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(-) Description

Title :  HIGH RESOLUTION STRUCTURE OF HUMAN CD59
 
Authors :  K. J. Leath, S. Johnson, P. Roversi, B. P. Morgan, R. A. G. Smith, S. M. Lea
Date :  24 Oct 06  (Deposition) - 07 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Lipid-Binding Protein, Glycoprotein, Lipid-Binding Protein Mac, Membrane, Gpi-Anchor, Complement, Lipoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. J. Leath, S. Johnson, P. Roversi, T. R. Hughes, R. A. G. Smith, L. Mackenzie, B. P. Morgan, S. M. Lea
High-Resolution Structures Of Bacterially Expressed Soluble Human Cd59.
Acta Crystallogr. , Sect. F V. 63 648 2007
PubMed-ID: 17671359  |  Reference-DOI: 10.1107/S1744309107033477

(-) Compounds

Molecule 1 - CD59 GLYCOPROTEIN
    CellLYMPHOCYTES, ERYTHROCYTES, PLATELETS, ENDOTHELIA, EPITHELIA
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET59-06
    Expression System StrainUT5600 (DE3)
    Expression System Taxid562
    FragmentMATURE POLYPEPTIDE, RESIDUES 26-103
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsPURIFIED FROM INCLUSION BODIES AFTER EXPRESSION IN ESCHERICHIA COLI
    SynonymMEMBRANE ATTACK COMPLEX INHIBITION FACTOR, MACIF, MAC-INHIBITORY PROTEIN, MAC-IP, PROTECTIN, MEM43 ANTIGEN, MEMBRANE INHIBITOR OF REACTIVE LYSIS, MIRL, 20 KDA HOMOLOGOUS RESTRICTION FACTOR, HRF-20,HRF20,1F5 ANTIGEN, CD59

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2J8B)

(-) Sites  (0, 0)

(no "Site" information available for 2J8B)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:3 -A:26
2A:6 -A:13
3A:19 -A:39
4A:45 -A:63
5A:45 -A:63
6A:64 -A:69

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2J8B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_070124C89YCD59_HUMANDisease (HACD59)397514767AC64Y

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LY6_UPARPS00983 Ly-6 / u-PAR domain signature.CD59_HUMAN27-70  1A:2-45

(-) Exons   (2, 2)

Asymmetric/Biological Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003958501bENSE00002148709chr11:33757985-3375792858CD59_HUMAN-00--
1.5eENST000003958505eENSE00000824399chr11:33744009-3374392585CD59_HUMAN1-23230--
1.6bENST000003958506bENSE00000710249chr11:33739017-33738916102CD59_HUMAN23-57351A:0-3233
1.8lENST000003958508lENSE00002144344chr11:33731889-337302461644CD59_HUMAN57-128721A:32-7746

(-) 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:78
 aligned with CD59_HUMAN | P13987 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:78
                                    34        44        54        64        74        84        94        
           CD59_HUMAN    25 SLQCYNCPNPTADCKTAVNCSSDFDACLITKAGLQVYNKCWKFEHCNFNDVTTRLRENELTYYCCKKDLCNFNEQLEN 102
               SCOP domains d2j8ba_ A: CD59                                                                SCOP domains
               CATH domains 2j8bA00 A:0-77 CD59                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee...........eee......eeeeeee..eeeeeeehhhhhhhhhhhhhhh....eeeee......hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------Y------------- SAPs(SNPs)
                    PROSITE --LY6_UPAR  PDB: A:2-45 UniProt: 27-70        -------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6b  PDB: A:0-32           --------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.8l  PDB: A:32-77 UniProt: 57-128        Transcript 1 (2)
                 2j8b A   0 MLQCYNCPNPTADCKTAVNCSSDFDACLITKAGLQVYNKCWKFEHCNFNDVTTRLRENELTYYCCKKDLCNFNEQLEN  77
                                     9        19        29        39        49        59        69        

   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J8B)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CD59_HUMAN | P13987)
molecular function
    GO:0001848    complement binding    Interacting selectively and non-covalently with any component or product of the complement cascade.
    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).
biological process
    GO:0048208    COPII vesicle coating    The addition of COPII proteins and adaptor proteins to ER membranes during the formation of transport vesicles, forming a vesicle coat.
    GO:0006888    ER to Golgi vesicle-mediated transport    The directed movement of substances from the endoplasmic reticulum (ER) to the Golgi, mediated by COP II vesicles. Small COP II coated vesicles form from the ER and then fuse directly with the cis-Golgi. Larger structures are transported along microtubules to the cis-Golgi.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0001775    cell activation    A change in the morphology or behavior of a cell resulting from exposure to an activating factor such as a cellular or soluble ligand.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0001971    negative regulation of activation of membrane attack complex    Any process that stops, prevents, or reduces the frequency, rate or extent of the activation of the membrane attack complex components of the complement cascade.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0030449    regulation of complement activation    Any process that modulates the frequency, rate or extent of complement activation.
cellular component
    GO:0012507    ER to Golgi transport vesicle membrane    The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0031362    anchored component of external side of plasma membrane    The component of the plasma membrane consisting of the gene products that are tethered to the external side of the membrane only by a covalently attached anchor, such as a lipid group embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0031225    anchored component of membrane    The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0043218    compact myelin    The portion of the myelin sheath in which layers of cell membrane are tightly juxtaposed, completely excluding cytoplasm. The juxtaposed cytoplasmic surfaces form the major dense line, while the juxtaposed extracellular surfaces form the interperiod line visible in electron micrographs.
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0033116    endoplasmic reticulum-Golgi intermediate compartment membrane    The lipid bilayer surrounding any of the compartments of the endoplasmic reticulum (ER)-Golgi intermediate compartment system.
    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: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: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: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.
    GO:0042383    sarcolemma    The outer membrane of a muscle cell, consisting of the plasma membrane, a covering basement membrane (about 100 nm thick and sometimes common to more than one fiber), and the associated loose network of collagen fibers.
    GO:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CD59_HUMAN | P139871cdq 1cdr 1cds 1erg 1erh 2ofs 2uwr 2ux2 4bik 5imt 5imy

(-) Related Entries Specified in the PDB File

1cdq CD59 (NMR, 20 STRUCTURES)
1cdr CD59 COMPLEXED WITH GLCNAC-BETA-1,4-GLCNAC -BETA-1 (NMR, 10 STRUCTURES)
1cds CD59 COMPLEXED WITH GLCNAC-BETA-1,4-(FUC- ALPHA-1,6)- GLCNAC-BETA-1 (NMR, 10 STRUCTURES)
1erg
1erh
2uwr HIGH RESOLUTION STRUCTURE OF HUMAN CD59
2ux2 HIGH RESOLUTION STRUCTURE OF HUMAN CD59