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(-) Description

Title :  CRYSTAL STRUCTURE OF COMPLEMENT PROTEIN C8 IN COMPLEX WITH A PEPTIDE CONTAINING THE C8 BINDING SITE ON C8
 
Authors :  L. L. Lovelace, B. Chiswell, D. J. Slade, J. M. Sodetz, L. Lebioda
Date :  20 Jul 07  (Deposition) - 16 Oct 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.81
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Beta Barrel, Lipocalin, Cleavage On Pair Of Basic Residues, Complement Alternate Pathway, Complement Pathway, Cytolysis, Egf-Like Domain, Glycoprotein, Immune Response, Innate Immunity, Membrane Attack Complex, Polymorphism, Secreted, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. L. Lovelace, B. Chiswell, D. J. Slade, J. M. Sodetz, L. Lebioda
Crystal Structure Of Complement Protein C8Gamma In Complex With A Peptide Containing The C8Gamma Binding Site On C8Alpha: Implications For C8Gamma Ligand Binding.
Mol. Immunol. V. 45 750 2008
PubMed-ID: 17692377  |  Reference-DOI: 10.1016/J.MOLIMM.2007.06.359
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COMPLEMENT COMPONENT 8, GAMMA POLYPEPTIDE
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: C8G
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - COMPLEMENT COMPONENT C8 ALPHA CHAIN
    Chains: A
    Engineered: YES
    Other Details: THIS SEQUENCE HAS BEEN MODIFIED FROM THE HUMAN
    Synonym: COMPLEMENT COMPONENT 8 SUBUNIT ALPHA
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2QOS)

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014668R69QCO8G_HUMANPolymorphism17614CR49Q
2UniProtVAR_044319D118GCO8G_HUMANPolymorphism7850844CG98G
3UniProtVAR_014669H124NCO8G_HUMANPolymorphism17613CH104N
  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  1C:21-34

(-) Exons   (8, 8)

Asymmetric/Biological Unit (8, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002241811bENSE00001834506chr9:139839713-139839910198CO8G_HUMAN1-46461C:10-2617
1.2ENST000002241812ENSE00000734163chr9:139840086-139840222137CO8G_HUMAN47-92461C:27-7246
1.3ENST000002241813ENSE00001194952chr9:139840381-13984045171CO8G_HUMAN92-116251C:72-9625
1.4aENST000002241814aENSE00000734168chr9:139840537-139840644108CO8G_HUMAN116-152371C:96-13237
1.6cENST000002241816cENSE00000734170chr9:139840917-139841018102CO8G_HUMAN152-186351C:132-16635
1.7aENST000002241817aENSE00001407255chr9:139841103-13984114139CO8G_HUMAN186-199141C:166-17914
1.7cENST000002241817cENSE00001902507chr9:139841220-139841419200CO8G_HUMAN199-20241C:179-1824
2.1ENST000003612491ENSE00001436108chr1:57320479-57320651173CO8A_HUMAN1-26260--
2.2ENST000003612492ENSE00001390177chr1:57333282-5733337594CO8A_HUMAN26-57320--
2.3ENST000003612493ENSE00001436153chr1:57340622-57340766145CO8A_HUMAN58-106490--
2.4ENST000003612494ENSE00001030576chr1:57341735-57341882148CO8A_HUMAN106-155500--
2.5ENST000003612495ENSE00001381670chr1:57347118-57347307190CO8A_HUMAN155-218641A:158-16811
2.6ENST000003612496ENSE00001030560chr1:57349154-57349354201CO8A_HUMAN219-285670--
2.7ENST000003612497ENSE00001436552chr1:57351600-57351840241CO8A_HUMAN286-366810--
2.8ENST000003612498ENSE00001382619chr1:57372340-57372465126CO8A_HUMAN366-408430--
2.9ENST000003612499ENSE00001030541chr1:57373629-57373786158CO8A_HUMAN408-460530--
2.10ENST0000036124910ENSE00001436003chr1:57378076-57378298223CO8A_HUMAN461-535750--
2.11ENST0000036124911ENSE00001422483chr1:57383238-57383894657CO8A_HUMAN535-584500--

(-) 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:11
 aligned with CO8A_HUMAN | P07357 from UniProtKB/Swiss-Prot  Length:584

    Alignment length:11
                                   197 
           CO8A_HUMAN   188 LRYDSTCERLY 198
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author .eee....eee Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
               Transcript 2 Exon 2.5    Transcript 2
                 2qos A 158 LRYDSTAERLY 168
                                   167 


Chain C from PDB  Type:PROTEIN  Length:173
 aligned with CO8G_HUMAN | P07360 from UniProtKB/Swiss-Prot  Length:202

    Alignment length:173
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199   
           CO8G_HUMAN    30 ASPISTIQPKANFDAQQFAGTWLLVAVGSACRFLQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQVRQLYGDTGVLGRFLLQARDARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQFHVLDEVRR 202
               SCOP domains d2qosc_ C: automated matches                                                                                                                                                  SCOP domains
               CATH domains 2qosC00 C:10-182  [code=2.40.128.20, no name defined]                                                                                                                         CATH domains
               Pfam domains ------------------Lipocalin-2qosC01 C:28-166                                                                                                                 ---------------- Pfam domains
         Sec.struct. author .hhhhhh......hhhhhheeeeeeeee..hhhhhhhhhhh...eeeeeee..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: C:27-72 UniProt: 47-92         -----------------------Exon 1.4a  PDB: C:96-132             ---------------------------------Exon 1.7a     --- Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------Exon 1.3  PDB: C:72-96   -----------------------------------Exon 1.6c  PDB: C:132-166          ------------1.7c Transcript 1 (2)
                 2qos C  10 ASPISTIQPKANFDAQQFAGTWLLVAVGSAARFLQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGICWQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQFHVLDEVRR 182
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (20, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CO8A_HUMAN | P07357)
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).
biological process
    GO:0006956    complement activation    Any process involved in the activation of any of the steps of the complement cascade, which allows for the direct killing of microbes, the disposal of immune complexes, and the regulation of other immune processes; the initial steps of complement activation involve one of three pathways, the classical pathway, the alternative pathway, and the lectin pathway, all of which lead to the terminal complement pathway.
    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:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    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: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: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.
    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 C   (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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CO8A_HUMAN | P07357: 2qqh 2rd7 3ojy
        CO8G_HUMAN | P07360: 1iw2 1lf7 2ova 2ovd 2ove 2rd7 3ojy

(-) Related Entries Specified in the PDB File

1iw2 1lf7 2ova 2ovd 2ove