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(-) Description

Title :  STRUCTURAL BASIS FOR SPECIFIC BINDING OF POLYCOMB CHROMODOMAIN TO HISTONE H3 METHYLATED AT K27
 
Authors :  J. R. Min, Y. Zhang, R. -M. Xu
Date :  24 May 03  (Deposition) - 07 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Chromatin, Histone Methylation, Polycomb, Chromodomain, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Min, Y. Zhang, R. -M. Xu
Structural Basis For Specific Binding Of Polycomb Chromodomain To Histone H3 Methylated At Lys 27.
Genes Dev. V. 17 1823 2003
PubMed-ID: 12897052  |  Reference-DOI: 10.1101/GAD.269603
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - POLYCOMB PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCHROMODOMAIN
    GenePC OR CG7618
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
 
Molecule 2 - HISTONE H3, EMBRYONIC
    ChainsB
    EngineeredYES
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED. IT IS NATURALLY FOUND IN STRONGYLOCENTROTUS PURPURATUS.
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)AB
Biological Unit 2 (2x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3CL2Ligand/IonCHLORIDE ION
4M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3CL-1Ligand/IonCHLORIDE ION
4M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2BME2Ligand/IonBETA-MERCAPTOETHANOL
3CL-1Ligand/IonCHLORIDE ION
4M3L2Mod. Amino AcidN-TRIMETHYLLYSINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:303BINDING SITE FOR RESIDUE CL A 203
2AC2SOFTWAREILE A:32 , GLN A:33 , HOH A:208BINDING SITE FOR RESIDUE CL A 204
3AC3SOFTWAREARG A:44 , ARG A:53 , TYR A:54 , HOH A:232BINDING SITE FOR RESIDUE BME A 202
4AC4SOFTWAREARG A:35 , LYS A:37 , ARG A:53 , HOH A:238 , HOH A:243 , HOH A:302 , HOH A:340BINDING SITE FOR RESIDUE ACY A 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.PC_DROME26-84  1A:26-77
2CHROMO_1PS00598 Chromo domain signature.PC_DROME43-63  1A:43-63
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.PC_DROME26-84  1A:26-77
2CHROMO_1PS00598 Chromo domain signature.PC_DROME43-63  1A:43-63
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHROMO_2PS50013 Chromo and chromo shadow domain profile.PC_DROME26-84  2A:26-77
2CHROMO_1PS00598 Chromo domain signature.PC_DROME43-63  2A:43-63

(-) Exons   (0, 0)

(no "Exon" information available for 1PFB)

(-) 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:55
 aligned with PC_DROME | P26017 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:55
                                    32        42        52        62        72     
              PC_DROME   23 DLVYAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNILDRRLIDIYEQTNK 77
               SCOP domains d1pfba_ A: Polycomb protein, Pc                         SCOP domains
               CATH domains 1pfbA00 A:23-77  [code=2.40.50.40, no name defined]     CATH domains
               Pfam domains ---Chromo-1pfbA01 A:26-75                            -- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeee..eeeeeeee...hhhhheeee.hhh..hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---CHROMO_2  PDB: A:26-77 UniProt: 26-84                PROSITE (1)
                PROSITE (2) --------------------CHROMO_1  PDB: A:43-6-------------- PROSITE (2)
                 Transcript ------------------------------------------------------- Transcript
                  1pfb A 23 DLVYAAEKIIQKRVKKGVVEYRVKWKGWNQRYNTWEPEVNILDRRLIDIYEQTNK 77
                                    32        42        52        62        72     

Chain B from PDB  Type:PROTEIN  Length:11
 aligned with H3_STRPU | P06352 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:11
                                    30 
              H3_STRPU   21 LATKAARKSAP 31
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ...eeeee... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                  1pfb B 20 LATKAARkSAP 30
                                   |29 
                                  27-M3L

   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, 1)

Asymmetric Unit

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: Tudor (88)

(-) Gene Ontology  (23, 24)

Asymmetric Unit(hide GO term definitions)
Chain A   (PC_DROME | P26017)
molecular function
    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: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.
biological process
    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:2001229    negative regulation of response to gamma radiation    Any process that stops, prevents or reduces the frequency, rate or extent of response to gamma radiation.
    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:0016322    neuron remodeling    The developmentally regulated remodeling of neuronal projections such as pruning to eliminate the extra dendrites and axons projections set up in early stages of nervous system development.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007385    specification of segmental identity, abdomen    The specification of the characteristic structures of the abdominal segments following establishment of segment boundaries. Identity is considered to be the aggregate of characteristics by which a structure is recognized.
    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.
    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.
    GO:0042060    wound healing    The series of events that restore integrity to a damaged tissue, following an injury.
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:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    GO:0005725    intercalary heterochromatin    Any of the regions of heterochromatin that form a reproducible set of dense bands scattered along the euchromatic arms in polytene chromosomes.
    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   (H3_STRPU | P06352)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
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:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    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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        PC_DROME | P260171pdq

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