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(-) Description

Title :  SOLUTION STRUCTURE OF THE SH3 DOMAIN OF THE PROTEIN ARGININE N-METHYLTRANSFERASE 2
 
Authors :  E. Chikayama, T. Kigawa, K. Saito, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  26 Apr 05  (Deposition) - 26 Oct 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Sh3 Domain, Protein Arginine N-Methyltransferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Chikayama, T. Kigawa, K. Saito, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The Sh3 Domain Of The Protein Arginine N-Methyltransferase 2
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN ARGININE N-METHYLTRANSFERASE 2
    ChainsA
    EC Number2.1.1.-
    EngineeredYES
    Expression System PlasmidP040531-04
    Expression System Vector TypePLASMID
    FragmentSH3 DOMAIN
    GeneHRMT1L1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1X2P)

(-) Sites  (0, 0)

(no "Site" information available for 1X2P)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1X2P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1X2P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1X2P)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SH3PS50002 Src homology 3 (SH3) domain profile.ANM2_HUMAN30-89  1A:10-62
2SAM_MT_PRMTPS51678 SAM-dependent methyltransferase PRMT-type domain profile.ANM2_HUMAN99-432  1A:66-68

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003976381bENSE00001529496chr21:48055527-48055675149ANM2_HUMAN-00--
1.2ENST000003976382ENSE00001336411chr21:48056808-4805690295ANM2_HUMAN1-13131A:1-6 (gaps)12
1.3bENST000003976383bENSE00001051368chr21:48063447-48063551105ANM2_HUMAN14-48351A:7-23 (gaps)35
1.4aENST000003976384aENSE00001051367chr21:48064218-48064400183ANM2_HUMAN49-109611A:24-68 (gaps)59
1.5bENST000003976385bENSE00001242460chr21:48068370-48068531162ANM2_HUMAN110-163540--
1.6cENST000003976386cENSE00001051373chr21:48069487-48069651165ANM2_HUMAN164-218550--
1.9cENST000003976389cENSE00001336310chr21:48078657-48078832176ANM2_HUMAN219-277590--
1.10aENST0000039763810aENSE00001051359chr21:48080745-48080874130ANM2_HUMAN277-320440--
1.10dENST0000039763810dENSE00001299450chr21:48081712-48081848137ANM2_HUMAN321-366460--
1.11ENST0000039763811ENSE00001801241chr21:48083295-48083466172ANM2_HUMAN366-423580--
1.12bENST0000039763812bENSE00001529484chr21:48084207-48084863657ANM2_HUMAN424-433100--

(-) Sequences/Alignments

NMR Structure
   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 ANM2_HUMAN | P55345 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:106
                                    11        21        31        41        51        61        71        81        91       101      
           ANM2_HUMAN     2 ATSGDCPRSESQGEEPAECSEAGLLQEGVQPEEFVAIADYAATDETQLSFLRGEKILILRQTTADWWWGERAGCCGYIPANHVGKHVDEYDPEDTWQDEEYFGSYG 107
               SCOP domains d1x2      pa_ A                  : automated matches                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------SH3_1-1x2pA01 A:11-56                         -------------------------- Pfam domains
         Sec.struct. author ....------....e------------------eee..................eeeeee.....eeeee.....eeee...ee...---..-----------... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------SH3  PDB: A:10-62 UniProt: 30-89                            ---------SAM_MT_PR PROSITE
               Transcript 1 Exon 1.2    Exon 1.3b  PDB: A:7-23 (gaps)      Exon 1.4a  PDB: A:24-68 (gaps) UniProt: 49-109 [INCOMPLETE] Transcript 1
                 1x2p A   1 GSSG------SSGEE------------------FVAIADYAATDETQLSFLRGEKILILRQTTADWWWGERAGCCGYIPANHVGKHS---GP-----------SSG  68
                               |     -|   |    -         -   |    16        26        36        46        56      |  -||       -   |  
                               4      5   9                 10                                                   63  64|          66  
                                                                                                                      65              

   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)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1X2P)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: SH3 (175)

(-) Gene Ontology  (36, 36)

NMR Structure(hide GO term definitions)
Chain A   (ANM2_HUMAN | P55345)
molecular function
    GO:0050681    androgen receptor binding    Interacting selectively and non-covalently with an androgen receptor.
    GO:0030331    estrogen receptor binding    Interacting selectively and non-covalently with an estrogen receptor.
    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:0008469    histone-arginine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + (histone)-arginine = S-adenosyl-L-homocysteine + (histone)-N-methyl-arginine.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0042975    peroxisome proliferator activated receptor binding    Interacting selectively and non-covalently with any of the peroxisome proliferator activated receptors, alpha, beta or gamma.
    GO:0033142    progesterone receptor binding    Interacting selectively and non-covalently with a progesterone receptor.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0016274    protein-arginine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + (protein)-arginine = S-adenosyl-L-homocysteine + (protein)-N-methyl-arginine.
    GO:0035242    protein-arginine omega-N asymmetric methyltransferase activity    Catalysis of the addition of a second methyl group to methylated peptidyl-arginine. Methylation is on the same terminal nitrogen (omega nitrogen) residue that was previously methylated, resulting in asymmetrical peptidyl-N(omega),N(omega)-dimethylated arginine residues.
    GO:0042974    retinoic acid receptor binding    Interacting selectively and non-covalently with the retinoic acid receptor, a ligand-regulated transcription factor belonging to the nuclear receptor superfamily.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
    GO:0046966    thyroid hormone receptor binding    Interacting selectively and non-covalently with a thyroid hormone receptor.
    GO:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    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.
biological process
    GO:0048588    developmental cell growth    The growth of a cell, where growth contributes to the progression of the cell over time from one condition to another.
    GO:0034969    histone arginine methylation    The modification of a histone by addition of a methyl group to an arginine 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:2000134    negative regulation of G1/S transition of mitotic cell cycle    Any cell cycle regulatory process that prevents the commitment of a cell from G1 to S phase of the mitotic cell cycle.
    GO:0032088    negative regulation of NF-kappaB transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
    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:0035246    peptidyl-arginine N-methylation    The addition of a methyl group onto a nitrogen atom of an arginine residue in a protein.
    GO:0019919    peptidyl-arginine methylation, to asymmetrical-dimethyl arginine    The process of methylation of peptidyl-arginine to form peptidyl-N(omega),N(omega)-dimethyl-L-arginine.
    GO:0043065    positive regulation of apoptotic process    Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
    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:0006479    protein methylation    The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
    GO:0060765    regulation of androgen receptor signaling pathway    Any process that modulates the rate, frequency, or extent of the androgen receptor signaling pathway.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
    GO:0035189    Rb-E2F complex    A multiprotein complex containing a heterodimeric E2F transcription factor and a Retinoblastoma (Rb) family member. This complex is capable of repressing transcription of E2F-regulated genes in order to regulate cell cycle progression.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    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: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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