt: 217-277                      PROSITE (1)
                PROSITE (2) ------------------------------------------------HOMEOBOX_1  PDB: A:34-57-- PROSITE (2)
                 Transcript -------------------------------------------------------------------------- Transcript
                 3cmy A   0 G--------------QRRSRTTFTAEQLEELERAFERTHYPDIYTREELAQRAKLTEARVQVWFSNRRARWRKQ  59
                            |        -     |   5        15        25        35        45        55    
                            |              1                                                          
                            0                                                                         

Chain B from PDB  Type:DNA  Length:8
                                        
                 3cmy B   1 ACATAATC   8

Chain C from PDB  Type:DNA  Length:7
                                       
                 3cmy C   8 GATTATG  14

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3CMY)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (20, 20)

Asymmetric Unit(hide GO term definitions)
Chain A   (PAX3_HUMAN | P23760)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0071837    HMG box domain binding    Interacting selectively and non-covalently with an HMG box domain, a protein domain that consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin.
    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:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    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:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
    GO:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0014029    neural crest formation    The formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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