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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CUB1-EGF INTERACTION DOMAIN OF COMPLEMENT PROTEASE C1S
 
Authors :  L. A. Gregory, N. M. Thielens, G. J. Arlaud, J. C. Fontecilla-Camps, C. Gaboriaud
Date :  18 Feb 03  (Deposition) - 10 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Calcium, Complement, Innate Immunity, Modular Structure, Cub, Egf, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. A. Gregory, N. M. Thielens, G. J. Arlaud, J. C. Fontecilla-Camps, C. Gaboriaud
X-Ray Structure Of The Ca2+-Binding Interaction Domain Of C1S. Insights Into The Assembly Of The C1 Complex Of Complement
J. Biol. Chem. V. 278 32157 2003
PubMed-ID: 12788922  |  Reference-DOI: 10.1074/JBC.M305175200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COMPLEMENT C1S COMPONENT
    ChainsA, B
    EC Number3.4.21.42
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Cell LineHIGH FIVE INSECT CELLS
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    Expression System VectorPBC1S
    Expression System Vector TypeBACULOVIRUS
    FragmentCALCIUM-DEPENDENT INTERACTION DOMAIN
    GeneC1S
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:116 , ILE A:117 , GLU A:119 , ASN A:134 , PHE A:135 , GLY A:138 , HOH A:1005BINDING SITE FOR RESIDUE CA A 1001
2AC2SOFTWAREASP B:116 , ILE B:117 , GLU B:119 , ASN B:134 , PHE B:135 , GLY B:138 , HOH B:1010BINDING SITE FOR RESIDUE CA B 1002
3AC3SOFTWAREGLU A:45 , ASP A:53 , ASP A:98 , HOH A:1109 , HOH A:1110BINDING SITE FOR RESIDUE MG A 1003
4AC4SOFTWAREGLU B:45 , ASP B:53 , ASP B:98 , HOH B:1122 , HOH B:1134BINDING SITE FOR RESIDUE MG B 1004

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:50 -A:68
2A:120 -A:132
3A:128 -A:141
4A:143 -A:156
5B:50 -B:68
6B:120 -B:132
7B:128 -B:141
8B:143 -B:156

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:13 -Pro A:14
2Tyr B:13 -Pro B:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric/Biological Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_033643R119HC1S_HUMANPolymorphism12146727A/BR104H

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

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1EGF_CAPS01187 Calcium-binding EGF-like domain signature.C1S_HUMAN131-156
 
  2A:116-141
B:116-141
2ASX_HYDROXYLPS00010 Aspartic acid and asparagine hydroxylation site.C1S_HUMAN147-158
 
  2A:132-143
B:132-143

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.5bENST000003608175bENSE00001554821chr12:7167980-7168181202C1S_HUMAN-00--
1.6dENST000003608176dENSE00001805598chr12:7169143-716922179C1S_HUMAN1-220--
1.7bENST000003608177bENSE00001609294chr12:7169779-7169986208C1S_HUMAN2-71702A:1-56
B:3-56
56
54
1.8cENST000003608178cENSE00001307751chr12:7170194-7170371178C1S_HUMAN72-131602A:57-116 (gaps)
B:57-116 (gaps)
60
60
1.10eENST0000036081710eENSE00001327036chr12:7171571-7171696126C1S_HUMAN131-173432A:116-158 (gaps)
B:116-158
43
43
1.11bENST0000036081711bENSE00001308911chr12:7172404-7172603200C1S_HUMAN173-239672A:158-159
B:158-159
2
2
1.12bENST0000036081712bENSE00001322783chr12:7173121-7173274154C1S_HUMAN240-291520--
1.12gENST0000036081712gENSE00001560603chr12:7173822-7173937116C1S_HUMAN291-329390--
1.12jENST0000036081712jENSE00001319673chr12:7174343-717442179C1S_HUMAN330-356270--
1.13cENST0000036081713cENSE00001777929chr12:7174947-7175075129C1S_HUMAN356-399440--
1.15bENST0000036081715bENSE00001604953chr12:7175760-717583475C1S_HUMAN399-424260--
1.17cENST0000036081717cENSE00001884879chr12:7177159-71782471089C1S_HUMAN424-6882650--

(-) 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:155
 aligned with C1S_HUMAN | P09871 from UniProtKB/Swiss-Prot  Length:688

    Alignment length:159
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165         
            C1S_HUMAN    16 EPTMYGEILSPNYPQAYPSEVEKSWDIEVPEGYGIHLYFTHLDIELSENCAYDSVQIISGDTEEGRLCGQRSSNNPHSPIVEEFQVPYNKLQVIFKSDFSNEERFTGFAAYYVATDINECTDFVDVPCSHFCNNFIGGYFCSCPPEYFLHDDMKNCGVN 174
               SCOP domains d1nzia1 A:1-117 Complement C1S component                                                                             d1nzi a2 A:118-159 Complement C1S componen SCOP domains
               CATH domains 1nziA01 A:1-117  [code=2.60.120.290, no name defined]                                                                1nziA 02 A:118-159 Laminin                 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...........eeeeeeee....eeeeeeeeeee...hhhhh..eeeee.---..eee..ee..........eeeee...eeeeeeee.........eeeeeeeeee......-.......eeeee..eeeee.....ee......ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------H------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------------------------------------EGF_CA  PDB: A:116-141    ------------------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------ASX_HYDROXYL---------------- PROSITE (2)
           Transcript 1 (1) Exon 1.7b  PDB: A:1-56 UniProt: 2-71 [INCOMPLETE]       -----------------------------------------------------------Exon 1.10e  PDB: A:116-158 (gaps)          - Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.8c  PDB: A:57-116 (gaps) UniProt: 72-131             -----------------------------------------1. Transcript 1 (2)
                 1nzi A   1 EPTMYGEILSPNYPQAYPSEVEKSWDIEVPEGYGIHLYFTHLDIELSENCAYDSVQIIS---EEGRLCGQRSSNNPHSPIVEEFQVPYNKLQVIFKSDFSNEERFTGFAAYYVATDINECTD-VDVPCSHFCNNFIGGYFCSCPPEYFLHDDMKNCGVN 159
                                    10        20        30        40        50        |-  |     70        80        90       100       110       120 | |   130       140       150         
                                                                                     59  63                                                        122 |                                   
                                                                                                                                                     124                                   

Chain B from PDB  Type:PROTEIN  Length:156
 aligned with C1S_HUMAN | P09871 from UniProtKB/Swiss-Prot  Length:688

    Alignment length:157
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       
            C1S_HUMAN    18 TMYGEILSPNYPQAYPSEVEKSWDIEVPEGYGIHLYFTHLDIELSENCAYDSVQIISGDTEEGRLCGQRSSNNPHSPIVEEFQVPYNKLQVIFKSDFSNEERFTGFAAYYVATDINECTDFVDVPCSHFCNNFIGGYFCSCPPEYFLHDDMKNCGVN 174
               SCOP domains d1nzib1 B:3-117 Complement C1S component                                                                           d1nzib2 B:118-159 Complement C1S component SCOP domains
               CATH domains 1nziB01 B:3-117  [code=2.60.120.290, no name defined]                                                              1nziB02 B:118-159 Laminin                  CATH domains
           Pfam domains (1) CUB-1nziB01 B:3-112                                                                                           ----------------------------------------------- Pfam domains (1)
           Pfam domains (2) CUB-1nziB02 B:3-112                                                                                           ----------------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeee...........eeeeeeee....eeeeeeeeeeee..hhhhh..eeeee....eeeee.eee..-.......eeeee...eeeeeeee.........eeeeeeeeee..............eeeee..eeeee.....ee......ee.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------H------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------EGF_CA  PDB: B:116-141    ------------------ PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------ASX_HYDROXYL---------------- PROSITE (2)
           Transcript 1 (1) Exon 1.7b  PDB: B:3-56 UniProt: 2-71 [INCOMPLETE]     -----------------------------------------------------------Exon 1.10e  PDB: B:116-158 UniProt: 131-173- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------Exon 1.8c  PDB: B:57-116 (gaps) UniProt: 72-131             -----------------------------------------1. Transcript 1 (2)
                 1nzi B   3 TMYGEILSPNYPQAYPSEVEKSWDIEVPEGYGIHLYFTHLDIELSENCAYDSVQIISGDTEEGRLCGQRSS-NPHSPIVEEFQVPYNKLQVIFKSDFSNEERFTGFAAYYVATDINECTDFVDVPCSHFCNNFIGGYFCSCPPEYFLHDDMKNCGVN 159
                                    12        22        32        42        52        62        72| |     82        92       102       112       122       132       142       152       
                                                                                                 73 |                                                                                    
                                                                                                   75                                                                                    

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: CUB (11)
(-)
Family: CUB (11)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (C1S_HUMAN | P09871)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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
        C1S_HUMAN | P098711elv 4j1y 4lmf 4lor 4los 4lot

(-) Related Entries Specified in the PDB File

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