Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN COMPLEMENT PROTEIN C8GAMMA AT 1.2 A RESOLUTION
 
Authors :  E. Ortlund, C. L. Parker, S. F. Schreck, S. Ginell, W. Minor, J. M. Sodetz, L. Lebioda
Date :  10 Apr 02  (Deposition) - 12 Jun 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Lipocalin, Beta Barrel, Calyx, Complement, Mac, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Ortlund, C. L. Parker, S. F. Schreck, S. Ginell, W. Minor, J. M. Sodetz, L. Lebioda
Crystal Structure Of Human Complement Protein C8Gamma At 1. 2 A Resolution Reveals A Lipocalin Fold And A Distinct Ligand Binding Site.
Biochemistry V. 41 7030 2002
PubMed-ID: 12033936  |  Reference-DOI: 10.1021/BI025696I
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COMPLEMENT PROTEIN C8GAMMA
    ChainsA
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Cell LineHIGH FIVE
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    Expression System VectorPBLUEBAC
    Expression System Vector TypeBACULOVIRUS
    Gene9Q34.3
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCOMPLEMENT COMPONENT C8 GAMMA CHAIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:33 , ARG A:70 , ARG A:122 , LYS A:129 , PHE A:162 , HOH A:386 , HOH A:390 , HOH A:468BINDING SITE FOR RESIDUE CIT A 200

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:76 -A:168

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:135 -Pro A:136

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014668R69QCO8G_HUMANPolymorphism17614AR49Q
2UniProtVAR_044319D118GCO8G_HUMANPolymorphism7850844AG98G
3UniProtVAR_014669H124NCO8G_HUMANPolymorphism17613AH104N

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPOCALINPS00213 Lipocalin signature.CO8G_HUMAN41-54  1A:21-34

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002241811bENSE00001834506chr9:139839713-139839910198CO8G_HUMAN1-46461A:10-2617
1.2ENST000002241812ENSE00000734163chr9:139840086-139840222137CO8G_HUMAN47-92461A:27-72 (gaps)46
1.3ENST000002241813ENSE00001194952chr9:139840381-13984045171CO8G_HUMAN92-116251A:72-9625
1.4aENST000002241814aENSE00000734168chr9:139840537-139840644108CO8G_HUMAN116-152371A:96-13237
1.6cENST000002241816cENSE00000734170chr9:139840917-139841018102CO8G_HUMAN152-186351A:132-16635
1.7aENST000002241817aENSE00001407255chr9:139841103-13984114139CO8G_HUMAN186-199141A:166-17914
1.7cENST000002241817cENSE00001902507chr9:139841220-139841419200CO8G_HUMAN199-20241A:179-1802

(-) 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:164
 aligned with CO8G_HUMAN | P07360 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:171
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199 
           CO8G_HUMAN    30 ASPISTIQPKANFDAQQFAGTWLLVAVGSACRFLQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQVRQLYGDTGVLGRFLLQARDARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQFHVLDEV 200
               SCOP domains d1lf7a_ A: Complement protein C8       gamma                                                                                                                                SCOP domains
               CATH domains 1lf7A00 A:10-180  [code=2.40.128       .20, no name defined]                                                                                                                CATH domains
               Pfam domains ------------------Lipocalin-1lf7       A01 A:28-166                                                                                                          -------------- Pfam domains
         Sec.struct. author .hhhhhh......hhhhhheeeeeeeee....-------....eeeeeeee..eeeeeeeeee..eeeeeeeeeee.....eeee........eeeeeeee....eeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhh..hhh.eee..........hhh.eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------Q------------------------------------------------G-----N---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------LIPOCALIN     -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b        Exon 1.2  PDB: A:27-72 (gaps) UniProt: 47-92  -----------------------Exon 1.4a  PDB: A:96-132             ---------------------------------Exon 1.7a     - Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------Exon 1.3  PDB: A:72-96   -----------------------------------Exon 1.6c  PDB: A:132-166          ------------1. Transcript 1 (2)
                 1lf7 A  10 ASPISTIQPKANFDAQQFAGTWLLVAVGSAGR-------RAEATTLHVAPQGTAMAVSTFRKLDGICWQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQFHVLDEV 180
                                    19        29        39 |      49        59        69        79        89        99       109       119       129       139       149       159       169       179 
                                                          41      49                                                                                                                                   

   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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Calycin (163)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CO8G_HUMAN | P07360)
molecular function
    GO:0001848    complement binding    Interacting selectively and non-covalently with any component or product of the complement cascade.
    GO:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019841    retinol binding    Interacting selectively and non-covalently with retinol, vitamin A1, 2,6,6-trimethyl-1-(9'-hydroxy-3',7'-dimethylnona-1',3',5',7'-tetraenyl)cyclohex-1-ene, one of the three components that makes up vitamin A. Retinol is an intermediate in the vision cycle and it also plays a role in growth and differentiation.
    GO:0036094    small molecule binding    Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
biological process
    GO:0006957    complement activation, alternative pathway    Any process involved in the activation of any of the steps of the alternative pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes.
    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:0019835    cytolysis    The rupture of cell membranes and the loss of cytoplasm.
    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:0030449    regulation of complement activation    Any process that modulates the frequency, rate or extent of complement activation.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    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:0005579    membrane attack complex    A protein complex produced by sequentially activated components of the complement cascade inserted into a target cell membrane and forming a pore leading to cell lysis via ion and water flow.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:135 - Pro A:136   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1lf7
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CO8G_HUMAN | P07360
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  CO8G_HUMAN | P07360
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CO8G_HUMAN | P073601iw2 2ova 2ovd 2ove 2qos 2rd7 3ojy

(-) Related Entries Specified in the PDB File

1iw2 1IW2 CONTAINS X-RAY STRUCTURE OF THE SAME PROTEIN AT PH 7.0