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(-) Description

Title :  DROSOPHILA HP1A CHROMO SHADOW DOMAIN
 
Authors :  D. Kim, M. Chruszcz, W. Minor, S. Khorasanizadeh
Date :  12 Oct 10  (Deposition) - 02 Feb 11  (Release) - 11 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Heterochromatin Protein 1, Chromo Shadow Domain, Gene Silencing, Epigenetics, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. L. Mendez, D. Kim, M. Chruszcz, G. E. Stephens, W. Minor, S. Khorasanizadeh, S. C. Elgin
The Hp1A Disordered C Terminus And Chromo Shadow Domain Cooperate To Select Target Peptide Partners.
Chembiochem V. 12 1084 2011
PubMed-ID: 21472955  |  Reference-DOI: 10.1002/CBIC.201000598

(-) Compounds

Molecule 1 - HETEROCHROMATIN PROTEIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21-CODONPLUS (DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 131-206
    Gene: SU(VAR)205, HP1, CG8409
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227
    Synonym: HP1, NON-HISTONE CHROMOSOMAL PROTEIN C1A9 ANTIGEN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:173 , ALA A:174 , LEU B:153 , GLN B:167 , ASP B:172 , GLN B:173 , ALA B:174BINDING SITE FOR RESIDUE GOL B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P7J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P7J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P7J)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.HP1_DROME24-82
147-205
 		  2-
A:147-199
B:147-201
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.HP1_DROME24-82
147-205
 		  2-
A:147-199
B:147-201
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.HP1_DROME24-82
147-205
 		  2-
A:147-199
B:147-201

(-) Exons   (0, 0)

(no "Exon" information available for 3P7J)

(-) 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:59
 aligned with HP1_DROME | P05205 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:59
                                   150       160       170       180       190         
            HP1_DROME   141 TGFDRGLEAEKILGASDNNGRLTFLIQFKGVDQAEMVPSSVANEKIPRMVIHFYEERLS 199
               SCOP domains d3p7ja_ A: automated matches                                SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee..eeeeeeee......eeeehhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------CHROMO_2  PDB: A:147-199 UniProt: 147-205             PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 3p7j A 141 TGFDRGLEAEKILGASDNNGRLTFLIQFKGVDQAEMVPSSVANEKIPRMVIHFYEERLS 199
                                   150       160       170       180       190         


Chain B from PDB  Type:PROTEIN  Length:61
 aligned with HP1_DROME | P05205 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:61
                                   150       160       170       180       190       200 
            HP1_DROME   141 TGFDRGLEAEKILGASDNNGRLTFLIQFKGVDQAEMVPSSVANEKIPRMVIHFYEERLSWY 201
               SCOP domains d3p7jb_ B: automated matches                                  SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Chromo_shadow-3p7jB01 B:145-201                           Pfam domains (1)
           Pfam domains (2) ----Chromo_shadow-3p7jB02 B:145-201                           Pfam domains (2)
         Sec.struct. author hhhhhh..eeeeeeeeee..eeeeeeee......eeeehhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------CHROMO_2  PDB: B:147-201 UniProt: 147-205               PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 3p7j B 141 TGFDRGLEAEKILGASDNNGRLTFLIQFKGVDQAEMVPSSVANEKIPRMVIHFYEERLSWY 201
                                   150       160       170       180       190       200
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P7J)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Tudor (88)

(-) Gene Ontology  (43, 43)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HP1_DROME | P05205)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
    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:0000182    rDNA binding    Interacting selectively and non-covalently with DNA sequences encoding ribosomal RNA.
    GO:0003696    satellite DNA binding    Interacting selectively and non-covalently with satellite DNA, the many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA.
biological process
    GO:0044026    DNA hypermethylation    An increase in the epigenetic methylation of cytosine and adenosine residues in DNA.
    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:0030702    chromatin silencing at centromere    Repression of transcription of centromeric DNA by altering the structure of chromatin.
    GO:0051276    chromosome organization    A process that is carried out at the cellular level that results in the assembly, arrangement of constituent parts, or disassembly of chromosomes, structures composed of a very long molecule of DNA and associated proteins that carries hereditary information. This term covers covalent modifications at the molecular level as well as spatial relationships among the major components of a chromosome.
    GO:0006343    establishment of chromatin silencing    The initial formation of a transcriptionally silent chromatin structure such as 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:0031507    heterochromatin assembly    The assembly of chromatin into heterochromatin, a compact and highly condensed form that is often, but not always, transcriptionally silent.
    GO:0034773    histone H4-K20 trimethylation    The modification of histone H4 by addition of three methyl groups to lysine at position 20 of the histone.
    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:0033697    positive regulation of extent of heterochromatin assembly    Any process that increases the extent of heterochromatin formation; increases the size of a chromosomal region converted to heterochromatin.
    GO:1900111    positive regulation of histone H3-K9 dimethylation    Any process that activates or increases the frequency, rate or extent of histone H3-K9 dimethylation.
    GO:0090309    positive regulation of methylation-dependent chromatin silencing    Any process that increases the rate, frequency, or extent of the repression of transcription by methylation of DNA, leading to the formation of heterochromatin.
    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:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0031060    regulation of histone methylation    Any process that modulates the frequency, rate or extent of the covalent addition of methyl groups to histones.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0000723    telomere maintenance    Any process that contributes to the maintenance of proper telomeric length and structure by affecting and monitoring the activity of telomeric proteins, the length of telomeric DNA and the replication and repair of the DNA. These processes includes those that shorten, lengthen, replicate and repair the telomeric DNA sequences.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0000793    condensed chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.
    GO:0000780    condensed nuclear chromosome, centromeric region    The region of a condensed nuclear chromosome that includes the centromere and associated proteins, including the kinetochore. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000791    euchromatin    A dispersed and relatively uncompacted form of chromatin.
    GO:0000792    heterochromatin    A compact and highly condensed form of chromatin.
    GO:0005720    nuclear heterochromatin    A condensed form of chromatin, occurring in the nucleus during interphase, that stains strongly with basophilic dyes. The DNA of heterochromatin is typically replicated at a later stage in the cell-division cycle than euchromatin.
    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.
    GO:0005721    pericentric heterochromatin    Heterochromatin that is located adjacent to the CENP-A rich centromere 'central core' and characterized by the modified histone H3K9me3.
    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.
    GO:0005704    polytene chromosome band    A stretch of densely packed chromatin along the polytene chromosome, visible as a morphologically distinct band.
    GO:0005701    polytene chromosome chromocenter    A region at which the centric regions of polytene chromosomes are joined together.
    GO:0005703    polytene chromosome puff    A swelling at a site along the length of a polytene chromosome, thought to be the site of active transcription.
    GO:0035012    polytene chromosome, telomeric region    The terminal region of a polytene chromosome.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HP1_DROME | P05205: 1kna 1kne 1q3l

(-) Related Entries Specified in the PDB File

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