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(-) Description

Title :  SOLUTION STRUCTURE OF THE RING DOMAIN OF THE HUMAN CELLULAR MODULATOR OF IMMUNE RECOGNITION PROTEIN
 
Authors :  K. Miyamoto, T. Kigawa, T. Tomizawa, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  08 Dec 05  (Deposition) - 08 Jun 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Cellular Modulator Of Immune Recognition, C-Mir, March8, Ring Domain, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Miyamoto, T. Kigawa, T. Tomizawa, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The Ring Domain Of The Human Cellular Modulator Of Immune Recognition Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CELLULAR MODULATOR OF IMMUNE RECOGNITION
    ChainsA
    EngineeredYES
    Expression System PlasmidP041123-09
    Expression System Vector TypePLASMID
    FragmentRING DOMAIN
    GeneMARCH8
    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  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:18 , CYS A:21 , HIS A:45 , CYS A:48BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:35 , CYS A:37 , CYS A:61 , CYS A:64BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2D8S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D8S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

NMR Structure (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_030266P92SMARH8_HUMANPolymorphism3764990AP30S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_RING_CHPS51292 Zinc finger RING-CH-type profile.MARH8_HUMAN72-133  1A:10-71

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000003957692ENSE00001522774chr10:46030819-46030659161MARH8_HUMAN-00--
1.4bENST000003957694bENSE00001191569chr10:46028737-46028558180MARH8_HUMAN1-34340--
1.5ENST000003957695ENSE00001191553chr10:45984865-4598481551MARH8_HUMAN35-51170--
1.6ENST000003957696ENSE00001191549chr10:45959775-4595968789MARH8_HUMAN52-81301A:1-19 (gaps)29
1.8cENST000003957698cENSE00001140823chr10:45956859-45956679181MARH8_HUMAN81-141611A:19-7557
1.9ENST000003957699ENSE00001092853chr10:45954715-45954568148MARH8_HUMAN142-191501A:76-805
1.10bENST0000039576910bENSE00001870745chr10:45953991-459529541038MARH8_HUMAN191-2911011A:80-801

(-) 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:80
 aligned with MARH8_HUMAN | Q5T0T0 from UniProtKB/Swiss-Prot  Length:291

    Alignment length:139
                                    62        72        82        92       102       112       122       132       142       152       162       172       182         
          MARH8_HUMAN    53 GSPPSASAPAPVSSFSRTSITPSSQDICRICHCEGDDESPLITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMETKLKPLRKWEKLQMTSSERRKIMCSVTFHVIAITCVVWSLYVLIDRTAEEIKQGQATG 191
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..--...--------.........................ee...........ee.hhhhhhhhhhh..................-------------------------------------------------..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------S--------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------ZF_RING_CH  PDB: A:10-71 UniProt: 72-133                      ---------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:1-19 (gaps) -------------------------------------------------------------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) ----------------------------Exon 1.8c  PDB: A:19-75 UniProt: 81-141 [INCOMPLETE]         Exon 1.9  PDB: A:76-80 UniProt: 142-191            Transcript 1 (2)
                 2d8s A   1 GS--SGS--------SGTSITPSSQDICRICHCEGDDESPLITPCHCTGSLHFVHQACLQQWIKSSDTRCCELCKYEFIMETKLS-------------------------------------------------GPSSG  80
                             |  | |  -     |  10        20        30        40        50        60        70    |    -         -         -         -         -    |    
                             2  3 5        6                                                                   75                                                76    

   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  (0, 0)

(no "SCOP Domain" information available for 2D8S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D8S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D8S)

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (MARH8_HUMAN | Q5T0T0)
molecular function
    GO:0042289    MHC class II protein binding    Interacting selectively and non-covalently with major histocompatibility complex class II molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0002495    antigen processing and presentation of peptide antigen via MHC class II    The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045347    negative regulation of MHC class II biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class II.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
cellular component
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0030659    cytoplasmic vesicle membrane    The lipid bilayer surrounding a cytoplasmic vesicle.
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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