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(-) Description

Title :  EUHMT1 (GLP) ANKYRIN REPEAT DOMAIN (STRUCTURE 1)
 
Authors :  R. E. Collins, J. R. Horton, X. Cheng
Date :  30 Oct 07  (Deposition) - 12 Feb 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.99
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ankyrin Repeat, Alternative Splicing, Ank Repeat, Chromatin Regulator, Methyltransferase, Nucleus, Phosphorylation, Polymorphism, S-Adenosyl-L-Methionine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. E. Collins, J. P. Northrop, J. R. Horton, D. Y. Lee, X. Zhang, M. R. Stallcup, X. Cheng
The Ankyrin Repeats Of G9A And Glp Histone Methyltransferases Are Mono- And Dimethyllysine Binding Modules
Nat. Struct. Mol. Biol. V. 15 245 2008
PubMed-ID: 18264113  |  Reference-DOI: 10.1038/NSMB.1384
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EUCHROMATIC HISTONE-LYSINE N-METHYLTRANSFERASE 1
    ChainsA, B
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21 (DE3) CODONPLUS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentANKYRIN REPEAT DOMAINS 2-7
    GeneEHMT1, EUHMTASE1, KIAA1876
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC 5, HISTONE H3-K9 METHYLTRANSFERASE 5, H3-K9- HMTASE 5, EU-HMTASE1, G9A- LIKE PROTEIN 1, GLP1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:920 , TYR A:921 , ASP A:922BINDING SITE FOR RESIDUE SO4 A 5
2AC2SOFTWAREASN A:786 , HIS A:820 , TYR A:821 , GLU A:822BINDING SITE FOR RESIDUE SO4 A 6
3AC3SOFTWARELYS A:853 , HIS A:854 , VAL A:855 , ASP A:856BINDING SITE FOR RESIDUE SO4 A 7
4AC4SOFTWAREASN A:786 , HIS A:787 , LEU A:788 , GLU A:789 , HOH A:976BINDING SITE FOR RESIDUE SO4 A 8
5AC5SOFTWAREASN B:919 , ARG B:920 , TYR B:921 , ASP B:922BINDING SITE FOR RESIDUE SO4 B 1
6AC6SOFTWARELYS B:853 , ARG B:920BINDING SITE FOR RESIDUE SO4 B 2
7AC7SOFTWAREHIS B:820 , TYR B:821 , GLU B:822BINDING SITE FOR RESIDUE SO4 B 3
8AC8SOFTWAREGLY B:753 , HIS B:754 , VAL B:755 , ASP B:756BINDING SITE FOR RESIDUE SO4 B 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B7B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B7B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B7B)

(-) PROSITE Motifs  (1, 9)

Asymmetric Unit (1, 9)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ANK_REPEATPS50088 Ankyrin repeat profile.EHMT1_HUMAN772-804
805-837
 
838-862
 
872-904
 
938-970
 
  9A:741-773
A:774-806
B:774-806
A:807-831
B:807-831
A:841-873
B:841-873
A:907-939
B:907-939
Biological Unit 1 (1, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ANK_REPEATPS50088 Ankyrin repeat profile.EHMT1_HUMAN772-804
805-837
 
838-862
 
872-904
 
938-970
 
  5A:741-773
A:774-806
-
A:807-831
-
A:841-873
-
A:907-939
-
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ANK_REPEATPS50088 Ankyrin repeat profile.EHMT1_HUMAN772-804
805-837
 
838-862
 
872-904
 
938-970
 
  4-
-
B:774-806
-
B:807-831
-
B:841-873
-
B:907-939

(-) Exons   (0, 0)

(no "Exon" information available for 3B7B)

(-) 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:236
 aligned with EHMT1_HUMAN | Q9H9B1 from UniProtKB/Swiss-Prot  Length:1298

    Alignment length:236
                                   772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992      
          EHMT1_HUMAN   763 DPNFKMEHQNKRSPLHAAAEAGHVDICHMLVQAGANIDTCSEDQRTPLMEAAENNHLEAVKYLIKAGALVDPKDAEGSTCLHLAAKKGHYEVVQYLLSNGQMDVNCQDDGGWTPMIWATEYKHVDLVKLLLSKGSDINIRDNEENICLHWAAFSGCVDIAEILLAAKCDLHAVNIHGDSPLHIAARENRYDCVVLFLSRDSDVTLKNKEGETPLQCASLNSQVWSALQMSKALQDS 998
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------d3b7ba1 A:879-954 automated matches                                         ------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhh.............hhhhhhhhh.hhhhhhhhhh..............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhh.............hhhhhhhhh.hhhhhhhhhh.............hhhhhh...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------ANK_REPEAT  PDB: A:741-773       ANK_REPEAT  PDB: A:774-806       ANK_REPEAT  PDB: A:807-83---------ANK_REPEAT  PDB: A:841-873       ---------------------------------ANK_REPEAT  PDB: A:907-939       ---------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b7b A   1 HMNFKMEHQNKRSPLHAAAEAGHVDICHMLVQAGANIDTCSEDQRTPLMEAAENNHLEAVKYLIKAGALVDPKDAEGSTCLHLAAKKGHYEVVQYLLSNGQMDVNCQDDGGWTPMIWATEYKHVDLVKLLLSKGSDINIRDNEENICLHWAAFSGCVDIAEILLAAKCDLHAVNIHGDSPLHIAARENRYDCVVLFLSRDSDVTLKNKEGETPLQCASLNSQVWSALQMSKALQDS 967
                            |||    741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961      
                            |||                                                                                                                                                                                                                                         
                            1||                                                                                                                                                                                                                                         
                             0|                                                                                                                                                                                                                                         
                            734                                                                                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:224
 aligned with EHMT1_HUMAN | Q9H9B1 from UniProtKB/Swiss-Prot  Length:1298

    Alignment length:224
                                   784       794       804       814       824       834       844       854       864       874       884       894       904       914       924       934       944       954       964       974       984       994    
          EHMT1_HUMAN   775 SPLHAAAEAGHVDICHMLVQAGANIDTCSEDQRTPLMEAAENNHLEAVKYLIKAGALVDPKDAEGSTCLHLAAKKGHYEVVQYLLSNGQMDVNCQDDGGWTPMIWATEYKHVDLVKLLLSKGSDINIRDNEENICLHWAAFSGCVDIAEILLAAKCDLHAVNIHGDSPLHIAARENRYDCVVLFLSRDSDVTLKNKEGETPLQCASLNSQVWSALQMSKALQDS 998
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.hhhhhhhhhhhh...........hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhh...............hhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhh..............hhhhh...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ANK_REPEAT  PDB: -            ANK_REPEAT  PDB: B:774-806       ANK_REPEAT  PDB: B:807-83---------ANK_REPEAT  PDB: B:841-873       ---------------------------------ANK_REPEAT  PDB: B:907-939       ---------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b7b B 744 SPLHAAAEAGHVDICHMLVQAGANIDTCSEDQRTPLMEAAENNHLEAVKYLIKAGALVDPKDAEGSTCLHLAAKKGHYEVVQYLLSNGQMDVNCQDDGGWTPMIWATEYKHVDLVKLLLSKGSDINIRDNEENICLHWAAFSGCVDIAEILLAAKCDLHAVNIHGDSPLHIAARENRYDCVVLFLSRDSDVTLKNKEGETPLQCASLNSQVWSALQMSKALQDS 967
                                   753       763       773       783       793       803       813       823       833       843       853       863       873       883       893       903       913       923       933       943       953       963    

   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  (0, 0)

(no "CATH Domain" information available for 3B7B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B7B)

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (EHMT1_HUMAN | Q9H9B1)
molecular function
    GO:0070742    C2H2 zinc finger domain binding    Interacting selectively and non-covalently with a C2H2-type zinc finger domain of a protein. The C2H2 zinc finger is the classical zinc finger domain, in which two conserved cysteines and histidines co-ordinate a zinc ion.
    GO:0046976    histone methyltransferase activity (H3-K27 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 27) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 27). This reaction is the addition of a methyl group onto lysine at position 27 of the histone H3 protein.
    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:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    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:0016279    protein-lysine N-methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue in a protein substrate.
    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:0006306    DNA methylation    The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
    GO:0009790    embryo development    The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
    GO:0070734    histone H3-K27 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 27 of the histone.
    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:0016571    histone methylation    The modification of histones by addition of methyl groups.
    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: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:0018027    peptidyl-lysine dimethylation    The methylation of peptidyl-lysine to form peptidyl-N6,N6-dimethyl-L-lysine.
    GO:0018026    peptidyl-lysine monomethylation    The methylation of peptidyl-lysine to form peptidyl-N6-methyl-L-lysine.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0060992    response to fungicide    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 fungicide stimulus. Fungicides are chemicals used to kill fungi.
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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        EHMT1_HUMAN | Q9H9B12igq 2rfi 3b95 3fpd 3hna 3mo0 3mo2 3mo5 3sw9 3swc 4i51 5ttg 5tuz 5vsd 5vsf

(-) Related Entries Specified in the PDB File

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