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(-) Description

Title :  H-FICOLIN COMPLEXED TO D-FUCOSE
 
Authors :  V. Garlatti, C. Gaboriaud
Date :  21 Sep 06  (Deposition) - 23 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Hydroxylation, Alternative Splicing, Lectin, Collagen, Immunology, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Garlatti, N. Belloy, L. Martin, M. Lacroix, M. Matsushita, Y. Endo, T. Fujita, J. C. Fontecilla-Camps, G. J. Arlaud, N. M. Thielens, C. Gaboriaud
Structural Insights Into The Innate Immune Recognition Specificities Of L- And H-Ficolins.
Embo J. V. 26 623 2007
PubMed-ID: 17215869  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601500

(-) Compounds

Molecule 1 - FICOLIN-3
    ChainsA, B, C
    EngineeredYES
    Expression System Vector TypeBACULOVIRUS
    FragmentBINDING DOMAIN, RESIDUES 79-299
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCOLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 3, COLLAGEN/FIBRINOGEN DOMAIN-CONTAINING LECTIN 3 P35, HAKATA ANTIGEN, H-FICOLIN
    TissuePLASMA

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1ABE2Ligand/IonABEQUOSE
2ACT1Ligand/IonACETATE ION
3CA3Ligand/IonCALCIUM ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ABE1Ligand/IonABEQUOSE
2ACT1Ligand/IonACETATE ION
3CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ABE1Ligand/IonABEQUOSE
2ACT-1Ligand/IonACETATE ION
3CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1ABE-1Ligand/IonABEQUOSE
2ACT-1Ligand/IonACETATE ION
3CA-1Ligand/IonCALCIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:235 , TYR A:236 , TYR A:254 , VAL A:264BINDING SITE FOR RESIDUE ABE A1277
2AC2SOFTWAREARG A:128 , HOH A:2071 , CYS B:235 , TYR B:236 , TYR B:254 , VAL B:264BINDING SITE FOR RESIDUE ABE B1277
3AC3SOFTWAREASP A:214 , ASP A:216 , SER A:218 , SER A:220 , HOH A:2057 , HOH A:2058BINDING SITE FOR RESIDUE CA A1278
4AC4SOFTWAREGLU A:143 , HIS A:146 , GLY A:179 , GLU A:180 , VAL A:181 , HOH A:2073 , SER B:220 , HOH B:2062BINDING SITE FOR RESIDUE ACT A1279
5AC5SOFTWAREASP B:214 , ASP B:216 , SER B:218 , SER B:220 , HOH B:2057 , HOH B:2060BINDING SITE FOR RESIDUE CA B1278
6AC6SOFTWAREASP C:214 , ASP C:216 , SER C:218 , ASN C:219 , SER C:220 , HOH C:2033BINDING SITE FOR RESIDUE CA C1277

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1A:63 -A:87
2A:70 -A:98
3A:222 -A:235
4B:70 -B:98
5B:222 -B:235
6C:70 -C:98
7C:222 -C:235

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser A:234 -Cys A:235
2Ser B:234 -Cys B:235
3Ser C:234 -Cys C:235

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2J60)

(-) PROSITE Motifs  (1, 3)

Asymmetric Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRINOGEN_C_1PS00514 Fibrinogen C-terminal domain signature.FCN3_HUMAN253-265
 
 
  3A:230-242
B:230-242
C:230-242
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRINOGEN_C_1PS00514 Fibrinogen C-terminal domain signature.FCN3_HUMAN253-265
 
 
  1A:230-242
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRINOGEN_C_1PS00514 Fibrinogen C-terminal domain signature.FCN3_HUMAN253-265
 
 
  1-
B:230-242
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRINOGEN_C_1PS00514 Fibrinogen C-terminal domain signature.FCN3_HUMAN253-265
 
 
  1-
-
C:230-242

(-) Exons   (5, 15)

Asymmetric Unit (5, 15)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002708791aENSE00001153243chr1:27701315-2770121997FCN3_HUMAN1-31310--
1.2aENST000002708792aENSE00000956155chr1:27700942-2770084796FCN3_HUMAN31-63330--
1.2cENST000002708792cENSE00000956156chr1:27700500-2770045645FCN3_HUMAN63-78160--
1.2eENST000002708792eENSE00000956157chr1:27700011-2769997933FCN3_HUMAN78-89123A:63-66
B:64-66
C:66-66
4
3
1
1.2fENST000002708792fENSE00000956158chr1:27699754-27699627128FCN3_HUMAN89-131433A:66-108
B:66-108
C:66-108
43
43
43
1.3ENST000002708793ENSE00000956159chr1:27697463-27697334130FCN3_HUMAN132-175443A:109-152
B:109-152
C:109-152
44
44
44
1.4aENST000002708794aENSE00000956160chr1:27697221-27697087135FCN3_HUMAN175-220463A:152-197
B:152-197
C:152-197
46
46
46
1.5ENST000002708795ENSE00001037666chr1:27695968-27695603366FCN3_HUMAN220-299803A:197-276
B:197-276
C:197-276
80
80
80

(-) Sequences/Alignments

Asymmetric 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:214
 aligned with FCN3_HUMAN | O75636 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:214
                                    95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295    
           FCN3_HUMAN    86 CQEGPRNCRELLSQGATLSGWYHLCLPEGRALPVFCDMDTEGGGWLVFQRRQDGSVDFFRSWSSYRAGFGNQESEFWLGNENLHQLTLQGNWELRVELEDFNGNRTFAHYATFRLLGEVDHYQLALGKFSEGTAGDSLSLHSGRPFTTYDADHDSSNSNCAVIVHGAWWYASCYRSNLNGRYAVSEAAAHKYGIDWASGRGVGHPYRRVRMMLR 299
               SCOP domains d2j60a_ A: automated matches                                                                                                                                                                                           SCOP domains
               CATH domains 2j60A01 A:63-196,A:270-276 Gamma Fibrinogen, chain A, domain 1                                                                        2j60A02 A:197-269 Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2  2j60A01 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhh.....eeeeee.....eeeeeee.hhhhh.eeeeeee.........hhhhhhhhee.....ee.hhhhhhhhh.....eeeeeee.....eeeeee..eee.hhhhh..eee..eee......hhhhh................hhhhhhh..........................................eeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------FIBRINOGEN_C_---------------------------------- PROSITE
           Transcript 1 (1) 1.2e------------------------------------------Exon 1.3  PDB: A:109-152 UniProt: 132-175   --------------------------------------------Exon 1.5  PDB: A:197-276 UniProt: 220-299                                        Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.2f  PDB: A:66-108 UniProt: 89-131   -------------------------------------------Exon 1.4a  PDB: A:152-197 UniProt: 175-220    ------------------------------------------------------------------------------- Transcript 1 (2)
                 2j60 A  63 CQEGPRNCRELLSQGATLSGWYHLCLPEGRALPVFCDMDTEGGGWLVFQRRQDGSVDFFRSWSSYRAGFGNQESEFWLGNENLHQLTLQGNWELRVELEDFNGNRTFAHYATFRLLGEVDHYQLALGKFSEGTAGDSLSLHSGRPFTTYDADHDSSNSNCAVIVHGAWWYASCYRSNLNGRYAVSEAAAHKYGIDWASGRGVGHPYRRVRMMLR 276
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272    

Chain B from PDB  Type:PROTEIN  Length:213
 aligned with FCN3_HUMAN | O75636 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:213
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296   
           FCN3_HUMAN    87 QEGPRNCRELLSQGATLSGWYHLCLPEGRALPVFCDMDTEGGGWLVFQRRQDGSVDFFRSWSSYRAGFGNQESEFWLGNENLHQLTLQGNWELRVELEDFNGNRTFAHYATFRLLGEVDHYQLALGKFSEGTAGDSLSLHSGRPFTTYDADHDSSNSNCAVIVHGAWWYASCYRSNLNGRYAVSEAAAHKYGIDWASGRGVGHPYRRVRMMLR 299
               SCOP domains d2j60b_ B: automated matches                                                                                                                                                                                          SCOP domains
               CATH domains 2j60B01 B:64-196,B:270-276 Gamma Fibrinogen, chain A, domain 1                                                                       2j60B02 B:197-269 Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2  2j60B01 CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhh...eeeeeeeee...eeeeeeee.hhhhh.eeeeeee.........hhhhhhhhee.....ee.hhhhhhhhhh...eeeeeeee.....eeeeeeeeeee.hhhhh................hhhhh................hhhhhhh...................hhhhh..................eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------FIBRINOGEN_C_---------------------------------- PROSITE
           Transcript 1 (1) 1.2------------------------------------------Exon 1.3  PDB: B:109-152 UniProt: 132-175   --------------------------------------------Exon 1.5  PDB: B:197-276 UniProt: 220-299                                        Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2f  PDB: B:66-108 UniProt: 89-131   -------------------------------------------Exon 1.4a  PDB: B:152-197 UniProt: 175-220    ------------------------------------------------------------------------------- Transcript 1 (2)
                 2j60 B  64 QEGPRNCRELLSQGATLSGWYHLCLPEGRALPVFCDMDTEGGGWLVFQRRQDGSVDFFRSWSSYRAGFGNQESEFWLGNENLHQLTLQGNWELRVELEDFNGNRTFAHYATFRLLGEVDHYQLALGKFSEGTAGDSLSLHSGRPFTTYDADHDSSNSNCAVIVHGAWWYASCYRSNLNGRYAVSEAAAHKYGIDWASGRGVGHPYRRVRMMLR 276
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273   

Chain C from PDB  Type:PROTEIN  Length:211
 aligned with FCN3_HUMAN | O75636 from UniProtKB/Swiss-Prot  Length:299

    Alignment length:211
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298 
           FCN3_HUMAN    89 GPRNCRELLSQGATLSGWYHLCLPEGRALPVFCDMDTEGGGWLVFQRRQDGSVDFFRSWSSYRAGFGNQESEFWLGNENLHQLTLQGNWELRVELEDFNGNRTFAHYATFRLLGEVDHYQLALGKFSEGTAGDSLSLHSGRPFTTYDADHDSSNSNCAVIVHGAWWYASCYRSNLNGRYAVSEAAAHKYGIDWASGRGVGHPYRRVRMMLR 299
               SCOP domains d2j60c_ C: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains 2j60C01 C:66-196,C:270-276 Gamma Fibrinogen, chain A, domain 1                                                                     2j60C02 C:197-269 Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2  2j60C01 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh........................hhhhh.eeeeeee.........hhhhhhhheee....ee.hhhhhhhhhh........................eee.hhhhh..eee...........hhhhh................hhhhhh.................................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------FIBRINOGEN_C_---------------------------------- PROSITE
           Transcript 1 (1) 1------------------------------------------Exon 1.3  PDB: C:109-152 UniProt: 132-175   --------------------------------------------Exon 1.5  PDB: C:197-276 UniProt: 220-299                                        Transcript 1 (1)
           Transcript 1 (2) Exon 1.2f  PDB: C:66-108 UniProt: 89-131   -------------------------------------------Exon 1.4a  PDB: C:152-197 UniProt: 175-220    ------------------------------------------------------------------------------- Transcript 1 (2)
                 2j60 C  66 GPRNCRELLSQGATLSGWYHLCLPEGRALPVFCDMDTEGGGWLVFQRRQDGSVDFFRSWSSYRAGFGNQESEFWLGNENLHQLTLQGNWELRVELEDFNGNRTFAHYATFRLLGEVDHYQLALGKFSEGTAGDSLSLHSGRPFTTYDADHDSSNSNCAVIVHGAWWYASCYRSNLNGRYAVSEAAAHKYGIDWASGRGVGHPYRRVRMMLR 276
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275 

   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 Unit

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J60)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (FCN3_HUMAN | O75636)
molecular function
    GO:0003823    antigen binding    Interacting selectively and non-covalently with an antigen, any substance which is capable of inducing a specific immune response and of reacting with the products of that response, the specific antibody or specifically sensitized T-lymphocytes, or both. Binding may counteract the biological activity of the antigen.
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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).
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:0001867    complement activation, lectin pathway    Any process involved in the activation of any of the steps of the lectin pathway of the complement cascade which allows for the direct killing of microbes and the regulation of other immune processes.
    GO:0051607    defense response to virus    Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
    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:1902679    negative regulation of RNA biosynthetic process    Any process that stops, prevents or reduces the frequency, rate or extent of RNA biosynthetic process.
    GO:0046597    negative regulation of viral entry into host cell    Any process that stops, prevents, or reduces the frequency, rate or extent of the entry of viral entry into a host cell.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0043654    recognition of apoptotic cell    The process in which a cell interprets signals (in the form of specific proteins and lipids) on the surface of a dying cell which it will engulf and remove by phagocytosis.
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:0005581    collagen trimer    A protein complex consisting of three collagen chains assembled into a left-handed triple helix. These trimers typically assemble into higher order structures.
    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
        FCN3_HUMAN | O756361la5 2j5z 2j64

(-) Related Entries Specified in the PDB File

1la5 THEORITICAL MODEL OF HUMAN FICOLIN PRECURSOR
2j5z H-FICOLIN COMPLEXED TO GALACTOSE
2j61 L-FICOLIN COMPLEXED TO N-ACETYLGALACTOSAMINE (FORME C)