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(-) Description

Title :  MONOMERIC STRUCTURE OF THE ZYMOGEN OF COMPLEMENT PROTEASE C1R
 
Authors :  M. Budayova-Spano, W. Grabarse, N. M. Thielens, H. Hillen, M. Lacroix, M. Schmidt, J. Fontecilla-Camps, G. J. Arlaud, C. Gaboriaud
Date :  07 Aug 02  (Deposition) - 07 Aug 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Complement, Innate Immunity, Serine Protease, Activation, Substrate Specificity, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Budayova-Spano, W. Grabarse, N. M. Thielens, H. Hillen, M. Lacroix, M. Schmidt, J. Fontecilla-Camps, G. J. Arlaud, C. Gaboriaud
Monomeric Structures Of The Zymogen And Active Catalytic Domain Of Complement Protease C1R: Further Insights Into The C1 Activation Mechanism
Structure V. 10 1509 2002
PubMed-ID: 12429092  |  Reference-DOI: 10.1016/S0969-2126(02)00881-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - C1R COMPLEMENT SERINE PROTEASE
    ChainsA
    EC Number3.4.21.41
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Cell LineHIGH FIVETM
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    Expression System VectorPNT-BAC
    Expression System Vector TypeBACULOVIRUS
    FragmentC-TERMINAL CCP-SP DOMAIN
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCOMPLEMENT C1R COMPONENT

 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
1NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:497BINDING SITE FOR RESIDUE NDG A 1001

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:359 -A:412
2A:389 -A:430
3A:434 -A:560
4A:603 -A:622
5A:633 -A:663

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:391 -Pro A:392

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_077119W435RC1R_HUMANUnclassified (EDSPD1)  ---AW418R

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.C1R_HUMAN464-702  1A:447-685
2TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.C1R_HUMAN648-659  1A:631-642

(-) Exons   (0, 0)

(no "Exon" information available for 1MD7)

(-) 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 C1R_HUMAN | P00736 from UniProtKB/Swiss-Prot  Length:705

    Alignment length:328
                                   384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694        
            C1R_HUMAN   375 DCGQPRNLPNGDFRYTTTMGVNTYKARIQYYCHEPYYKMQTRAGSRESEQGVYTCTAQGIWKNEQKGEKIPRCLPVCGKPVNPVEQRQRIIGGQKAKMGNFPWQVFTNIHGRGGGALLGDRWILTAAHTLYPKEHEAQSNASLDVFLGHTNVEELMKLGNHPIRRVSVHPDYRQDESYNFEGDIALLELENSVTLGPNLLPICLPDNDTFYDLGLMGYVSGFGVMEEKIAHDLRFVRLPVANPQACENWLRGKNRMDVFSQNMFCAGHPSLKQDACQGDSGGVFAVRDPNTDRWVATGIVSWGIGCSRGYGFYTKVLNYVDWIKKEME 702
               SCOP domains d1md7a2 A:358-433 Complement C1R protease         domains                   d1md7a1 A    :434-685 Complement C1R protease, catalytic domain                                                                                                                                                                                              SCOP domains
               CATH domains 1md7A01 A:358-433 Complement Module, doma        in 1                       ---------    --1md7A02     1md7A03 A:461-558,A:676-683 Trypsin-like serine proteases                                         -1md7A02 A:449-460,A:5      60-675 Trypsin-like s      erine proteases                                               1md7A03 -- CATH domains
               Pfam domains -Sushi-1md7A02 A:359-430                                                 ------------    Trypsin-1md7A01 A:447-680                                                                                                                                                                                                                 ----- Pfam domains
         Sec.struct. author ..........eeeee...........eeeeee....eee..--------..eeee.....ee..........eee..........----..............eeeee...eeeeeee...eeeehhhhhh.............eee...hhhhhhhhh...eeeeee................eeeee.................hhhhh....eeeeee..------....eeeeee...........------......eeeee...hhhhhhh......eee........eeeeee.........eeeeee...hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------R--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------TRYPSIN_DOM  PDB: A:447-685 UniProt: 464-702                                                                                                                                                                                                    PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1md7 A 358 DCGQPRNLPNGDFRYTTTMGVNTYKARIQYYCHEPYYKMQT--------QGVYTCTAQGIWKNEQKGEKIPRCLPVCGKPVNPVE----IIGGQKAKMGNFPWQVFTNIHGRGGGALLGDRWILTAAHTLYPKEHEAQSNASLDVFLGHTNVEELMKLGNHPIRRVSVHPDYRQDESYNFEGDIALLELENSVTLGPNLLPICLPDNDTFYDLGLMGYVSGFG------AHDLRFVRLPVANPQACENWL------DVFSQNMFCAGHPSLKQDACQGDAGGVFAVRDPNTDRWVATGIVSWGIGCSRGYGFYTKVLNYVDWIKKEME 685
                                   367       377       387       397|      407       417       427       437    |  447       457       467       477       487       497       507       517       527       537       547       557       567       577  |    587       597       607      |617       627       637       647       657       667       677        
                                                                  398      407                                442  447                                                                                                                                  580    587                 607    614                                                                       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (C1R_HUMAN | P00736)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
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: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: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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        C1R_HUMAN | P007361apq 1gpz 1md8 2qy0

(-) Related Entries Specified in the PDB File

1gpz 1GPZ CONTAINS THE SAME PROTEIN, IN THE SAME ZYMOGEN STATE, A LONGER FRAGMENT(CCP1-CCP2-SP), A DIMERIC ASSEMBLY
1md8 1MD8 CONTAINS THE ACTIVE CATALYTIC DOMAIN OF COMPLEMENT PROTEASE C1R