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(-) Description

Title :  HUMAN COMPLEMENT FACTOR B
 
Authors :  F. J. Milder, L. Gomes, A. Schouten, B. J. C. Janssen, E. G. Huizinga, R. A W. Hemrika, A. Roos, M. R. Daha, P. Gros
Date :  16 Jan 07  (Deposition) - 27 Feb 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Pro-Enzyme, Serine Protease Domain, Von Willebrand Factor-A Domain, Ccp Domain, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. J. Milder, L. Gomes, A. Schouten, B. J. Janssen, E. G. Huizinga, R. A. Romijn, W. Hemrika, A. Roos, M. R. Daha, P. Gros
Factor B Structure Provides Insights Into Activation Of The Central Protease Of The Complement System.
Nat. Struct. Mol. Biol. V. 14 224 2007
PubMed-ID: 17310251  |  Reference-DOI: 10.1038/NSMB1210

(-) Compounds

Molecule 1 - COMPLEMENT FACTOR B
    Chains: A
    EC Number: 3.4.21.47
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Common: HUMAN
    Expression System Plasmid: PABC
    Expression System Strain: HUMAN
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: CFB, BF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Strain: HUMAN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 24)

Asymmetric/Biological Unit (4, 24)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2GOL13Ligand/IonGLYCEROL
3MAN4Ligand/IonALPHA-D-MANNOSE
4NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:95 , ASN A:97 , NAG A:1098 , HOH A:1424BINDING SITE FOR RESIDUE NAG A 1097
02AC2SOFTWAREGLN A:706 , NAG A:1097 , BMA A:1099 , MAN A:1100 , MAN A:1101BINDING SITE FOR RESIDUE NAG A 1098
03AC3SOFTWAREGLU A:182 , NAG A:1098 , MAN A:1100 , MAN A:1103BINDING SITE FOR RESIDUE BMA A 1099
04AC4SOFTWAREGLY A:183 , NAG A:1098 , BMA A:1099 , MAN A:1101 , MAN A:1102 , HOH A:1512 , HOH A:1546BINDING SITE FOR RESIDUE MAN A 1100
05AC5SOFTWAREGLU A:72 , ARG A:74 , NAG A:1098 , MAN A:1100BINDING SITE FOR RESIDUE MAN A 1101
06AC6SOFTWARELYS A:20 , TYR A:139 , GLY A:183 , GLY A:184 , LYS A:707 , MAN A:1100 , GOL A:1365 , HOH A:1520BINDING SITE FOR RESIDUE MAN A 1102
07AC7SOFTWARELYS A:391 , BMA A:1099BINDING SITE FOR RESIDUE MAN A 1103
08AC8SOFTWAREASN A:117 , THR A:587 , NAG A:1118 , HOH A:1508BINDING SITE FOR RESIDUE NAG A 1117
09AC9SOFTWARENAG A:1117BINDING SITE FOR RESIDUE NAG A 1118
10BC1SOFTWAREASN A:260 , ASN A:318BINDING SITE FOR RESIDUE NAG A 1260
11BC2SOFTWAREASN A:353 , HOH A:1514BINDING SITE FOR RESIDUE NAG A 1353
12BC3SOFTWAREASP A:200 , THR A:201 , PRO A:202 , VAL A:430 , LYS A:431 , ASN A:435BINDING SITE FOR RESIDUE GOL A 1354
13BC4SOFTWAREILE A:76 , ASN A:123 , ARG A:125 , PHE A:197 , TYR A:199 , LYS A:431 , HOH A:1591BINDING SITE FOR RESIDUE GOL A 1355
14BC5SOFTWAREVAL A:152 , GLY A:153 , SER A:161 , THR A:163 , ARG A:177BINDING SITE FOR RESIDUE GOL A 1356
15BC6SOFTWAREARG A:92 , ASP A:735 , LEU A:736 , GLY A:737 , HOH A:1399 , HOH A:1444 , HOH A:1600 , HOH A:1601BINDING SITE FOR RESIDUE GOL A 1357
16BC7SOFTWARECYS A:590 , LYS A:594 , PHE A:721 , ALA A:740 , ALA A:742BINDING SITE FOR RESIDUE GOL A 1358
17BC8SOFTWARETYR A:42 , HIS A:77 , ASP A:195 , PHE A:197 , GOL A:1362BINDING SITE FOR RESIDUE GOL A 1359
18BC9SOFTWAREGLU A:519 , LEU A:523 , LEU A:561 , LYS A:562 , ILE A:567 , HOH A:1560BINDING SITE FOR RESIDUE GOL A 1360
19CC1SOFTWAREGLY A:21 , PRO A:38 , PHE A:41 , CYS A:73 , ALA A:665BINDING SITE FOR RESIDUE GOL A 1361
20CC2SOFTWARETYR A:42 , TYR A:44 , PRO A:45 , THR A:62 , GLN A:63 , GOL A:1359BINDING SITE FOR RESIDUE GOL A 1362
21CC3SOFTWAREASP A:634 , ALA A:711 , HIS A:712 , ARG A:714BINDING SITE FOR RESIDUE GOL A 1363
22CC4SOFTWAREGLY A:16 , GLU A:18 , ARG A:113 , GLY A:114 , GLN A:129 , HOH A:1461BINDING SITE FOR RESIDUE GOL A 1364
23CC5SOFTWAREGLY A:136 , GLY A:138 , TYR A:139 , CYS A:140 , SER A:141 , GLY A:184 , MAN A:1102 , HOH A:1661BINDING SITE FOR RESIDUE GOL A 1365
24CC6SOFTWARELYS A:556 , GLU A:734BINDING SITE FOR RESIDUE GOL A 1366

(-) SS Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1A:12 -A:51
2A:37 -A:73
3A:78 -A:120
4A:106 -A:133
5A:140 -A:180
6A:166 -A:193
7A:453 -A:571
8A:486 -A:502
9A:574 -A:590
10A:631 -A:657
11A:670 -A:700

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Tyr A:44 -Pro A:45
2Trp A:90 -Pro A:91
3Tyr A:319 -Glu A:320
4Gly A:538 -Lys A:539
5Ser A:662 -Pro A:663
6Gln A:706 -Lys A:707
7Lys A:707 -Gln A:708

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (11, 11)

Asymmetric/Biological Unit (11, 11)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_063659S166PCFAB_HUMANDisease (AHUS4)  ---AS141P
02UniProtVAR_063660R203QCFAB_HUMANDisease (AHUS4)745794224AR178Q
03UniProtVAR_063661I242LCFAB_HUMANDisease (AHUS4)144812066AI217L
04UniProtVAR_063221F286LCFAB_HUMANDisease (AHUS4)117905900AF261L
05UniProtVAR_063222K323ECFAB_HUMANDisease (AHUS4)121909748AK298E
06UniProtVAR_063662K323QCFAB_HUMANDisease (AHUS4)  ---AK298Q
07UniProtVAR_063663M458ICFAB_HUMANDisease (AHUS4)200837114AM433I
08UniProtVAR_063664K533RCFAB_HUMANDisease (AHUS4)149101394AK508R
09UniProtVAR_016277K565ECFAB_HUMANPolymorphism4151659AK540E
10UniProtVAR_016278D651ECFAB_HUMANPolymorphism4151660AD626E
11UniProtVAR_006495A736SCFAB_HUMANPolymorphism  ---AA711S
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (5, 7)

Asymmetric/Biological Unit (5, 7)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SUSHIPS50923 Sushi/CCP/SCR domain profile.CFAB_HUMAN35-100
101-160
163-220		  3A:10-75
A:76-135
A:138-195
2VWFAPS50234 VWFA domain profile.CFAB_HUMAN270-469  1A:245-444
3TRYPSIN_DOMPS50240 Serine proteases, trypsin domain profile.CFAB_HUMAN477-757  1A:452-732
4TRYPSIN_HISPS00134 Serine proteases, trypsin family, histidine active site.CFAB_HUMAN522-527  1A:497-502
5TRYPSIN_SERPS00135 Serine proteases, trypsin family, serine active site.CFAB_HUMAN693-704  1A:668-679

(-) Exons   (0, 0)

(no "Exon" information available for 2OK5)

(-) 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:710
 aligned with CFAB_HUMAN | P00751 from UniProtKB/Swiss-Prot  Length:764

    Alignment length:734
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    764   
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763|   
           CFAB_HUMAN    34 QGSCSLEGVEIKGGSFRLLQEGQALEYVCPSGFYPYPVQTRTCRSTGSWSTLKTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYYNVSDEISFHCYDGYTLRGSANRTCQVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQYRLEDSVTYHCSRGLTLRGSQRRTCQEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTETIEGVDAEDGHGPGEQQKRKIVLDPSGSMNIYLVLDGSDSIGASNFTGAKKCLVNLIEKVASYGVKPRYGLVTYATYPKIWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDVPPEGWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLVNQVNINALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQAKISVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNYNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQKEELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPRFLCTGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGVVDVCKNQKRQKQVPAHARDFHINLFQVLPWLKEKLQDEDLGFL---   -
               SCOP domains d2ok5a4 A:9-76 Complement factor B                                  d2ok5a3 A:77-137 Complement factor B                         d2ok5a2 A:138-199 Complement factor B                         d2ok5a1 A:200-452                Complement factor B domain                                                                                                                                                                                                  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------Sushi-2ok5A02 A:140-193                               ------------------------               ------------VWA-2ok5A05 A:245-443                                                                                                                                                                                  ------------Trypsin-2ok5A01 A:456-727                                                                                                                                                                                                                                                       --------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------Sushi-2ok5A03 A:140-193                               --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------------------------------------------------------Sushi-2ok5A04 A:140-193                               --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author ..............eeeeehhh.eeeee....eeee...eee.....................eeee.ee........eeee.....ee...eeeeee....eee...eee............eee...............eee........eeeee.....eee...eee............eee......hhhhhhhhhhhhhh...---------------..........eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh.....eeeeeee...eeeee........hhhhhhhhhhh....------..hhhhhhhhhhhhhh.---....hhh.eeeeeeeee.........hhhhhhhhhhhh.........hhh.eeeeeeee....hhhhhhhhh........eeee.hhhhhhhhhhhhhhh................hhhhhh..eeeeee.......eeeeeee....eeeehhhhh....hhh.eeeee........eeeeee......................eeeee.................hhhhhhhh......hhhhhhhhhh...eeeeeeeeee..eeeeeeeeee...hhhhhhhhhhhh.......hhhhh....eeeee..........hhhhh..eeeeee..eeeeeeeeeee...hhhhh..........eeeeee...hhhhhhhhh........... Sec.struct. author
             SAPs(SNPs) (1) ------------------------------------------------------------------------------------------------------------------------------------P------------------------------------Q--------------------------------------L-------------------------------------------L------------------------------------E--------------------------------------------------------------------------------------------------------------------------------------I--------------------------------------------------------------------------R-------------------------------E-------------------------------------------------------------------------------------E------------------------------------------------------------------------------------S------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Q------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (2)
                PROSITE (1) -SUSHI  PDB: A:10-75 UniProt: 35-100                               SUSHI  PDB: A:76-135 UniProt: 101-160                       --SUSHI  PDB: A:138-195 UniProt: 163-220                    -------------------------------------------------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
                 2ok5 A   9 QGSCSLEGVEIKGGSFRLLQEGQALEYVCPSGFYPYPVQTRTCRSTGSWSTLKTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYYNVSDEISFHCYDGYTLRGSANRTCQVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQYRLEDSVTYHCSRGLTLRGSQRRTCQEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTETI---------------KRKIVLDPSGSMNIYLVLDGSDSIGASNFTGAKKCLVNLIEKVASYGVKPRYGLVTYATYPKIWVKVSEADSSNADWVTKQLNEINYE------GTNTKKALQAVYSMMSW---VPPEGWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLVNQVNINALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQAKISVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPNYNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQKEELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPRFLCTGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGVVDVCKNQKRQKQVPAHARDFHINLFQVLPWLKEKLQDEDLGFLAAA 742
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208        |-         -    |  238       248       258       268       278       288       298       308       318 |     328       338    |  348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738    
                                                                                                                                                                                                                                          217             233                                                                                    320    327             343 347
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2OK5)

(-) Pfam Domains  (3, 5)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_PA (797)
(-)
Clan: no clan defined [family: Sushi] (50)
(-)
Family: Sushi (50)
(-)
Homo sapiens (Human) (42)
2aSushi-2ok5A02A:140-193
2bSushi-2ok5A03A:140-193
2cSushi-2ok5A04A:140-193
(-)
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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  2ok5
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  CFAB_HUMAN | P00751
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  3.4.21.47
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  612924
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  CFAB_HUMAN | P00751
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UniProtKB/Swiss-Prot
        CFAB_HUMAN | P00751: 1dle 1q0p 1rrk 1rs0 1rtk 2win 2xwb 2xwj 3hrz 3hs0 5m6w

(-) Related Entries Specified in the PDB File

2i6q COMPLEMENT COMPONENT C2A