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(-) Description

Title :  CRYSTAL STRUCTURE OF CARBOHYDRATE RECOGNITION DOMAIN OF BLOOD DENDRITIC CELL ANTIGEN-2 (BDCA2) LECTIN (CRYSTAL FORM-1)
 
Authors :  M. Nagae, A. Ikeda, Y. Kitago, N. Matsumoto, K. Yamamoto, Y. Yamaguchi
Date :  20 May 13  (Deposition) - 25 Dec 13  (Release) - 09 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  C-Type Lectin Fold, Immune Receptor, Complex-Type N-Glycan, Carbohydrate Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Nagae, A. Ikeda, Y. Kitago, N. Matsumoto, K. Yamamoto, Y. Yamaguchi
Crystal Structures Of Carbohydrate Recognition Domain Of Blood Dendritic Cell Antigen-2 (Bdca2) Reveal A Common Domain-Swapped Dimer
Proteins 2013
PubMed-ID: 24425442  |  Reference-DOI: 10.1002/PROT.24504

(-) Compounds

Molecule 1 - C-TYPE LECTIN DOMAIN FAMILY 4 MEMBER C
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCOLD-TEV VECTOR
    Expression System Strain: ROSETTA2 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 83-210
    Gene: BDCA2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BLOOD DENDRITIC CELL ANTIGEN 2, BDCA-2, C-TYPE LECTIN SUPERFAMILY MEMBER 7, DENDRITIC LECTIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:98 , THR A:99 , ASN A:110BINDING SITE FOR RESIDUE EDO A 1001
2AC2SOFTWARESER B:98 , THR B:99 , GLY B:100 , ASN B:110BINDING SITE FOR RESIDUE EDO B 301

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:83 -A:94
2A:111 -A:206
3A:180 -A:198
4B:83 -B:94
5B:111 -B:206
6B:180 -B:198

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:172 -Pro A:173
2Glu B:172 -Pro B:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WBP)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.CLC4C_HUMAN90-207
 		  2A:90-207
B:90-207
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.CLC4C_HUMAN180-206
 		  2A:180-206
B:180-206

(-) Exons   (0, 0)

(no "Exon" information available for 3WBP)

(-) 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:128
 aligned with CLC4C_HUMAN | Q8WTT0 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:129
                                    91       101       111       121       131       141       151       161       171       181       191       201         
          CLC4C_HUMAN    82 CCPTPWTSFQSSCYFISTGMQSWTKSQKNCSVMGADLVVINTREEQDFIIQNLKRNSSYFLGLSDPGGRRHWQWVDQTPYNENVTFWHSGEPNNLDERCAIINFRSSEEWGWNDIHCHVPQKSICKMKK 210
               SCOP domains d3wbpa_ A: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeee.....hhhhhhhhhhh...ee....hhhhhhhhhhh......eeeeeee...............hhhhh............eeeeeee...-.eeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: A:90-207 UniProt: 90-207                                                                        --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1            ---- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wbp A  82 SCPTPWTSFQSSCYFISTGMQSWTKSQKNCSVMGADLVVINTREEQDFIIQNLKRNSSYFLGLSDPGGRRHWQWVDQTPYNENVTFWHSGEPNNLDERCAIINFRSS-EWGWNDIHCHVPQKSICKMKK 210
                                    91       101       111       121       131       141       151       161       171       181      |191       201         
                                                                                                                                    188 |                    
                                                                                                                                      190                    


Chain B from PDB  Type:PROTEIN  Length:127
 aligned with CLC4C_HUMAN | Q8WTT0 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:129
                                    91       101       111       121       131       141       151       161       171       181       191       201         
          CLC4C_HUMAN    82 CCPTPWTSFQSSCYFISTGMQSWTKSQKNCSVMGADLVVINTREEQDFIIQNLKRNSSYFLGLSDPGGRRHWQWVDQTPYNENVTFWHSGEPNNLDERCAIINFRSSEEWGWNDIHCHVPQKSICKMKK 210
               SCOP domains d3wbpb_ B: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeee.....hhhhhhhhhhh...ee....hhhhhhhhhhh......eeeeeee...............hhhhh............eeeeeee..--.eeeeee......eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: B:90-207 UniProt: 90-207                                                                        --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1            ---- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wbp B  82 SCPTPWTSFQSSCYFISTGMQSWTKSQKNCSVMGADLVVINTREEQDFIIQNLKRNSSYFLGLSDPGGRRHWQWVDQTPYNENVTFWHSGEPNNLDERCAIINFRS--EWGWNDIHCHVPQKSICKMKK 210
                                    91       101       111       121       131       141       151       161       171       181     | 191       201         
                                                                                                                                   187  |                    
                                                                                                                                      190
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CLC4C_HUMAN | Q8WTT0)
molecular function
    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.
biological process
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    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:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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
        CLC4C_HUMAN | Q8WTT0: 3wbq 3wbr 4zes 4zet

(-) Related Entries Specified in the PDB File

3wbq 3wbr