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(-) Description

Title :  FITTED STRUCTURE OF SCR4 OF DAF INTO CRYOEM DENSITY
 
Authors :  S. Hafenstein, V. D. Bowman, P. R. Chipman, C. M. Bator Kelly, F. Lin, M. M. G. Rossmann
Date :  16 Aug 07  (Deposition) - 30 Oct 07  (Release) - 30 May 12  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  14.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Scr4 Of Daf From 1Ojv Fitted Into Cryoem Density, Blood Group Antigen, Complement Pathway, Glycoprotein, Gpi-Anchor, Immune Response, Innate Immunity, Lipoprotein, Membrane, Sushi, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Hafenstein, V. D. Bowman, P. R. Chipman, C. M. Bator Kelly, F. Lin, M. E. Medof, M. G. Rossmann
Interaction Of Decay-Accelerating Factor With Coxsackieviru B3.
J. Virol. V. 81 12927 2007
PubMed-ID: 17804498  |  Reference-DOI: 10.1128/JVI.00931-07

(-) Compounds

Molecule 1 - COMPLEMENT DECAY-ACCELERATING FACTOR
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentSCR4 DOMAIN
    GeneCD55, CR, DAF
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCD55 ANTIGEN

 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 2QZD)

(-) Sites  (0, 0)

(no "Site" information available for 2QZD)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:1193 -A:1235
2A:1221 -A:1251

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:1253 -Cys A:1254

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_002001A227PDAF_HUMANPolymorphism60822373AA1195P
2UniProtVAR_015884R240HDAF_HUMANPolymorphism199705465AR1208H

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUSHIPS50923 Sushi/CCP/SCR domain profile.DAF_HUMAN96-160
34-94
161-222
223-285
  1-
-
-
A:1191-1253

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003670641aENSE00001840627chr1:207494853-207495210358DAF_HUMAN1-34340--
1.3ENST000003670643ENSE00001443405chr1:207495727-207495912186DAF_HUMAN34-96630--
1.4bENST000003670644bENSE00001443404chr1:207497904-207498095192DAF_HUMAN96-160650--
1.5ENST000003670645ENSE00001069638chr1:207498967-207499066100DAF_HUMAN160-193340--
1.6ENST000003670646ENSE00001069637chr1:207500097-20750018286DAF_HUMAN193-222301A:1190-11901
1.7ENST000003670647ENSE00000960173chr1:207504453-207504641189DAF_HUMAN222-285641A:1190-125364
1.8bENST000003670648bENSE00001041396chr1:207510038-207510163126DAF_HUMAN285-327431A:1253-12542
1.8dENST000003670648dENSE00001253047chr1:207510674-20751075481DAF_HUMAN327-354280--
1.9ENST000003670649ENSE00001432766chr1:207512742-20751276221DAF_HUMAN354-36180--
1.15fENST0000036706415fENSE00001631743chr1:207532891-2075343111421DAF_HUMAN361-381210--

(-) 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:65
 aligned with DAF_HUMAN | P08174 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:65
                                   231       241       251       261       271       281     
           DAF_HUMAN    222 EIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEWSGPPPECRGK  286
               SCOP domains -d2qzda1 A:1191-1254                                              SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ---Sushi-2qzdA01 A:1193-1251                                  --- Pfam domains
         Sec.struct. author ............eee...........eeeeee....eee...eeeeeee..eeee.....eee.. Sec.struct. author
                 SAPs(SNPs) -----P------------H---------------------------------------------- SAPs(SNPs)
                    PROSITE SSUSHI  PDB: A:1191-1253 UniProt: 223-285                       - PROSITE
           Transcript 1 (1) 1--------------------------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) Exon 1.7  PDB: A:1190-1253 UniProt: 222-285                     - Transcript 1 (2)
                2qzd A 1190 EIYCPAPPQIDNGIIQGERDHYGYRQSVTYACNKGFTMIGEHSIYCTVNNDEGEWSGPPPECRGC 1254
                                  1199      1209      1219      1229      1239      1249     

   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 2QZD)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (28, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DAF_HUMAN | P08174)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    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:0001618    virus receptor activity    Combining with a virus component and mediating entry of the virus into the cell.
biological process
    GO:0035743    CD4-positive, alpha-beta T cell cytokine production    Any process that contributes to cytokine production by a CD4-positive, alpha-beta T cell.
    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:0006958    complement activation, classical pathway    Any process involved in the activation of any of the steps of the classical pathway of the complement cascade which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes.
    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:0045916    negative regulation of complement activation    Any process that stops, prevents, or reduces the frequency, rate or extent of complement activation.
    GO:2000516    positive regulation of CD4-positive, alpha-beta T cell activation    Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell activation.
    GO:2000563    positive regulation of CD4-positive, alpha-beta T cell proliferation    Any process that activates or increases the frequency, rate or extent of CD4-positive, alpha-beta T cell proliferation.
    GO:0007204    positive regulation of cytosolic calcium ion concentration    Any process that increases the concentration of calcium ions in the cytosol.
    GO:0030449    regulation of complement activation    Any process that modulates the frequency, rate or extent of complement activation.
    GO:0031664    regulation of lipopolysaccharide-mediated signaling pathway    Any process that modulates the frequency, rate or extent of signaling in response to detection of lipopolysaccharide.
    GO:0045730    respiratory burst    A phase of elevated metabolic activity, during which oxygen consumption increases; this leads to the production, by an NADH dependent system, of hydrogen peroxide (H2O2), superoxide anions and hydroxyl radicals.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    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: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: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:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    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:0030133    transport vesicle    Any of the vesicles of the constitutive secretory pathway, which carry cargo from the endoplasmic reticulum to the Golgi, between Golgi cisternae, from the Golgi to the ER (retrograde transport) or to destinations within or outside the cell.

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    Gly A:1253 - Cys A:1254   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        DAF_HUMAN | P081741h03 1h04 1h2p 1h2q 1m11 1nwv 1ojv 1ojw 1ojy 1ok1 1ok2 1ok3 1ok9 1uot 1upn 2c8i 2qzf 2qzh 3iyp 3j24 5foa

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2QZD)