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(-) Description

Title :  SCM SAM DOMAIN
 
Authors :  C. A. Kim, M. R. Sawaya, D. Cascio, W. Kim, J. U. Bowie
Date :  04 Jun 03  (Deposition) - 15 Feb 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Sam Domain, Polymer, Transcriptional Repression, Transcription Repression (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. A. Kim, M. R. Sawaya, D. Cascio, W. Kim, J. U. Bowie
Structural Organization Of A Sex-Comb-On-Midleg/Polyhomeotic Copolymer.
J. Biol. Chem. V. 280 27769 2005
PubMed-ID: 15905166  |  Reference-DOI: 10.1074/JBC.M503055200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SEX COMB ON MIDLEG CG9495-PA
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-3C
    Expression System StrainBL21(DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentSEQUENCE DATABASE RESIDUE 795-871, SAM DOMAIN OF SCM
    GeneSCM
    MutationYES
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymSCM

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1BME3Ligand/IonBETA-MERCAPTOETHANOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:53 , ASN A:54 , CYS A:73 , ASN A:77BINDING SITE FOR RESIDUE BME A 1001
2AC2SOFTWARELEU B:53 , ASN B:54 , CYS B:73 , ASN B:77BINDING SITE FOR RESIDUE BME B 1002
3AC3SOFTWARELEU C:53 , ASN C:54 , CYS C:73 , ASN C:77BINDING SITE FOR RESIDUE BME C 1003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1PK3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PK3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PK3)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_DOMAINPS50105 SAM domain profile.SCM_DROME806-856
 
 
  3A:17-67
B:17-67
C:17-67
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_DOMAINPS50105 SAM domain profile.SCM_DROME806-856
 
 
  1A:17-67
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_DOMAINPS50105 SAM domain profile.SCM_DROME806-856
 
 
  1-
B:17-67
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_DOMAINPS50105 SAM domain profile.SCM_DROME806-856
 
 
  1-
-
C:17-67

(-) Exons   (0, 0)

(no "Exon" information available for 1PK3)

(-) 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:76
 aligned with SCM_DROME | Q9VHA0 from UniProtKB/Swiss-Prot  Length:877

    Alignment length:76
                                   803       813       823       833       843       853       863      
            SCM_DROME   794 LANSHLRSQPIDWTIEEVIQYIESNDNSLAVHGDLFRKHEIDGKALLLLNSEMMMKYMGLKLGPALKICNLVNKVN 869
               SCOP domains -d1pk3a1 A:6-79 Polycomb protein Scm                                       - SCOP domains
               CATH domains 1pk3A00 A:5-80 Transcription Factor, Ets-1                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------SAM_DOMAIN  PDB: A:17-67 UniProt: 806-856          ------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 1pk3 A   5 RANSHLRSQPIDWTIEEVIQYIESNDNSLAVHGDLFRKHEIDGKALLRLNSEMMMKYMGLKLGPALKICNLVNKVN  80
                                    14        24        34        44        54        64        74      

Chain B from PDB  Type:PROTEIN  Length:68
 aligned with SCM_DROME | Q9VHA0 from UniProtKB/Swiss-Prot  Length:877

    Alignment length:68
                                   811       821       831       841       851       861        
            SCM_DROME   802 QPIDWTIEEVIQYIESNDNSLAVHGDLFRKHEIDGKALLLLNSEMMMKYMGLKLGPALKICNLVNKVN 869
               SCOP domains d1pk3b_ B: automated matches                                         SCOP domains
               CATH domains 1pk3B00 B:13-80 Transcription Factor, Ets-1                          CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhh..hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SAM_DOMAIN  PDB: B:17-67 UniProt: 806-856          ------------- PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                 1pk3 B  13 QPIDWTIEEVIQYIESNDNSLAVHGDLFRKHEIDGKALLRLNSEMMMKYMGLKLGPALKICNLVNKVN  80
                                    22        32        42        52        62        72        

Chain C from PDB  Type:PROTEIN  Length:78
 aligned with SCM_DROME | Q9VHA0 from UniProtKB/Swiss-Prot  Length:877

    Alignment length:78
                                   801       811       821       831       841       851       861        
            SCM_DROME   792 SALANSHLRSQPIDWTIEEVIQYIESNDNSLAVHGDLFRKHEIDGKALLLLNSEMMMKYMGLKLGPALKICNLVNKVN 869
               SCOP domains d1pk3c_ C: automated matches                                                   SCOP domains
               CATH domains 1pk3C00 C:3-80 Transcription Factor, Ets-1                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------SAM_DOMAIN  PDB: C:17-67 UniProt: 806-856          ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 1pk3 C   3 KTRANSHLRSQPIDWTIEEVIQYIESNDNSLAVHGDLFRKHEIDGKALLRLNSEMMMKYMGLKLGPALKICNLVNKVN  80
                                    12        22        32        42        52        62        72        

   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  (2, 3)

Asymmetric Unit

(-) CATH Domains  (1, 3)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1PK3)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (SCM_DROME | Q9VHA0)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007409    axonogenesis    De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
    GO:0048749    compound eye development    The process whose specific outcome is the progression of the compound eye over time, from its formation to the mature structure. The compound eye is an organ of sight that contains multiple repeating units, often arranged hexagonally. Each unit has its own lens and photoreceptor cell(s) and can generate either a single pixelated image or multiple images, per eye.
    GO:0016458    gene silencing    Any process carried out at the cellular level that results in either long-term transcriptional repression via action on chromatin structure or RNA mediated, post-transcriptional repression of gene expression.
    GO:0030708    germarium-derived female germ-line cyst encapsulation    Formation of a single follicular epithelium around the germ-line derived cells of a cyst formed in the germarium. An example of this process is found in Drosophila melanogaster.
    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:0045926    negative regulation of growth    Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism.
    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:0022008    neurogenesis    Generation of cells within the nervous system.
    GO:0030713    ovarian follicle cell stalk formation    Development of ovarian follicle cells to create the interfollicular stalks that connect the egg chambers of progressive developmental stages. An example of this process is found in Drosophila melanogaster.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0007419    ventral cord development    The process whose specific outcome is the progression of the ventral cord over time, from its formation to the mature structure. The ventral cord is one of the distinguishing traits of the central nervous system of all arthropods (such as insects, crustaceans and arachnids) as well as many other invertebrates, such as the annelid worms.
cellular component
    GO:0035102    PRC1 complex    A multiprotein complex that mediates monoubiquitination of lysine residues of histone H2A (lysine-118 in Drosophila or lysine-119 in mammals). The complex is required for stable long-term maintenance of transcriptionally repressed states and is involved in chromatin remodeling.
    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:0005700    polytene chromosome    A type of chromosome in a polyploid cell, formed when multiple copies of homologous chromosomes are aligned side by side to give a giant chromosome in which distinct chromosome bands are readily visible.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SCM_DROME | Q9VHA01pk1 2r57 2r58 2r5a 2r5m 5j8y

(-) Related Entries Specified in the PDB File

1pk1 DIFFERENT MUTANT OF SAME PROTEIN COMPLEXED WITH PHSAM.