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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE BB SEGMENT OF FACTOR B COMPLEXED WITH 4-GUANIDINOBENZOIC ACID
 
Authors :  K. Ponnuraj, Y. Xu, K. Macon, D. Moore, J. E. Volanakis, S. V. Narayana
Date :  10 Dec 03  (Deposition) - 14 Dec 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Factor B, Bb, Factor Bb-Inhibitor Complex, Hormone/Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Ponnuraj, Y. Xu, K. Macon, D. Moore, J. E. Volanakis, S. V. Narayana
Structural Analysis Of Engineered Bb Fragment Of Complement Factor B: Insights Into The Activation Mechanism Of The Alternative Pathway C3-Convertase.
Mol. Cell V. 14 17 2004
PubMed-ID: 15068800  |  Reference-DOI: 10.1016/S1097-2765(04)00160-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COMPLEMENT FACTOR B
    ChainsA
    EC Number3.4.21.47
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System CellEGG
    Expression System Cell LineBTI-TN-5B1-4
    Expression System CommonCABBAGE LOOPER
    Expression System Taxid7111
    Expression System Vector TypeBACULOVIRUS
    FragmentCOMPLEMENT FACTOR B BB FRAGMENT
    GeneBF
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsSF9 CELLS WERE ALSO USED
    SynonymC3/C5 CONVERTASE, PROPERDIN FACTOR B, GLYCINE- RICH BETA GLYCOPROTEIN, GBG, PBF2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1GBS1Ligand/Ion4-GUANIDINOBENZOIC ACID
2IOD2Ligand/IonIODIDE ION
3MG1Ligand/IonMAGNESIUM ION
4NA7Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:531BINDING SITE FOR RESIDUE IOD A 740
2AC2SOFTWAREHIS A:466 , NA A:748BINDING SITE FOR RESIDUE IOD A 741
3AC3SOFTWARELYS A:594 , ASN A:719 , GLN A:722BINDING SITE FOR RESIDUE NA A 745
4AC4SOFTWAREARG A:580BINDING SITE FOR RESIDUE NA A 746
5AC5SOFTWAREALA A:290 , THR A:291 , TYR A:292 , HIS A:322 , LYS A:323 , LEU A:324 , IOD A:741BINDING SITE FOR RESIDUE NA A 748
6AC6SOFTWARESER A:253 , SER A:255 , THR A:328 , HOH A:989 , HOH A:990 , HOH A:991 , HOH A:992BINDING SITE FOR RESIDUE MG A 749
7AC7SOFTWAREHIS A:501 , THR A:669 , ARG A:671 , SER A:674 , SER A:693 , TRP A:694 , GLY A:695 , VAL A:697 , ASP A:698 , HOH A:879 , HOH A:945 , HOH A:1007 , HOH A:1016BINDING SITE FOR RESIDUE GBS A 750

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:428 -A:435
2A:453 -A:571
3A:486 -A:502
4A:574 -A:590
5A:631 -A:657
6A:670 -A:700

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:662 -Pro A:663

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

Asymmetric/Biological Unit (8, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_063221F286LCFAB_HUMANDisease (AHUS4)117905900AF261L
2UniProtVAR_063222K323ECFAB_HUMANDisease (AHUS4)121909748AK298E
3UniProtVAR_063662K323QCFAB_HUMANDisease (AHUS4)  ---AK298Q
4UniProtVAR_063663M458ICFAB_HUMANDisease (AHUS4)200837114AM433I
5UniProtVAR_063664K533RCFAB_HUMANDisease (AHUS4)149101394AK508R
6UniProtVAR_016277K565ECFAB_HUMANPolymorphism4151659AK540E
7UniProtVAR_016278D651ECFAB_HUMANPolymorphism4151660AD626E
8UniProtVAR_006495A736SCFAB_HUMANPolymorphism  ---AA711S

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

(-) PROSITE Motifs  (4, 4)

Asymmetric/Biological Unit (4, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1VWFAPS50234 VWFA domain profile.CFAB_HUMAN270-469  1A:245-444
2TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CFAB_HUMAN477-757  1A:452-732
3TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CFAB_HUMAN522-527  1A:497-502
4TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CFAB_HUMAN693-704  1A:668-679

(-) Exons   (0, 0)

(no "Exon" information available for 1RTK)

(-) 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:486
 aligned with CFAB_HUMAN | P00751 from UniProtKB/Swiss-Prot  Length:764

    Alignment length:497
                                   277       287       297       307       317       327       337       347       357       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       687       697       707       717       727       737       747       757       
           CFAB_HUMAN   268 SMNIYLVLDGSDSIGASNFTGAKKCLVNLIEKVASYGVKPRYGLVTYATYPKIWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPPEGWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLVNQVNINALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQAKISVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNYNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQKEELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPRFLCTGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGVVDVCKNQKRQKQVPAHARDFHINLFQVLPWLKEKLQDEDLGFL 764
               SCOP domains d1rtka2 A:243-452 Complement factor B domain                                                                                                                                                                      d1rtka1 A:453-739 Factor B                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 1rtkA01 A:243-451  [code=3.40.50.410, no name defined]                                                                                                                                                           1rtkA02 A:452-570 Trypsin-l  ike serine proteases                                                                      1rtkA03 A:571-739 Trypsin-like serine proteases                                                                                                                           CATH domains
               Pfam domains --VWA-1rtkA02 A:245-443                                                                                                                                                                                  ------------Trypsin-1rtkA01 A:456-7  27                                                                                                                                                                                                                                                     ------------ Pfam domains
         Sec.struct. author .eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...eeeee...hhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh..------hhhhheeeeeeee.........hhhhhhhhhhhh.........hhh.eeeeeee.....hhhhhhhhh........eee..hhhhhhhhhhhhhhhhhhh............hhhhhh..eeeeee..--...eeeeeee....eeeehhhhh....hhh.eeeee......eeeeeeee........hhhhh.........eeeee.................hhhhhhhh......hhhhhhhhhh...eeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhh.......hhhhh....eeeee..........hhhhh..eeeeee..eeeeeeeeeee.....---..........eeeeee...hhhhhhhhh........ Sec.struct. author
             SAPs(SNPs) (1) ------------------L------------------------------------E--------------------------------------------------------------------------------------------------------------------------------------I--------------------------------------------------------------------------R-------------------------------E-------------------------------------------------------------------------------------E------------------------------------------------------------------------------------S---------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------Q--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                PROSITE (1) --VWFA  PDB: A:245-444 UniProt: 270-469                                                                                                                                                                   -------TRYPSIN_DOM  PDB: A:452-732 UniProt: 477-757                                                                                                                                                                                                                                             ------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSI---------------------------------------------------------------------------------------------------------------------------------------------------------------------TRYPSIN_SER ------------------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rtk A 243 SMNIYLVLDGSDSIGASNFTGAKKVLVNLIEKVASYGVKPRYGLVTYATYPKIWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWP------GWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLVNQVNINALASKKDNEQHVCKVKDMECLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQAKISVIR--KGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNYNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQKEELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPRFLCTGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGVVDVC---KRQKQVPAHARDFHINLFQVLPWLKEKLQDEDLGFL 739
                                   252       262       272       282       292       302       312       322       332       342 |     352       362       372       382       392       402       412       422       432       442       452       462       472     | 482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       | - |     712       722       732       
                                                                                                                               344    351                                                                                                                            478  |                                                                                                                                                                                                                        700 704                                   
                                                                                                                                                                                                                                                                        481                                                                                                                                                                                                                                                                  

   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, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: vWA-like (60)
(-)
Family: VWA (50)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CFAB_HUMAN | P00751)
molecular function
    GO:0001848    complement binding    Interacting selectively and non-covalently with any component or product of the complement cascade.
    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: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: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: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.
    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: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
        CFAB_HUMAN | P007511dle 1q0p 1rrk 1rs0 2ok5 2win 2xwb 2xwj 3hrz 3hs0 5m6w

(-) Related Entries Specified in the PDB File

1rrk CRYSTAL STRUCTURE ANALYSIS OF THE BB SEGMENT OF FACTOR B
1rs0 CRYSTAL STRUCTURE ANALYSIS OF THE BB SEGMENT OF FACTOR B COMPLEXED WITH DI-ISOPROPYL-PHOSPHATE (DIP)