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(-) Description

Title :  THE CRYSTAL STRUCTURE OF C2B, A FRAGMENT OF COMPLEMENT COMPONENT C2 PRODUCED DURING C3-CONVERTASE FORMATION
 
Authors :  S. V. L. Narayan, V. Krishnan
Date :  01 Oct 08  (Deposition) - 10 Mar 09  (Release) - 10 Mar 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Complement Component C2B, C3/C5 Convertase, Complement Control Protein (Ccp), Short Consensus Repeat(Scr), Sushi Domain, Human Complement System, Complement Second Component C2, Complement Pathway, Disease Mutation, Glycoprotein, Hydrolase, Immune Response, Innate Immunity, Polymorphism, Protease, Secreted, Serine Protease, Sushi (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Krishnan, Y. Xu, K. Macon, J. E. Volanakis, S. V. Narayana
The Structure Of C2B, A Fragment Of Complement Component C2 Produced During C3 Convertase Formation
Acta Crystallogr. , Sect. D V. 65 266 2009
PubMed-ID: 19237749  |  Reference-DOI: 10.1107/S0907444909000389
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COMPLEMENT C2
    ChainsA
    EC Number3.4.21.43
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Cell LineHIGH FIVE(BTI-TN-5B1-4)
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    FragmentCOMPLEMENT C2B FRAGMENT, N-TERMINAL FRAGMENT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymC3/C5 CONVERTASE, COMPLEMENT C2B FRAGMENT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3ERB)

(-) Sites  (0, 0)

(no "Site" information available for 3ERB)

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:44
2A:31 -A:64
3A:69 -A:111
4A:97 -A:124
5A:131 -A:171
6A:157 -A:184

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:38 -Pro A:39
2Thr A:81 -Pro A:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_008544C131YCO2_HUMANDisease (C2D)760744400AC111Y
2UniProtVAR_008545S209FCO2_HUMANDisease (C2D)28934590AS189F

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUSHIPS50923 Sushi/CCP/SCR domain profile.CO2_HUMAN22-86
87-146
149-206
  2-
A:67-126
A:129-186

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.25aENST0000038336225aENSE00001853166HSCHR6_MHC_QBL:31885665-31885971307CO2_HUMAN1-16160--
1.25kENST0000038336225kENSE00002156028HSCHR6_MHC_QBL:31886128-31886337210CO2_HUMAN16-86711A:3-66 (gaps)64
1.25mENST0000038336225mENSE00001594373HSCHR6_MHC_QBL:31886905-31887090186CO2_HUMAN86-148631A:66-12863
1.33eENST0000038336233eENSE00002151523HSCHR6_MHC_QBL:31891783-31891956174CO2_HUMAN148-206591A:128-18659
1.33gENST0000038336233gENSE00002200460HSCHR6_MHC_QBL:31892040-3189213899CO2_HUMAN206-239341A:186-19712
1.33jENST0000038336233jENSE00001787345HSCHR6_MHC_QBL:31892339-31892472134CO2_HUMAN239-283450--
1.36hENST0000038336236hENSE00001794636HSCHR6_MHC_QBL:31894096-31894234139CO2_HUMAN284-330470--
1.36xENST0000038336236xENSE00002172075HSCHR6_MHC_QBL:31895492-31895632141CO2_HUMAN330-377480--
1.37bENST0000038336237bENSE00002191951HSCHR6_MHC_QBL:31897404-3189749390CO2_HUMAN377-407310--
1.48bENST0000038336248bENSE00002174341HSCHR6_MHC_QBL:31901133-31901273141CO2_HUMAN407-454480--
1.49bENST0000038336249bENSE00002169338HSCHR6_MHC_QBL:31901399-3190149395CO2_HUMAN454-485320--
1.50aENST0000038336250aENSE00002167630HSCHR6_MHC_QBL:31901590-31901701112CO2_HUMAN486-523380--
1.51bENST0000038336251bENSE00002150511HSCHR6_MHC_QBL:31901818-31901983166CO2_HUMAN523-578560--
1.51jENST0000038336251jENSE00002151638HSCHR6_MHC_QBL:31902091-3190216777CO2_HUMAN578-604270--
1.51kENST0000038336251kENSE00002180220HSCHR6_MHC_QBL:31902309-3190240092CO2_HUMAN604-634310--
1.52bENST0000038336252bENSE00002173165HSCHR6_MHC_QBL:31902901-31903027127CO2_HUMAN635-677430--
1.53cENST0000038336253cENSE00001729514HSCHR6_MHC_QBL:31903154-3190320350CO2_HUMAN677-693170--
1.54eENST0000038336254eENSE00001787775HSCHR6_MHC_QBL:31903352-31903846495CO2_HUMAN694-752590--

(-) 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:188
 aligned with CO2_HUMAN | P06681 from UniProtKB/Swiss-Prot  Length:752

    Alignment length:195
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212     
            CO2_HUMAN    23 SCPQNVNISGGTFTLSHGWAPGSLLTYSCPQGLYPSPASRLCKSSGQWQTPGATRSLSKAVCKPVRCPAPVSFENGIYTPRLGSYPVGGNVSFECEDGFILRGSPVRQCRPNGMWDGETAVCDNGAGHCPNPGISLGAVRTGFRFGHGDKVRYRCSSNLVLTGSSERECQGNGVWSGTEPICRQPYSYDFPEDVA 217
               SCOP domains d3erba1 A:3-67 automated matches                                 d3erba2 A:68-128 automated matches                           d3erba3 A:129-197 automated matches                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee........eeeee....eeee..eeee.....ee..-------..eeee.eee.......eeee....eee...eeeeee....eee...eee............eee..............eeee........eeeeee....eee...eee............eeehhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------Y-----------------------------------------------------------------------------F-------- SAPs(SNPs)
                    PROSITE SUSHI  PDB: - UniProt: 22-86                                    SUSHI  PDB: A:67-126 UniProt: 87-146                        --SUSHI  PDB: A:129-186 UniProt: 149-206                    ----------- PROSITE
           Transcript 1 (1) Exon 1.25k  PDB: A:3-66 (gaps) UniProt: 16-86 [INCOMPLETE]      -------------------------------------------------------------Exon 1.33e  PDB: A:128-186 UniProt: 148-206                ----------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------Exon 1.25m  PDB: A:66-128 UniProt: 86-148                      ---------------------------------------------------------Exon 1.33g   Transcript 1 (2)
                 3erb A   3 SCPQNVNISGGTFTLSHGWAPGSLLTYSCPQGLYPSPASRLCKSSGQWQTP-------KAVCKPVRCPAPVSFENGIYTPRLGSYPVGGNVSFECEDGFILRGSPVRQCRPNGMWDGETAVCDNGAGHCPNPGISLGAVRTGFRFGHGDKVRYRCSSNLVLTGSSERECQGNGVWSGTEPICRQPYSYDFPEDVA 197
                                    12        22        32        42        52|       62        72        82        92       102       112       122       132       142       152       162       172       182       192     
                                                                             53      61                                                                                                                                        

   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, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ERB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ERB)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CO2_HUMAN | P06681)
molecular function
    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: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: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:2000427    positive regulation of apoptotic cell clearance    Any process that activates or increases the frequency, rate or extent of apoptotic cell clearance.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0030449    regulation of complement activation    Any process that modulates the frequency, rate or extent of complement activation.
    GO:0007584    response to nutrient    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
cellular component
    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.

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    Ser A:38 - Pro A:39   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        CO2_HUMAN | P066812i6q 2i6s 2odp 2odq

(-) Related Entries Specified in the PDB File

2odp COMPLEMENT COMPONENT C2A, THE CATALYTIC FRAGMENT OF C3- AND C5-CONVERTASE
2odq COMPLEMENT COMPONENT C2A, THE CATALYTIC FRAGMENT OF C3- AND C5-CONVERTASE