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(-) Description

Title :  MOLECULAR MODEL OF DOMAINS 3 AND 4 OF MEMBRANE COFACTOR PROTEIN (MCP, CD46)
 
Authors :  T. S. Jokiranta, C. Bagley, D. L. Gordon
Date :  20 Dec 00  (Deposition) - 28 Jun 02  (Release) - 01 Nov 02  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Mcp, Cd46, Theoretical Model, Sushi-Domain, Scr-Domain, Short Consensus Repeat Domain, Complement (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Giannakis, T. S. Jokiranta, R. J. Ormsby, T. G. Duthy, D. A. Male, D. Christiansen, V. A. Fischetti, C. Bagley, B. E. Loveland, D. L. Gordon
Identification Of The Streptococcal M Protein Binding Site On Membrane Cofactor Protein (Cd46).
J. Immunol. V. 168 4585 2002
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MEMBRANE COFACTOR PROTEIN
    ChainsA
    FragmentDOMAINS 3-4, RESIDUES 159-284
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymMCP, CD46, TROPHOBLAST LEUCOCYTE COMMON ANTIGEN, TLX

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1HR4)

(-) Sites  (0, 0)

(no "Site" information available for 1HR4)

(-) SS Bonds  (4, 4)

Theoretical Model
No.Residues
1A:4 -A:52
2A:33 -A:65
3A:70 -A:112
4A:98 -A:125

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1HR4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 7)

Theoretical Model (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_026569P165SMCP_HUMANDisease (AHUS2)759136081AP7S
2UniProtVAR_063657W216CMCP_HUMANDisease (AHUS2)  ---AW58C
3UniProtVAR_035828C228YMCP_HUMANUnclassified  ---AC70Y
4CancerSNPVAR_MCP_HUMAN_CCDS1479_1_01 *C228YMCP_HUMANDisease (Colorectal cancer)  ---AC70Y
5UniProtVAR_063658P231RMCP_HUMANDisease (AHUS2)  ---AP73R
6UniProtVAR_026570S240PMCP_HUMANDisease (AHUS2)121909589AS82P
7UniProtVAR_022262D266NMCP_HUMANPolymorphism17006830AD108N
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 2)

Theoretical Model (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUSHIPS50923 Sushi/CCP/SCR domain profile.MCP_HUMAN33-96
97-159
160-225
226-285
  2-
-
A:2-67
A:68-126

(-) Exons   (3, 3)

Theoretical Model (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003581701aENSE00001225216chr1:207925402-207925654253MCP_HUMAN1-33330--
1.2ENST000003581702ENSE00001600549chr1:207930359-207930547189MCP_HUMAN33-96640--
1.3ENST000003581703ENSE00001725236chr1:207930885-207930987103MCP_HUMAN96-130350--
1.4aENST000003581704aENSE00001719360chr1:207932984-20793306986MCP_HUMAN130-159301A:1-11
1.4dENST000003581704dENSE00001167611chr1:207934594-207934791198MCP_HUMAN159-225671A:1-6767
1.5bENST000003581705bENSE00001167601chr1:207940358-207940540183MCP_HUMAN225-286621A:67-12660
1.5eENST000003581705eENSE00001320886chr1:207940952-20794099645MCP_HUMAN286-301160--
1.5fENST000003581705fENSE00000792032chr1:207941124-20794116845MCP_HUMAN301-316160--
1.5jENST000003581705jENSE00001167583chr1:207943666-20794370742MCP_HUMAN316-330150--
1.6aENST000003581706aENSE00001167577chr1:207956637-20795667539MCP_HUMAN330-343140--
1.7ENST000003581707ENSE00001167569chr1:207958416-20795845136MCP_HUMAN343-355130--
1.8aENST000003581708aENSE00001167565chr1:207958964-20795902764MCP_HUMAN355-376220--
1.9bENST000003581709bENSE00001162717chr1:207963598-20796369093MCP_HUMAN376-392170--
1.10eENST0000035817010eENSE00001643557chr1:207966864-2079688581995MCP_HUMAN-00--

(-) Sequences/Alignments

Theoretical Model
   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:126
 aligned with MCP_HUMAN | P15529 from UniProtKB/Swiss-Prot  Length:392

    Alignment length:126
                                   168       178       188       198       208       218       228       238       248       258       268       278      
            MCP_HUMAN   159 KVLCTPPPKIKNGKHTFSEVEVFEYLDAVTYSCDPAPGPDPFSLIGESTIYCGDNSVWSRAAPECKVVKCRFPVVENGKQISGFGKKFYYKATVMFECDKGFYLDGSDTIVCDSNSTWDPPVPKCL 284
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........................ee....................ee............................eee............eee.....ee....................ee Sec.struct. author
             SAPs(SNPs) (1) ------S--------------------------------------------------C-----------Y--R--------P-------------------------N------------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------Y-------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE SSUSHI  PDB: A:2-67 UniProt: 160-225                               SUSHI  PDB: A:68-126 UniProt: 226-285                       PROSITE
           Transcript 1 (1) 1-----------------------------------------------------------------Exon 1.5b  PDB: A:67-126 UniProt: 225-286 [INCOMPLETE]       Transcript 1 (1)
           Transcript 1 (2) Exon 1.4d  PDB: A:1-67 UniProt: 159-225                            ----------------------------------------------------------- Transcript 1 (2)
                 1hr4 A   1 KVLCTPPPKIKNGKHTFSEVEVFEYLDAVTYSCDPAPGPDPFSLIGESTIYCGDNSVWSRAAPECKVVKCRFPVVENGKQISGFGKKFYYKATVMFECDKGFYLDGSDTIVCDSNSTWDPPVPKCL 126
                                    10        20        30        40        50        60        70        80        90       100       110       120      

   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 1HR4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1HR4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1HR4)

(-) Gene Ontology  (42, 42)

Theoretical Model(hide GO term definitions)
Chain A   (MCP_HUMAN | P15529)
molecular function
    GO:0045296    cadherin binding    Interacting selectively and non-covalently with cadherin, a type I membrane protein involved in cell adhesion.
    GO:0001848    complement binding    Interacting selectively and non-covalently with any component or product of the complement cascade.
    GO:0004175    endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
    GO:0004857    enzyme inhibitor activity    Binds to and stops, prevents or reduces the activity of an enzyme.
    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:0004872    receptor activity    Combining with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0001618    virus receptor activity    Combining with a virus component and mediating entry of the virus into the cell.
biological process
    GO:0002456    T cell mediated immunity    Any process involved in the carrying out of an immune response by a T cell.
    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:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0032613    interleukin-10 production    The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0045916    negative regulation of complement activation    Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0032733    positive regulation of interleukin-10 production    Any process that activates or increases the frequency, rate, or extent of interleukin-10 production.
    GO:0043382    positive regulation of memory T cell differentiation    Any process that activates or increases the frequency, rate or extent of memory T cell differentiation.
    GO:0045591    positive regulation of regulatory T cell differentiation    Any process that activates or increases the frequency, rate or extent of differentiation of regulatory T cells.
    GO:0071636    positive regulation of transforming growth factor beta production    Any process that activates or increases the frequency, rate, or extent of production of transforming growth factor-beta.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0008593    regulation of Notch signaling pathway    Any process that modulates the frequency, rate or extent of the Notch signaling pathway.
    GO:0030449    regulation of complement activation    Any process that modulates the frequency, rate or extent of complement activation.
    GO:0035581    sequestering of extracellular ligand from receptor    The process of binding or confining an extracellular signaling ligand, such that the ligand is unable to bind to its cell surface receptor.
    GO:0007338    single fertilization    The union of male and female gametes to form a zygote.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0001669    acrosomal vesicle    A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.
    GO:0016323    basolateral plasma membrane    The region of the plasma membrane that includes the basal end and sides of the cell. Often used in reference to animal polarized epithelial membranes, where the basal membrane is the part attached to the extracellular matrix, or in plant cells, where the basal membrane is defined with respect to the zygotic axis.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0002079    inner acrosomal membrane    The acrosomal membrane region that underlies the acrosomal vesicle and is located toward the sperm nucleus. This region is responsible for molecular interactions allowing the sperm to penetrate the zona pellucida and fuses with the egg plasma membrane.
    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:0005887    integral component of plasma membrane    The component of the plasma 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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MCP_HUMAN | P155291ckl 2o39 3inb 3l89 3o8e 5fo8

(-) Related Entries Specified in the PDB File

1ckl STRUCTURE OF CD46 (MCP) DOMAINS 1 AND 2