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(-) Description

Title :  STRUCTURE OF C8A-MACPF REVEALS MECHANISM OF MEMBRANE ATTACK IN COMPLEMENT IMMUNE DEFENSE
 
Authors :  M. A. Hadders, P. Gros
Date :  26 Jul 07  (Deposition) - 25 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Macpf, Membrane Perforation, 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, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Hadders, D. X. Beringer, P. Gros
Structure Of C8Alpha-Macpf Reveals Mechanism Of Membrane Attack In Complement Immune Defense.
Science V. 317 1552 2007
PubMed-ID: 17872444  |  Reference-DOI: 10.1126/SCIENCE.1147103
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COMPLEMENT COMPONENT C8 ALPHA CHAIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET
    Expression System StrainORIGAMI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneC8A
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCOMPLEMENT COMPONENT 8 SUBUNIT ALPHA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric/Biological Unit (3, 16)
No.NameCountTypeFull Name
1NI1Ligand/IonNICKEL (II) ION
2SO43Ligand/IonSULFATE ION
3UNK12Mod. Amino Acid

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:118 , SER A:119 , GLN A:120 , LYS A:121 , HOH A:515 , HOH A:531BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWAREARG A:394BINDING SITE FOR RESIDUE SO4 A 466
3AC3SOFTWARELYS A:275 , ARG A:439 , HIS A:440 , HOH A:542BINDING SITE FOR RESIDUE SO4 A 467
4AC4SOFTWAREHIS A:186 , GLU A:188 , HIS A:270 , HOH A:524 , HOH A:529BINDING SITE FOR RESIDUE NI A 500

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:110 -A:147

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_033800D458NCO8A_HUMANPolymorphism17114555AD428N
2UniProtVAR_011891R485LCO8A_HUMANPolymorphism1620075AR455L

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MACPF_2PS51412 Membrane attack complex/perforin (MACPF) domain profile.CO8A_HUMAN135-498  1A:105-462
2MACPF_1PS00279 Membrane attack complex/perforin (MACPF) domain signature.CO8A_HUMAN330-341  1A:300-311

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003612491ENSE00001436108chr1:57320479-57320651173CO8A_HUMAN1-26260--
1.2ENST000003612492ENSE00001390177chr1:57333282-5733337594CO8A_HUMAN26-57320--
1.3ENST000003612493ENSE00001436153chr1:57340622-57340766145CO8A_HUMAN58-106490--
1.4ENST000003612494ENSE00001030576chr1:57341735-57341882148CO8A_HUMAN106-155501A:102-12524
1.5ENST000003612495ENSE00001381670chr1:57347118-57347307190CO8A_HUMAN155-218641A:125-188 (gaps)64
1.6ENST000003612496ENSE00001030560chr1:57349154-57349354201CO8A_HUMAN219-285671A:189-25567
1.7ENST000003612497ENSE00001436552chr1:57351600-57351840241CO8A_HUMAN286-366811A:256-33580
1.8ENST000003612498ENSE00001382619chr1:57372340-57372465126CO8A_HUMAN366-408431A:2-1211
1.9ENST000003612499ENSE00001030541chr1:57373629-57373786158CO8A_HUMAN408-460531A:13-430 (gaps)52
1.10ENST0000036124910ENSE00001436003chr1:57378076-57378298223CO8A_HUMAN461-535751A:431-46333
1.11ENST0000036124911ENSE00001422483chr1:57383238-57383894657CO8A_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:304
 aligned with CO8A_HUMAN | P07357 from UniProtKB/Swiss-Prot  Length:584

    Alignment length:362
                                   141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491  
           CO8A_HUMAN   132 DVRAIDEDCSQYEPIPGSQKAALGYNILTQEDAQSVYDASYYGGQCETVYNGEWRELRYDSTCERLYYGDDEKYFRKPYNFLKYHFEALADTGISSEFYDNANDLLSKVKKDKSDSFGVTIGIGPAGSPLLVGVGVSHSQDTSFLNELNKYNEKKFIFTRIFTKVQTAHFKMRKDDIMLDEGMLQSLMELPDQYNYGMYAKFINDYGTHYITSGSMGGIYEYILVIDKAKMESLGITSRDITTCFGGSLGIQYEDKINVGGGLSGDHCKKFGGGKTERARKAMAVEDIISRVRGGSSGWSGGLAQNRSTITYRSWGRSLKYNPVVIDFEMQPIHEVLRHTSLGPLEAKRQNLRRALDQYLME 493
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------            ------------------------------------------------------------------MACPF-2qqhA01 A:237-460                                                                                                                                                                                                         --- Pfam domains
         Sec.struct. author ................hhhhhheee......eeee............eee.......------------....eee....eeeeeeeeeeee........hhhhhhhhhhhhhhhhhh.eeee......ee.....hhhhhhhhhhhhhh......eeeeeeeeeeeeeeee.......hhhhhhhhhh.....hhhhhhhhhhhhh.eeeeeeeeeeeeeeeeeehhhhhhhh-hhhhhhhhhhh-------------------------------h-.........eeeee.....-------------.hhhhhhhhhh.eeeeeeeee.hhhhh....hhh................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N--------------------------L-------- SAPs(SNPs)
                PROSITE (1) ---MACPF_2  PDB: A:105-462 UniProt: 135-498                                                                                                                                                                                                                                                                                                                                PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MACPF_1     -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.4  PDB: A:102-125---------------------------------------------------------------Exon 1.6  PDB: A:189-255 UniProt: 219-285                          Exon 1.7  PDB: A:256-335 UniProt: 286-366 [INCOMPLETE]                           -----------------------------------------Exon 1.9  PDB: A:13-430 (gaps) UniProt: 408-460      Exon 1.10  PDB: A:431-463         Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.5  PDB: A:125-188 (gaps) UniProt: 155-218                ---------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:2-12 UniProt: 366-408     ------------------------------------------------------------------------------------- Transcript 1 (2)
                 2qqh A 102 SVRAIDEDCSQYEPIPGSQKAALGYNILTQEDAQSVYDASYYGGQCETVYNGEWREL------------DDEKYFRKPYNFLKYHFEALADTGISSEFYDNANDLLSKVKKDKSDSFGVTIGIGPAGSPLLVGVGVSHSQDTSFLNELNKYNEKKFIFTRIFTKVQTAHFKMRKDDIMLDEGMLQSLMELPDQYNYGMYAKFINDYGTHYITSGSMGGIYEYILVIDKAKMESL-xxxxxxxxxxx-------------------------------x-RKAMAVEDIISRVRGGSSG-------------YRSWGRSLKYNPVVIDFEMQPIHEVLRHTSLGPLEAKRQNLRRALDQYLMA 463
                                   111       121       131       141       151      |  -       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331   | ||||6||||||   -         -         -       381       391       | -         - |     421       431       441       451       461  
                                                                                  158          171                                                                                                                                                                 335 |||||||10-UNK                            13-UNK             399           413                                                  
                                                                                                                                                                                                                                                                       2-UNK|||11-UNK                            381                                                                                  
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                                                                                                                                                                                                                                                                            7-UNK                                                                                                                     
                                                                                                                                                                                                                                                                             8-UNK                                                                                                                    
                                                                                                                                                                                                                                                                              9-UNK                                                                                                                   

   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  (0, 0)

(no "SCOP Domain" information available for 2QQH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2QQH)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: CDC (6)

(-) Gene Ontology  (18, 18)

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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CO8A_HUMAN | P073572qos 2rd7 3ojy

(-) Related Entries Specified in the PDB File

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