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(-) Description

Title :  HETERO SAM DOMAIN STRUCTURE OF PH AND SCM.
 
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 :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Hetero Sam Domain, Polymers, 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 - POLYHOMEOTIC-PROXIMAL CHROMATIN PROTEIN
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-3C
    Expression System StrainBL21(DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUE 1502-1577, PH SAM DOMAIN
    GenePH-P
    MutationYES
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
 
Molecule 2 - SEX COMB ON MIDLEG CG9495-PA
    ChainsB, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-3C
    Expression System StrainBL21(DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUE 795-871, SCM SAM DOMAIN
    GeneSEX COMB ON MIDLEG
    MutationYES
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1PK1)

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:32 -C:32

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PK1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PK1)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_DOMAINPS50105 SAM domain profile.SCM_DROME806-856
 
  2B:17-67
D:17-67
PHP_DROME1513-1577
 
  2A:17-79
C:17-78
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_DOMAINPS50105 SAM domain profile.SCM_DROME806-856
 
  1B:17-67
-
PHP_DROME1513-1577
 
  1A:17-79
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_DOMAINPS50105 SAM domain profile.SCM_DROME806-856
 
  1-
D:17-67
PHP_DROME1513-1577
 
  1-
C:17-78

(-) Exons   (0, 0)

(no "Exon" information available for 1PK1)

(-) 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:68
 aligned with PHP_DROME | P39769 from UniProtKB/Swiss-Prot  Length:1589

    Alignment length:68
                                  1517      1527      1537      1547      1557      1567        
           PHP_DROME   1508 PPISSWSVDDVSNFIRELPGCQDYVDDFIQQEIDGQALLLLKEKHLVNAMGMKLGPALKIVAKVESIK 1575
               SCOP domains d1pk1a1 A:12-79 Polyhomeotic                                         SCOP domains
               CATH domains 1pk1A00 A:12-79 Transcription Factor, Ets-1                          CATH domains
               Pfam domains -------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh......hhhhhhhh..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SAM_DOMAIN  PDB: A:17-79 UniProt: 1513-1577                     PROSITE
                 Transcript -------------------------------------------------------------------- Transcript
                1pk1 A   12 PPISSWSVDDVSNFIRELPGCQDYVDDFIQQEIDGQALLLLKEKHLVNAmGmKLGPARKIVAKVESIK   79
                                    21        31        41        51        61 |      71        
                                                                            61-MSE              
                                                                              63-MSE            

Chain B from PDB  Type:PROTEIN  Length:70
 aligned with SCM_DROME | Q9VHA0 from UniProtKB/Swiss-Prot  Length:877

    Alignment length:70
                                   809       819       829       839       849       859       869
           SCM_DROME    800 RSQPIDWTIEEVIQYIESNDNSLAVHGDLFRKHEIDGKALLLLNSEMMMKYMGLKLGPALKICNLVNKVN  869
               SCOP domains ------d1pk1b1 B:17-79 Polycomb protein Scm                           - SCOP domains
               CATH domains 1pk1B00 B:11-80 Transcription Factor, Ets-1                            CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------SAM_DOMAIN  PDB: B:17-67 UniProt: 806-856          ------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                1pk1 B   11 RSQPIDWTIEEVIQYIESNDNSLAVHGDLFRKHEIDGKALLRLNSERMMKYMGLKLGPALKICNLVNKVN   80
                                    20        30        40        50        60        70        80

Chain C from PDB  Type:PROTEIN  Length:66
 aligned with PHP_DROME | P39769 from UniProtKB/Swiss-Prot  Length:1589

    Alignment length:66
                                  1518      1528      1538      1548      1558      1568      
           PHP_DROME   1509 PISSWSVDDVSNFIRELPGCQDYVDDFIQQEIDGQALLLLKEKHLVNAMGMKLGPALKIVAKVESI 1574
               SCOP domains d1pk1c_ C: Polyhomeotic                                            SCOP domains
               CATH domains 1pk1C00 C:13-78 Transcription Factor, Ets-1                        CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.....hhhhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----SAM_DOMAIN  PDB: C:17-78 UniProt: 1513-1577                    PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                1pk1 C   13 PISSWSVDDVSNFIRELPGCQDYVDDFIQQEIDGQALLLLKEKHLVNAmGmKLGPARKIVAKVESI   78
                                    22        32        42        52        62|       72      
                                                                           61-MSE             
                                                                             63-MSE           

Chain D from PDB  Type:PROTEIN  Length:67
 aligned with SCM_DROME | Q9VHA0 from UniProtKB/Swiss-Prot  Length:877

    Alignment length:67
                                   812       822       832       842       852       862       
           SCM_DROME    803 PIDWTIEEVIQYIESNDNSLAVHGDLFRKHEIDGKALLLLNSEMMMKYMGLKLGPALKICNLVNKVN  869
               SCOP domains d1pk1d_ D: automated matches                                        SCOP domains
               CATH domains 1pk1D00 D:14-80 Transcription Factor, Ets-1                         CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SAM_DOMAIN  PDB: D:17-67 UniProt: 806-856          ------------- PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                1pk1 D   14 PIDWTIEEVIQYIESNDNSLAVHGDLFRKHEIDGKALLRLNSERMMKYMGLKLGPALKICNLVNKVN   80
                                    23        33        43        53        63        73       

   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  (3, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1PK1)

(-) Gene Ontology  (30, 40)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (PHP_DROME | P39769)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0044547    DNA topoisomerase binding    Interacting selectively and non-covalently with a DNA topoisomerase.
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0001047    core promoter binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    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:0021954    central nervous system neuron development    The process whose specific outcome is the progression of a neuron whose cell body is located in the central nervous system, from initial commitment of the cell to a neuronal fate, to the fully functional differentiated neuron.
    GO:0006342    chromatin silencing    Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
    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:0000070    mitotic sister chromatid segregation    The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
    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: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:0035075    response to ecdysone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a ecdysone stimulus.
    GO:0035186    syncytial blastoderm mitotic cell cycle    Mitotic division cycles 10 to 13 of the insect embryo. This is the second phase of the syncytial period where nuclei divide in a common cytoplasm without cytokinesis. The majority of migrating nuclei reach the embryo surface during cycle 10, after which they divide less synchronously than before, and the syncytial blastoderm cycles lengthen progressively.
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:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.

Chain B,D   (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
        PHP_DROME | P397691kw4
        SCM_DROME | Q9VHA01pk3 2r57 2r58 2r5a 2r5m 5j8y

(-) Related Entries Specified in the PDB File

1pk3