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(-) Description

Title :  STRUCTURE OF THE IMMUNOGLOBULIN-SUPERFAMILY ECTODOMAIN OF HUMAN CD47
 
Authors :  D. Hatherley, S. C. Graham, J. Turner, K. Harlos, D. I. Stuart, A. N. Barclay
Date :  22 Apr 08  (Deposition) - 12 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Immunoglobulin Domain, Signal Regulatory Protein, Cd47, Membrane, Glycoprotein, Cell Adhesion, Immunoglobulin Superfamily, Pyrrolidone Carboxylic Acid, Transmembrane, Paired Receptor, Alternative Splicing (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Hatherley, S. C. Graham, J. Turner, K. Harlos, D. I. Stuart, A. N. Barclay
Paired Receptor Specificity Explained By Structures Of Signal Regulatory Proteins Alone And Complexed With Cd47.
Mol. Cell V. 31 266 2008
PubMed-ID: 18657508  |  Reference-DOI: 10.1016/J.MOLCEL.2008.05.026

(-) Compounds

Molecule 1 - LEUKOCYTE SURFACE ANTIGEN CD47
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System Cell LineCHO CELLS
    Expression System PlasmidPEE14
    Expression System Taxid10029
    Expression System VariantLEC3.2.8.1
    Expression System Vector TypePLASMID
    FragmentIMMUNOGLOBULIN-SUPERFAMILY ECTODOMAIN, RESIDUES 19-136
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymINTEGRIN-ASSOCIATED PROTEIN, IAP, ANTIGENIC SURFACE DETERMINANT PROTEIN OA3, PROTEIN MER6, CD47

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric Unit (3, 18)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PCA4Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PCA2Mod. Amino AcidPYROGLUTAMIC ACID
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PCA2Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:11 , ASN A:16 , VAL A:19 , VAL A:20 , HOH A:2074 , HOH A:2075BINDING SITE FOR RESIDUE NAG A1116
02AC2SOFTWAREASN A:32 , THR A:34 , NAG A:1118 , LYS D:56 , SER D:57BINDING SITE FOR RESIDUE NAG A1117
03AC3SOFTWARETHR A:34 , ASN A:55 , THR A:61 , NAG A:1117BINDING SITE FOR RESIDUE NAG A1118
04AC4SOFTWAREASN A:93 , GLU B:110BINDING SITE FOR RESIDUE NAG A1119
05AC5SOFTWAREGLU B:11 , ASN B:16 , VAL B:19 , VAL B:20 , HOH B:2102 , HOH B:2103 , HOH B:2104 , VAL C:25 , THR C:26 , HOH C:2026BINDING SITE FOR RESIDUE NAG B1116
06AC6SOFTWAREGLU A:110 , ASN B:93BINDING SITE FOR RESIDUE NAG B1117
07AC7SOFTWARELYS B:75 , GLU C:11 , ASN C:16 , VAL C:19 , VAL C:20 , HOH C:2022 , HOH C:2108BINDING SITE FOR RESIDUE NAG C1116
08AC8SOFTWAREASN A:27 , GLN B:31 , ASN C:32 , THR C:34 , HOH C:2109 , HOH C:2110 , HOH C:2111 , HOH C:2113BINDING SITE FOR RESIDUE NAG C1117
09AC9SOFTWARETHR C:34 , ASN C:55 , HOH C:2114BINDING SITE FOR RESIDUE NAG C1118
10BC1SOFTWAREARG A:114 , GLU B:11 , ASN C:93 , HOH C:2115 , HOH C:2116 , GLU D:110BINDING SITE FOR RESIDUE NAG C1119
11BC2SOFTWAREGLU D:11 , ASN D:16 , VAL D:19 , VAL D:20 , HOH D:2043BINDING SITE FOR RESIDUE NAG D1117
12BC3SOFTWAREGLU C:11 , ASN D:32 , ARG D:114BINDING SITE FOR RESIDUE NAG D1118
13BC4SOFTWARELEU A:101 , HOH A:2077 , HOH A:2078 , HOH A:2079 , HOH A:2080 , HOH A:2081 , HOH A:2082 , LEU B:101BINDING SITE FOR RESIDUE MG A1120
14BC5SOFTWAREHOH C:2119 , HOH C:2120 , HOH C:2121 , HOH C:2122 , HOH C:2123 , HOH C:2124BINDING SITE FOR RESIDUE MG C1120

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:23 -A:96
2B:23 -B:96
3C:23 -C:96
4D:23 -D:96

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2VSC)

(-) Exons   (0, 0)

(no "Exon" information available for 2VSC)

(-) Sequences/Alignments

Asymmetric 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:115
 aligned with CD47_HUMAN | Q08722 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:115
                                    28        38        48        58        68        78        88        98       108       118       128     
           CD47_HUMAN    19 QLLFNKTKSVEFTFCNDTVVIPCFVTNMEAQNTTEVYVKWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKGDASLKMDKSDAVSHTGNYTCEVTELTREGETIIELKYRV 133
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeee..............eeeeeee..eeeeeee....eee...........hhhhhh....eeeehhhhh...eeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2vsc A   1 xLLFNKTKSVEFTFGNDTVVIPCFVTNMEAQNTTEVYVKWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKGDASLKMDKSDAVSHTGNYTCEVTELTREGETIIELKYRV 115
                            |       10        20        30        40        50        60        70        80        90       100       110     
                            |                                                                                                                  
                            1-PCA                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:115
 aligned with CD47_HUMAN | Q08722 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:115
                                    28        38        48        58        68        78        88        98       108       118       128     
           CD47_HUMAN    19 QLLFNKTKSVEFTFCNDTVVIPCFVTNMEAQNTTEVYVKWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKGDASLKMDKSDAVSHTGNYTCEVTELTREGETIIELKYRV 133
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeee.....eeee..ee..........eeeeeee..eeeeeee....eeeee.........hhhhhh....eeeehhhhh...eeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2vsc B   1 xLLFNKTKSVEFTFGNDTVVIPCFVTNMEAQNTTEVYVKWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKGDASLKMDKSDAVSHTGNYTCEVTELTREGETIIELKYRV 115
                            |       10        20        30        40        50        60        70        80        90       100       110     
                            1-PCA                                                                                                              

Chain C from PDB  Type:PROTEIN  Length:115
 aligned with CD47_HUMAN | Q08722 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:115
                                    28        38        48        58        68        78        88        98       108       118       128     
           CD47_HUMAN    19 QLLFNKTKSVEFTFCNDTVVIPCFVTNMEAQNTTEVYVKWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKGDASLKMDKSDAVSHTGNYTCEVTELTREGETIIELKYRV 133
               SCOP domains ------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeee..............eeeeeee..eeeeeee....eeeee.........hhhhhh....eeeehhhhh...eeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 2vsc C   1 xLLFNKTKSVEFTFGNDTVVIPCFVTNMEAQNTTEVYVKWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKGDASLKMDKSDAVSHTGNYTCEVTELTREGETIIELKYRV 115
                            |       10        20        30        40        50        60        70        80        90       100       110     
                            1-PCA                                                                                                              

Chain D from PDB  Type:PROTEIN  Length:116
 aligned with CD47_HUMAN | Q08722 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:116
                                    28        38        48        58        68        78        88        98       108       118       128      
           CD47_HUMAN    19 QLLFNKTKSVEFTFCNDTVVIPCFVTNMEAQNTTEVYVKWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKGDASLKMDKSDAVSHTGNYTCEVTELTREGETIIELKYRVV 134
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -V-set_CD47-2vscD01 D:2-116                                                                                          Pfam domains (1)
           Pfam domains (2) -V-set_CD47-2vscD02 D:2-116                                                                                          Pfam domains (2)
           Pfam domains (3) -V-set_CD47-2vscD03 D:2-116                                                                                          Pfam domains (3)
           Pfam domains (4) -V-set_CD47-2vscD04 D:2-116                                                                                          Pfam domains (4)
         Sec.struct. author ........eeee.....eeee..............eeeeeee..eeeeeee....eee...........hhhhhh....eeeehhhhh...eeeeeeeee..eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 2vsc D   1 xLLFNKTKSVEFTFGNDTVVIPCFVTNMEAQNTTEVYVKWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKGDASLKMDKSDAVSHTGNYTCEVTELTREGETIIELKYRVV 116
                            |       10        20        30        40        50        60        70        80        90       100       110      
                            1-PCA                                                                                                               

   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 2VSC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CD47_HUMAN | Q08722)
molecular function
    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:0070053    thrombospondin receptor activity    Combining with thrombospondin and transmitting the signal to initiate a change in cell activity.
biological process
    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:0030198    extracellular matrix organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of an extracellular matrix.
    GO:0007229    integrin-mediated signaling pathway    A series of molecular signals initiated by the binding of extracellular ligand to an integrin on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    GO:0008228    opsonization    The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody.
    GO:0050870    positive regulation of T cell activation    Any process that activates or increases the frequency, rate or extent of T cell activation.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0022409    positive regulation of cell-cell adhesion    Any process that activates or increases the rate or extent of cell adhesion to another cell.
    GO:0050729    positive regulation of inflammatory response    Any process that activates or increases the frequency, rate or extent of the inflammatory response.
    GO:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    GO:0009617    response to bacterium    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 a stimulus from a bacterium.
cellular component
    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: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
        CD47_HUMAN | Q087222jjs 2jjt 4cmm 4kjy 5iwl 5tz2 5tzt 5tzu

(-) Related Entries Specified in the PDB File

2jjs STRUCTURE OF HUMAN CD47 IN COMPLEX WITH HUMAN SIGNAL REGULATORY PROTEIN (SIRP) ALPHA
2jjt STRUCTURE OF HUMAN CD47 IN COMPLEX WITH HUMAN SIGNAL REGULATORY PROTEIN (SIRP) ALPHA