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(-) Description

Title :  NMR STRUCTURE OF THE MOUSE MFG-E8 C2 DOMAIN
 
Authors :  H. Ye, H. S. Yoon
Date :  21 Feb 11  (Deposition) - 29 Aug 12  (Release) - 20 Feb 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Apoptosis, Phosphatidylserine-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Ye, B. Li, V. Subramanian, B. H. Choi, Y. Liang, A. Harikishore, G. Chakraborty, K. Baek, H. S. Yoon
Nmr Solution Structure Of C2 Domain Of Mfg-E8 And Insights Into Its Molecular Recognition With Phosphatidylserine
Biochim. Biophys. Acta V. 1828 1083 2013
PubMed-ID: 23262193  |  Reference-DOI: 10.1016/J.BBAMEM.2012.12.009

(-) Compounds

Molecule 1 - LACTADHERIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET29B
    Expression System Vector TypeVECTOR
    FragmentC2 DOMAIN
    GeneMFGE8
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymMFGM, MILK FAT GLOBULE-EGF FACTOR 8, MFG-E8, SED1, SPERM SURFACE PROTEIN SP47, MP47

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2L9L)

(-) Sites  (0, 0)

(no "Site" information available for 2L9L)

(-) SS Bonds  (1, 1)

NMR Structure
No.Residues
1A:1 -A:156

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2L9L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2L9L)

(-) PROSITE Motifs  (3, 3)

NMR Structure (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FA58C_3PS50022 Coagulation factors 5/8 type C domain (FA58C) profile.MFGM_MOUSE148-303
308-463
  1-
A:1-156
2FA58C_1PS01285 Coagulation factors 5/8 type C domain (FA58C) signature 1.MFGM_MOUSE194-223
355-384
  1-
A:48-77
3FA58C_2PS01286 Coagulation factors 5/8 type C domain (FA58C) signature 2.MFGM_MOUSE287-303
447-463
  1-
A:140-156
NMR Structure * (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FA58C_3PS50022 Coagulation factors 5/8 type C domain (FA58C) profile.MFGM_MOUSE148-303
308-463
  1-
A:1-156
2FA58C_1PS01285 Coagulation factors 5/8 type C domain (FA58C) signature 1.MFGM_MOUSE194-223
355-384
  1-
A:48-77
3FA58C_2PS01286 Coagulation factors 5/8 type C domain (FA58C) signature 2.MFGM_MOUSE287-303
447-463
  1-
A:140-156

(-) Exons   (0, 0)

(no "Exon" information available for 2L9L)

(-) 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:164
 aligned with MFGM_MOUSE | P21956 from UniProtKB/Swiss-Prot  Length:463

    Alignment length:214
                                                                                                                                                                                                                                             463  
                                   261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461 |  
           MFGM_MOUSE   252 DESGGDKEFLGNLDNNSLKVNMFNPTLEAQYIKLYPVSCHRGCTLRFELLGCELHGCSEPLGLKNNTIPDSQMSASSSYKTWNLRAFGWYPHLGRLDNQGKINAWTAQSNSAKEWLQVDLGTQRQVTGIITQGARDFGHIQYVASYKVAHSDDGVQWTVYEEQGSSKVFQGNLDNNSHKKNIFEKPFMARYVRVLPVSWHNRITLRLELLGC--   -
               SCOP domains d2l9                                                  la_ A: automated matches                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....--------------------------------------------------..................eee.............................ee.........eeeeeeeeeeeeeeeeee.ee..ee.eeeeeeeeee.....ee..........ee........eee.....eeeeeeeeeeeeee...eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) FA58C_3  PDB: - UniProt: 148-303                    ----FA58C_3  PDB: A:1-156 UniProt: 308-463                                                                                                                      -- PROSITE (1)
                PROSITE (2) -----------------------------------FA58C_2  PDB: -  ---------------------------------------------------FA58C_1  PDB: A:48-77         --------------------------------------------------------------FA58C_2          -- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2l9l A  -5 MKSG--------------------------------------------------HGCSEPLGLKNNTIPDSQMSASSSYKTWNLRAFGWYPHLGRLDNQGKINAWTAQSNSAKEWLQVDLGTQRQVTGIITQGARDFGHIQYVASYKVAHSDDGVQWTVYEEQGSSKVFQGNLDNNSHKKNIFEKPFMARYVRVLPVSWHNRITLRLELLGCLE 158
                               |     -         -         -         -         -    |    4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154    
                              -2                                                 -1                                                                                                                                                               

   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 2L9L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2L9L)

(-) Gene Ontology  (20, 20)

NMR Structure(hide GO term definitions)
Chain A   (MFGM_MOUSE | P21956)
molecular function
    GO:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0008429    phosphatidylethanolamine binding    Interacting selectively and non-covalently with phosphatidylethanolamine, any of a class of glycerophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of ethanolamine.
    GO:0001786    phosphatidylserine binding    Interacting selectively and non-covalently with phosphatidylserine, a class of glycophospholipids in which a phosphatidyl group is esterified to the hydroxyl group of L-serine.
biological process
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0006911    phagocytosis, engulfment    The internalization of bacteria, immune complexes and other particulate matter or of an apoptotic cell by phagocytosis, including the membrane and cytoskeletal processes required, which involves one of three mechanisms: zippering of pseudopods around a target via repeated receptor-ligand interactions, sinking of the target directly into plasma membrane of the phagocytosing cell, or induced uptake via an enhanced membrane ruffling of the phagocytosing cell similar to macropinocytosis.
    GO:0006910    phagocytosis, recognition    The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
    GO:2000427    positive regulation of apoptotic cell clearance    Any process that activates or increases the frequency, rate or extent of apoptotic cell clearance.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    GO:0043627    response to estrogen    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 stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
    GO:0007338    single fertilization    The union of male and female gametes to form a zygote.
cellular component
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:1903561    extracellular vesicle    Any vesicle that is part of the extracellular region.
    GO:0019897    extrinsic component of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to one of its surfaces, but not integrated into the hydrophobic region.
    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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