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(-) Description

Title :  L-FICOLIN COMPLEXED TO N-ACETYLGLUCOSAMINE (FORME C)
 
Authors :  V. Garlatti, C. Gaboriaud
Date :  21 Sep 06  (Deposition) - 23 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycoprotein, Ficrinogen-Like, Innate Immunity, Pattern Recognition Protein, Lectin, Collagen, Immunology, Lectin- Like (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-2
    ChainsA
    EngineeredYES
    FragmentBINDING DOMAIN, RESIDUES 97-313
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCOLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 2, FICOLIN-B, FICOLIN B, SERUM LECTIN P35, EBP-37, HUCOLIN, L-FICOLIN
    TissuePLASMA
 
Molecule 2 - FICOLIN-2
    ChainsB
    EngineeredYES
    FragmentBINDING DOMAIN, RESIDUES 97-313
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCOLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 2, FICOLIN-B, FICOLIN B, SERUM LECTIN P35, EBP-37, HUCOLIN, L-FICOLIN
    TissuePLASMA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:109 , THR A:112 , ARG A:122 , SER A:143 , ASP A:169 , GLU A:282 , LYS A:284BINDING SITE FOR RESIDUE NAG A1290
2AC2SOFTWAREASP A:224 , ASP A:226 , ASN A:228 , THR A:229 , GLY A:230BINDING SITE FOR RESIDUE CA A1289
3AC3SOFTWAREASP B:224 , ASP B:226 , ASN B:228 , HOH B:2024BINDING SITE FOR RESIDUE CA B1289

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:73 -A:101
2A:80 -A:108
3A:232 -A:245
4B:73 -B:101
5B:80 -B:108
6B:232 -B:245

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:244 -Cys A:245
2Asn B:244 -Cys B:245

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 8)

Asymmetric Unit (4, 8)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049072H113YFCN2_HUMANPolymorphism17549179A/BH88Y
2UniProtVAR_049073G117SFCN2_HUMANPolymorphism12684476A/BG92S
3UniProtVAR_049074T236MFCN2_HUMANPolymorphism17549193A/BT211M
4UniProtVAR_049075A258SFCN2_HUMANPolymorphism7851696A/BA233S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049072H113YFCN2_HUMANPolymorphism17549179AH88Y
2UniProtVAR_049073G117SFCN2_HUMANPolymorphism12684476AG92S
3UniProtVAR_049074T236MFCN2_HUMANPolymorphism17549193AT211M
4UniProtVAR_049075A258SFCN2_HUMANPolymorphism7851696AA233S

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049072H113YFCN2_HUMANPolymorphism17549179BH88Y
2UniProtVAR_049073G117SFCN2_HUMANPolymorphism12684476BG92S
3UniProtVAR_049074T236MFCN2_HUMANPolymorphism17549193BT211M
4UniProtVAR_049075A258SFCN2_HUMANPolymorphism7851696BA233S

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRINOGEN_C_1PS00514 Fibrinogen C-terminal domain signature.FCN2_HUMAN265-277
 
  2A:240-252
B:240-252
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRINOGEN_C_1PS00514 Fibrinogen C-terminal domain signature.FCN2_HUMAN265-277
 
  1A:240-252
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIBRINOGEN_C_1PS00514 Fibrinogen C-terminal domain signature.FCN2_HUMAN265-277
 
  1-
B:240-252

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002917441bENSE00001890733chr9:137772658-137772767110FCN2_HUMAN1-34340--
1.2ENST000002917442ENSE00001051605chr9:137774372-137774485114FCN2_HUMAN34-72390--
1.3aENST000002917443aENSE00001051599chr9:137775148-13777520154FCN2_HUMAN72-90190--
1.4ENST000002917444ENSE00001247525chr9:137776586-13777661833FCN2_HUMAN90-101122A:73-76
B:73-76
4
4
1.5ENST000002917445ENSE00001643405chr9:137777085-137777212128FCN2_HUMAN101-143432A:76-118
B:76-118
43
43
1.6ENST000002917446ENSE00001786911chr9:137777614-137777743130FCN2_HUMAN144-187442A:119-162
B:119-162
44
44
1.7ENST000002917447ENSE00001656900chr9:137778276-137778410135FCN2_HUMAN187-232462A:162-207
B:162-207
46
46
1.8aENST000002917448aENSE00001941356chr9:137779014-137779366353FCN2_HUMAN232-313822A:207-288
B:207-288
82
82

(-) 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:216
 aligned with FCN2_HUMAN | Q15485 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:216
                                   107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307      
           FCN2_HUMAN    98 CLTGPRTCKDLLDRGHFLSGWHTIYLPDCRPLTVLCDMDTDGGGWTVFQRRVDGSVDFYRDWATYKQGFGSRLGEFWLGNDNIHALTAQGTSELRVDLVDFEDNYQFAKYRSFKVADEAEKYNLVLGAFVEGSAGDSLTFHNNQSFSTKDQDNDLNTGNCAVMFQGAWWYKNCHVSNLNGRYLRGTHGSFANGINWKSGKGYNYSYKVSEMKVRPA 313
               SCOP domains d2j61a_ A: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains 2j61A01 A:73-206,A:280-288 Gamma Fibrinogen, chain A, domain 1                                                                        2j61A02 A:207-279 Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2  2j61A01   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhh.....eeeeee.....eeeeeee.hhhhh.eeeeeee.........hhhhhhhhee.....ee.hhhhhhhhhh...eeeeeeee.....eeeeeeeeeee......................hhhhh....ee..........hhhhhhh.ee.......ee.......ee........eehhhhh..ee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------Y---S----------------------------------------------------------------------------------------------------------------------M---------------------S------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------FIBRINOGEN_C_------------------------------------ PROSITE
           Transcript 1 (1) 1.4 ------------------------------------------Exon 1.6  PDB: A:119-162 UniProt: 144-187   --------------------------------------------Exon 1.8a  PDB: A:207-288 UniProt: 232-313                                         Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.5  PDB: A:76-118 UniProt: 101-143   -------------------------------------------Exon 1.7  PDB: A:162-207 UniProt: 187-232     --------------------------------------------------------------------------------- Transcript 1 (2)
                 2j61 A  73 CLTGPRTCKDLLDRGHFLSGWHTIYLPDCRPLTVLCDMDTDGGGWTVFQRRVDGSVDFYRDWATYKQGFGSRLGEFWLGNDNIHALTAQGTSELRTDLVDFEDNYQFAKYRSFRVADEAEKYNLVLGAFVEGSAGDSLTFHNNQSFSTKDQDNDLNTGNCAVMFQGAWWYKNCHTSNLNGRYLRGTHGSFANGINWKSGKGYNYSYKVSEMKVRPA 288
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with FCN2_HUMAN | Q15485 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:216
                                   107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307      
           FCN2_HUMAN    98 CLTGPRTCKDLLDRGHFLSGWHTIYLPDCRPLTVLCDMDTDGGGWTVFQRRVDGSVDFYRDWATYKQGFGSRLGEFWLGNDNIHALTAQGTSELRVDLVDFEDNYQFAKYRSFKVADEAEKYNLVLGAFVEGSAGDSLTFHNNQSFSTKDQDNDLNTGNCAVMFQGAWWYKNCHVSNLNGRYLRGTHGSFANGINWKSGKGYNYSYKVSEMKVRPA 313
               SCOP domains d2j61b_ B: automated matches                                                                                                                                                                                             SCOP domains
               CATH domains 2j61B01 B:73-206,B:280-288 Gamma Fibrinogen, chain A, domain 1                                                                        2j61B02 B:207-279 Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2  2j61B01   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhh.....eeeeee.....eeeeeee.hhhhh.eeeeeee.........hhhhhhhhee.....ee.hhhhhhhhhh...eeeeeeee.....eee..............................hhhhh................hhhhhh....................ee.................ee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------Y---S----------------------------------------------------------------------------------------------------------------------M---------------------S------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------FIBRINOGEN_C_------------------------------------ PROSITE
           Transcript 1 (1) 1.4 ------------------------------------------Exon 1.6  PDB: B:119-162 UniProt: 144-187   --------------------------------------------Exon 1.8a  PDB: B:207-288 UniProt: 232-313                                         Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.5  PDB: B:76-118 UniProt: 101-143   -------------------------------------------Exon 1.7  PDB: B:162-207 UniProt: 187-232     --------------------------------------------------------------------------------- Transcript 1 (2)
                 2j61 B  73 CLTGPRTCKDLLDRGHFLSGWHTIYLPDCRPLTVLCDMDTDGGGWTVFQRRVDGSVDFYRDWATYKQGFGSRLGEFWLGNDNIHALTAQGTSELRTDLVDFEDNYQFAKYRSFKVADEAEKYNLVLGAFVEGSAGDSLTFHNNQSFSTKDQDNDLNTGNCAVMFQGAWWYKNCHTSNLNGRYLRGTHGSFANGINWKSGKGYNYSYKVSEMKVRPA 288
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      

   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, 2)

Asymmetric Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2J61)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (FCN2_HUMAN | Q15485)
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:0048306    calcium-dependent 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), in the presence of calcium.
    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:2001065    mannan binding    Interacting selectively and non-covalently with mannan.
    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:0043394    proteoglycan binding    Interacting selectively and non-covalently with a proteoglycan, any glycoprotein in which the carbohydrate units are glycosaminoglycans.
    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:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium 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:0008228    opsonization    The process in which a microorganism (or other particulate material) is rendered more susceptible to phagocytosis by coating with an opsonin, a blood serum protein such as a complement component or antibody.
    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: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
        FCN2_HUMAN | Q154852j0g 2j0h 2j0y 2j1g 2j2p 2j3f 2j3g 2j3o 2j3u 4nyt 4r9j 4r9t

(-) Related Entries Specified in the PDB File

2j0g L-FICOLIN COMPLEXED TO N-ACETYL-MANNOSAMINE
2j0h L-FICOLIN COMPLEXED TO ACETYL-CHOLINE
2j0y L-FICOLIN COMPLEXED TO B-1,3-D-GLUCAN
2j1g L-FICOLIN COMPLEXED TO N-ACETYL-CYSTEIN
2j2p L-FICOLIN COMPLEXED TO N-ACETYL-CYSTEIN (50MM)
2j3f L-FICOLIN COMPLEXED TO N-ACETYL-D- GALACTOSAMIN
2j3g L-FICOLIN
2j3o L-FICOLIN COMPLEXED TO N-ACETYL-D- GLUCOSAMIN
2j3u L-FICOLIN COMPLEXED TO GALACTOSE
2j5z H-FICOLIN COMPLEXED TO GALACTOSE
2j60 H-FICOLIN COMPLEXED TO D-FUCOSE