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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE MONOMERIC SRCR DOMAIN OF MOUSE MARCO
 
Authors :  J. R. M. Ojala, T. Pikkarainen, A. Tuuttila, T. Sandalova, K. Tryggvason
Date :  21 Feb 07  (Deposition) - 17 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A
Keywords :  Extracellular Matrix, Scavenger Receptor Cysteine-Rich (Srcr), Macrophage Receptor, Ligand Binding Domain, Basic Cluster, Acidic Cluster, Ligand Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Ojala, T. Pikkarainen, A. Tuuttila, T. Sandalova, K. Tryggvason
Crystal Structure Of The Cysteine-Rich Domain Of Scavenger Receptor Marco Reveals The Presence Of A Basic And An Acidic Cluster That Both Contribute To Ligand Recognition.
J. Biol. Chem. V. 282 16654 2007
PubMed-ID: 17405873  |  Reference-DOI: 10.1074/JBC.M701750200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MACROPHAGE RECEPTOR MARCO
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: EMBRYONIC KIDNEY CELLS
    Expression System Common: HUMAN
    Expression System Plasmid: PCEP-PU
    Expression System Strain: 293-EBNA
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN, SCAVENGER RECEPTOR CYSTEINE- RICH DOMAIN (SRCR)
    Gene: MARCO
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: C57BL/6
    Synonym: MACROPHAGE RECEPTOR WITH COLLAGENOUS STRUCTURE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:7 , HOH A:16 , HOH A:21 , HOH A:24 , HOH A:31 , ASP A:448BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWAREHOH A:15 , HOH A:53 , ASP A:449 , ASP A:451 , ASP A:454 , VAL A:485BINDING SITE FOR RESIDUE MG A 202

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:446 -A:507
2A:459 -A:517
3A:487 -A:497

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2OY3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OY3)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SRCR_2PS50287 SRCR domain profile.MARCO_MOUSE423-518  1A:423-518
2SRCR_1PS00420 SRCR domain signature.MARCO_MOUSE426-463  1A:426-463

(-) Exons   (0, 0)

(no "Exon" information available for 2OY3)

(-) Sequences/Alignments

Asymmetric/Biological 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:98
 aligned with MARCO_MOUSE | Q60754 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:98
                                   430       440       450       460       470       480       490       500       510        
          MARCO_MOUSE   421 QRVRIMGGTNRGRAEVYYNNEWGTICDDDWDNNDATVFCRMLGYSRGRALSSYGGGSGNIWLDNVNCRGTENSLWDCSKNSWGNHNCVHNEDAGVECS 518
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2oy3A00 A:421-518 Mac-2 Binding Protein;                                                           CATH domains
               Pfam domains -----SRCR-2oy3A01 A:426-518                                                                        Pfam domains
         Sec.struct. author ..eeeee...eeeeeeee..eeeee.....hhhhhhhhhhh....eeeee.........eee..........hhhhh..........hhhhh.eeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --SRCR_2  PDB: A:423-518 UniProt: 423-518                                                          PROSITE (1)
                PROSITE (2) -----SRCR_1  PDB: A:426-463                ------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 2oy3 A 421 QRVRIMGGTNRGRAEVYYNNEWGTICDDDWDNNDATVFCRMLGYSRGRALSSYGGGSGNIWLDNVNCRGTENSLWDCSKNSWGNHNCVHNEDAGVECS 518
                                   430       440       450       460       470       480       490       500       510
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 2OY3)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SRCR] (5)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MARCO_MOUSE | Q60754)
molecular function
    GO:0005044    scavenger receptor activity    Combining with any modified low-density lipoprotein (LDL) or other polyanionic ligand and delivering the ligand into the cell via endocytosis. Ligands include acetylated and oxidized LDL, Gram-positive and Gram-negative bacteria, apoptotic cells, amyloid-beta fibrils, and advanced glycation end products (AGEs).
biological process
    GO:0043277    apoptotic cell clearance    The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    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:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
cellular component
    GO:0005581    collagen trimer    A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
    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: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
        MARCO_MOUSE | Q60754: 2oya

(-) Related Entries Specified in the PDB File

2oya