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(-) Description

Title :  STRUCTURE OF THE NEUROSPORA SET DOMAIN PROTEIN DIM-5, A HISTONE LYSINE METHYLTRANSFERASE
 
Authors :  X. Zhang, H. Tamaru, S. I. Khan, J. R. Horton, L. J. Keefe, E. U. Selker, X. Cheng
Date :  30 Aug 02  (Deposition) - 23 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.98
Chains :  Asym./Biol. Unit :  A
Keywords :  Dim-5, Adomet-Dependent Methyltransferase Histone H3 Lysine- 9 Methylation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Zhang, H. Tamaru, S. I. Khan, J. R. Horton, L. J. Keefe, E. U. Selker, X. Cheng
Structure Of The Neurospora Set Domain Protein Dim-5, A Histone H3 Lysine Methyltransferase
Cell(Cambridge, Mass. ) V. 111 117 2002
PubMed-ID: 12372305  |  Reference-DOI: 10.1016/S0092-8674(02)00999-6
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HISTONE H3 METHYLTRANSFERASE DIM-5
    ChainsA
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPXC379
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 17-318
    Organism ScientificNEUROSPORA CRASSA
    Organism Taxid5141

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1UNK6Mod. Residue
2ZN3Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:66 , CYS A:81 , CYS A:128 , CYS A:132BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWARECYS A:74 , CYS A:128 , CYS A:134 , CYS A:138BINDING SITE FOR RESIDUE ZN A 2
3AC3SOFTWARECYS A:66 , CYS A:68 , CYS A:74 , CYS A:79BINDING SITE FOR RESIDUE ZN A 3

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1ML9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ML9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ML9)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PRE_SETPS50867 Pre-SET domain profile.DIM5_NEUCR77-159  1A:64-146
2SETPS50280 SET domain profile.DIM5_NEUCR162-297  1A:149-284
3POST_SETPS50868 Post-SET domain profile.DIM5_NEUCR315-331  1A:302-308

(-) Exons   (0, 0)

(no "Exon" information available for 1ML9)

(-) Sequences/Alignments

Asymmetric/Biological 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:260
 aligned with DIM5_NEUCR | Q8X225 from UniProtKB/Swiss-Prot  Length:331

    Alignment length:284
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317    
           DIM5_NEUCR    38 QLPISIVNREDDAFLNPNFRFIDHSIIGKNVPVADQSFRVGCSCASDEECMYSTCQCLDEMAPDSDEEADPYTRKKRFAYYSQGAKKGLLRDRVLQSQEPIYECHQGCACSKDCPNRVVERGRTVPLQIFRTKDRGWGVKCPVNIKRGQFVDRYLGEIITSEEADRRRAESTIARRKDVYLFALDKFSDPDSLDPLLAGQPLEVDGEYMSGPTRFINHSCDPNMAIFARVGDHADKHIHDLALFAIKDIPKGTELTFDYVNGLTGLESDAHDPSKISEMTKCLC 321
               SCOP domains d1ml9a_ A: Dim-5                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1ml9A00 A:25-308 SET domain                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains Pre-SET-1ml9A01 A:25-141                                                                                             ------------------SET-1ml9A02 A:160-284                                                                                                        -             ---------- Pfam domains
         Sec.struct. author ...eeee............ee....ee.......hhhhh........hhhhh..hhhhh.....-----------...............hhhhhhhh..ee..............hhhhhh....eeeee.....eeee.........eeee...eeehhhhhhhhhhhhhhhhhhhhheee..........hhhhhh...eee...eehhhhhhee.....eeeeeee.hhhhhhhheeeeee........eeee....-------------.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------PRE_SET  PDB: A:64-146 UniProt: 77-159                                             --SET  PDB: A:149-284 UniProt: 162-297                                                                                                    -----------------POST_SE PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ml9 A  25 QLPISIVNREDDAFLNPNFRFIDHSIIGKNVPVADQSFRVGCSCASDEECMYSTCQCLDEMAPD-----------KRFAYYSQGAKKGLLRDRVLQSQEPIYECHQGCACSKDCPNRVVERGRTVPLQIFRTKDRGWGVKCPVNIKRGQFVDRYLGEIITSEEADRRRAESTIARRKDVYLFALDKFSDPDSLDPLLAGQPLEVDGEYMSGPTRFINHSCDPNMAIFARVGDHADKHIHDLALFAIKDIPKGTELTFDYVN-------------KISEMTKCLC 308
                                    34        44        54        64        74        84   |     -     | 104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284|        -    |  304    
                                                                                          88         100                                                                                                                                                                                      285           299         

   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/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Family: SET (46)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DIM5_NEUCR | Q8X225)
molecular function
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0042054    histone methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone = S-adenosyl-L-homocysteine + methyl-histone. Histone methylation generally occurs on either an arginine or lysine residue.
    GO:0046974    histone methyltransferase activity (H3-K9 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 9) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 9). This reaction is the addition of a methyl group onto lysine at position 9 of the histone H3 protein.
    GO:0018024    histone-lysine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0003697    single-stranded DNA binding    Interacting selectively and non-covalently with single-stranded DNA.
    GO:0003727    single-stranded RNA binding    Interacting selectively and non-covalently with single-stranded RNA.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0051315    attachment of mitotic spindle microtubules to kinetochore    The cell cycle process in which spindle microtubules become physically associated with the proteins making up the kinetochore complex as part of mitotic metaphase plate congression.
    GO:0034613    cellular protein localization    Any process in which a protein is transported to, and/or maintained in, a specific location at the level of a cell. Localization at the cellular level encompasses movement within the cell, from within the cell to the cell surface, or from one location to another at the surface of a cell.
    GO:0030702    chromatin silencing at centromere    Repression of transcription of centromeric DNA by altering the structure of chromatin.
    GO:1990141    chromatin silencing at centromere outer repeat region    Repression of transcription of DNA at the outer repeat region of a regional centromere by altering the structure of chromatin.
    GO:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0030466    chromatin silencing at silent mating-type cassette    Repression of transcription at silent mating-type loci by alteration of the structure of chromatin.
    GO:0031048    chromatin silencing by small RNA    Repression of transcription by conversion of large regions of DNA into heterochromatin, directed by small RNAs sharing sequence identity to the repressed region.
    GO:0007535    donor selection    The process that determines which donor locus a cell uses, in preference to another, in mating type switching.
    GO:1902368    heterochromatin maintenance involved in chromatin silencing at centromere outer repeat region    Any heterochromatin maintenance that is involved in chromatin silencing at centromere outer repeat region.
    GO:0051567    histone H3-K9 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 9 of the histone.
    GO:0034968    histone lysine methylation    The modification of a histone by addition of one or more methyl groups to a lysine residue.
    GO:0045141    meiotic telomere clustering    The cell cycle process in which the dynamic reorganization of telomeres occurs in early meiotic prophase, during which meiotic chromosome ends are gathered in a bouquet arrangement at the inner surface of the nuclear envelope proximal to the spindle pole body. This plays an important role in progression through meiosis and precedes synapsis.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0090065    regulation of production of siRNA involved in RNA interference    Any process that modulates the frequency, rate or extent of the production of siRNA, the cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference.
cellular component
    GO:0043494    CLRC ubiquitin ligase complex    An cullin-dependent E3 ubiquitin ligase/histone H3-K9 methyltransferase complex essential for heterochromatin assembly by RNAi.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0034507    chromosome, centromeric outer repeat region    The portion of the centromeric region of a chromosome that flanks the core region, encompassing repeated regions of a chromosome centromere and the proteins that bind to it.
    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:0044732    mitotic spindle pole body    The microtubule organizing center that forms as part of the mitotic cell cycle; functionally homologous to the animal cell centrosome.
    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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        DIM5_NEUCR | Q8X2251peg

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