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(-) Description

Title :  STRUCTURE OF HUMAN CD47 IN COMPLEX WITH HUMAN SIGNAL REGULATORY PROTEIN (SIRP) ALPHA V1
 
Authors :  D. Hatherley, S. M. Lea, S. Johnson, A. N. Barclay
Date :  16 Jan 14  (Deposition) - 26 Feb 14  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.92
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Signaling Protein, Paired Receptor, Immunological, Inhibitory (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Hatherley, S. M. Lea, S. Johnson, A. N. Barclay
Polymorphisms In The Human Inhibitory Signal-Regulatory Protein Alpha Do Not Affect Binding To Its Ligand Cd47.
J. Biol. Chem. V. 289 10024 2014
PubMed-ID: 24550402  |  Reference-DOI: 10.1074/JBC.M114.550558

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN PHOSPHATASE NON-RECEPTOR TYPE SUBSTRATE 1
    ChainsA
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System Cell LineCHO
    Expression System CommonCHINESE HAMSTER
    Expression System PlasmidPEE14
    Expression System Taxid10029
    Expression System VariantLEC3.2.8.1
    Expression System Vector TypePLASMID
    FragmentEXTRACELLULAR DOMAIN, RESIDUES 31-149
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSHP SUBSTRATE 1, SHPS-1, BRAIN IG-LIKE MOLECULE WITH TYROSINE-BASED ACTIVATION MOTIFS, BIT, CD172 ANTIGEN-LIKE FAMILY MEMBER A, INHIBITORY RECEPTOR SHPS-1, MACROPHAGE FUSION RECEPTOR, MYD-1 ANTIGEN, SIGNAL-REGULATORY PROTEIN ALPHA-1, SIRP-ALPHA-1, SIGNAL-REGULATORY PROTEIN ALPHA-2, SIRP-ALPHA-2, SIGNAL-REGULATORY PROTEIN ALPHA-3, SIRP-ALPHA-3, P84, SIGNAL REGULATORY PROTEIN SIRP ALPHA V1
 
Molecule 2 - LEUKOCYTE SURFACE ANTIGEN CD47
    ChainsB
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System Cell LineCHO
    Expression System CommonCHINESE HAMSTER
    Expression System PlasmidPEE14
    Expression System Taxid10029
    Expression System VariantLEC3.2.8.1
    Expression System Vector TypePLASMID
    FragmentEXTRACELLULAR DOMAIN, RESIDUES 19-136
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymANTIGENIC SURFACE DETERMINANT PROTEIN OA3, INTEGRIN- ASSOCIATED PROTEIN, IAP, PROTEIN MER6

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
2PCA1Mod. Amino AcidPYROGLUTAMIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:5 , PHE B:24 , LEU B:54 , LYS B:56 , HOH B:2076BINDING SITE FOR MONO-SACCHARIDE NAG B1123 BOUND TO ASN B 5
2AC2SOFTWAREGLU B:11 , ASN B:16 , VAL B:19 , VAL B:20 , HOH B:2074 , HOH B:2075BINDING SITE FOR MONO-SACCHARIDE NAG B1121 BOUND TO ASN B 16
3AC3SOFTWAREASN B:32BINDING SITE FOR MONO-SACCHARIDE NAG B1122 BOUND TO ASN B 32
4AC4SOFTWAREASN B:93 , GLU B:110 , HOH B:2077BINDING SITE FOR MONO-SACCHARIDE NAG B1124 BOUND TO ASN B 93

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:25 -A:91
2B:23 -B:96

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ile A:31 -Pro A:32
2Ser A:98 -Pro A:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (19, 19)

Asymmetric/Biological Unit (19, 19)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_015464D40ESHPS1_HUMANPolymorphism  ---AD10E
02UniProtVAR_015465L44SSHPS1_HUMANPolymorphism1135193AL14S
03UniProtVAR_015466T50SSHPS1_HUMANPolymorphism17855609AT20S
04UniProtVAR_015468T52ISHPS1_HUMANPolymorphism17855610AT22I
05UniProtVAR_015470R54HSHPS1_HUMANPolymorphism17855611AR24H
06UniProtVAR_015471A57VSHPS1_HUMANPolymorphism17855612AA27V
07UniProtVAR_015472I61NSHPS1_HUMANPolymorphism  ---AI31N
08UniProtVAR_015473W68RSHPS1_HUMANPolymorphism  ---AW38R
09UniProtVAR_015474G75ASHPS1_HUMANPolymorphism1057114AG45A
10UniProtVAR_015475E77KSHPS1_HUMANPolymorphism  ---AE47K
11UniProtVAR_015477N81HSHPS1_HUMANPolymorphism  ---AN51H
12UniProtVAR_015478D95ESHPS1_HUMANPolymorphism138283486AD65E
13UniProtVAR_015479L96SSHPS1_HUMANPolymorphism  ---AL66S
14UniProtVAR_015480N100ESHPS1_HUMANPolymorphism386811662AN70E
15UniProtVAR_015483R107SSHPS1_HUMANPolymorphism17855615AR77S
16UniProtVAR_015484G109SSHPS1_HUMANPolymorphism17855616AG79S
17UniProtVAR_015485R125QSHPS1_HUMANPolymorphism767136065AR95Q
18UniProtVAR_015486V132TSHPS1_HUMANPolymorphism386811663AV102T
19UniProtVAR_015487F134LSHPS1_HUMANPolymorphism  ---AF104L

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CMM)

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000004000681bENSE00001927472chr20:1875154-187516310SHPS1_HUMAN-00--
1.3bENST000004000683bENSE00001426544chr20:1876085-187617288SHPS1_HUMAN1-27270--
1.4ENST000004000684ENSE00001673100chr20:1895745-1896101357SHPS1_HUMAN27-1461201A:3-116114
1.5ENST000004000685ENSE00001805661chr20:1902041-1902358318SHPS1_HUMAN146-2521071A:116-1194
1.6ENST000004000686ENSE00001735773chr20:1902959-1903291333SHPS1_HUMAN252-3631120--
1.7ENST000004000687ENSE00000655714chr20:1905410-1905523114SHPS1_HUMAN363-401390--
1.8ENST000004000688ENSE00001043117chr20:1908521-190854525SHPS1_HUMAN401-40990--
1.9bENST000004000689bENSE00001541433chr20:1915361-191541252SHPS1_HUMAN409-426180--
1.10bENST0000040006810bENSE00001841036chr20:1917966-19205432578SHPS1_HUMAN427-508820--

(-) 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:117
 aligned with SHPS1_HUMAN | P78324 from UniProtKB/Swiss-Prot  Length:504

    Alignment length:117
                                    42        52        62        72        82        92       102       112       122       132       142       
          SHPS1_HUMAN    33 ELQVIQPDKSVLVAAGETATLRCTATSLIPVGPIQWFRGAGPGRELIYNQKEGHFPRVTTVSDLTKRNNMDFSIRIGNITPADAGTYYCVKFRKGSPDDVEFKSGAGTELSVRAKPS 149
               SCOP domains d4cmma_ A: automated matches                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeeee....eee..ee........eeeee......eeee.........eee.............eee...hhhhheeeeeeeee......eeeee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------E---S-----S-I-H--V---N------R------A-K---H-------------ES---E------S-S---------------Q------T-L--------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:3-116 UniProt: 27-146 [INCOMPLETE]                                                               --- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------1.5  Transcript 1 (2)
                 4cmm A   3 ELQVIQPDKSVLVAAGETATLRCTATSLIPVGPIQWFRGAGPGRELIYNQKEGHFPRVTTVSDLTKRNNMDFSIRIGNITPADAGTYYCVKFRKGSPDDVEFKSGAGTELSVRAKPS 119
                                    12        22        32        42        52        62        72        82        92       102       112       

Chain B from PDB  Type:PROTEIN  Length:120
 aligned with CD47_HUMAN | Q08722 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:120
                                    28        38        48        58        68        78        88        98       108       118       128       138
           CD47_HUMAN    19 QLLFNKTKSVEFTFCNDTVVIPCFVTNMEAQNTTEVYVKWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKGDASLKMDKSDAVSHTGNYTCEVTELTREGETIIELKYRVVSWFS 138
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeee.....eeee..........hhh.eeeeeee..eeeeeee.hhheee.hhhhh....hhhhhhhh...eeeehhhhhhh.eeeeeeeee..eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4cmm B   1 xLLFNKTKSVEFTFGNDTVVIPCFVTNMEAQNTTEVYVKWKFKGRDIYTFDGALNKSTVPTDFSSAKIEVSQLLKGDASLKMDKSDAVSHTGNYTCEVTELTREGETIIELKYRVVSWST 120
                            |       10        20        30        40        50        60        70        80        90       100       110       120
                            |                                                                                                                       
                            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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CMM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CMM)

(-) Gene Ontology  (19, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SHPS1_HUMAN | P78324)
molecular function
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
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:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
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: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.

Chain B   (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 2vsc 4kjy 5iwl 5tz2 5tzt 5tzu
        SHPS1_HUMAN | P783242jjs 2jjt 2uv3 2wng

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4CMM)