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(-) Description

Title :  STRUCTURE OF MURINE DECTIN-1
 
Authors :  J. Brown, C. A. O'Callaghan, A. S. J. Marshall, R. J. C. Gilbert, C. Siebo S. Gordon, G. D. Brown, E. Y. Jones
Date :  19 Apr 05  (Deposition) - 31 Aug 06  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Receptor, Dectin-1, Beta-Glucan, Fungal Recognition, C-Type Lectin- Like Domain, Ctld (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Brown, C. A. O'Callaghan, A. S. J. Marshall, R. J. C. Gilbert, C. Siebold, S. Gordon, G. D. Brown, E. Y. Jones
Structure Of The Fungal Beta-Glucan-Binding Immune Receptor Dectin-1: Implications For Function.
Protein Sci. V. 16 1042 2007
PubMed-ID: 17473009  |  Reference-DOI: 10.1110/PS.072791207

(-) Compounds

Molecule 1 - DECTIN-1
    Cell Line: RAW264.7
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: ROSETTA
    Expression System Plasmid: PET22B
    Expression System Taxid: 562
    Fragment: EXTRACELLULAR BETA-GLUCAN RECOGNITION DOMAIN RESIDUES 113- 244
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2CL4Ligand/IonCHLORIDE ION
3PG42Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:156 , ASP A:158 , GLU A:162 , GLU A:241 , HOH A:2042 , HOH A:2043BINDING SITE FOR RESIDUE CA A1245
2AC2SOFTWARELYS A:144 , LEU A:154 , GLU A:194 , HOH A:2029 , HOH A:2075BINDING SITE FOR RESIDUE CL A1246
3AC3SOFTWAREASN A:159 , ASN A:202 , SER A:203 , HOH A:2041BINDING SITE FOR RESIDUE CL A1247
4AC4SOFTWARELYS B:156 , ASP B:158 , GLU B:162 , GLU B:241 , HOH B:2035 , HOH B:2044BINDING SITE FOR RESIDUE CA B1245
5AC5SOFTWAREPHE A:204 , GLN A:205 , ARG A:207 , PHE B:204 , GLN B:205 , ARG B:207BINDING SITE FOR RESIDUE CL B1246
6AC6SOFTWARELYS B:144 , LEU B:154 , GLU B:194 , HOH B:2028BINDING SITE FOR RESIDUE CL B1247
7AC7SOFTWAREGLN A:117 , SER A:118 , CYS A:119 , PRO A:121 , HOH A:2108 , PHE B:135 , SER B:171 , SER B:172 , HIS B:173 , ARG B:174 , ILE B:175 , ASN B:176 , PHE B:178 , TYR B:237BINDING SITE FOR RESIDUE PG4 A1248
8AC8SOFTWAREPHE A:135 , SER A:171 , SER A:172 , HIS A:173 , ARG A:174 , ILE A:175 , ASN A:176 , PHE A:178 , TYR A:237 , GLN B:117 , SER B:118 , CYS B:119 , PRO B:121 , HOH B:2091 , HOH B:2092BINDING SITE FOR RESIDUE PG4 B1248

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:119 -A:130
2A:147 -A:240
3A:219 -A:232
4B:119 -B:130
5B:147 -B:240
6B:219 -B:232

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BPE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.CLC7A_MOUSE126-241
 		  2A:126-241
B:126-241

(-) Exons   (0, 0)

(no "Exon" information available for 2BPE)

(-) 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:129
 aligned with CLC7A_MOUSE | Q6QLQ4 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:129
                                                                                                                                                         244 
                                   126       136       146       156       166       176       186       196       206       216       226       236       | 
          CLC7A_MOUSE   117 QPCLPNWIMHGKSCYLFSFSGNSWYGSKRHCSQLGAHLLKIDNSKEFEFIESQTSSHRINAFWIGLSRNQSEGPWFWEDGSAFFPNSFQVRNTAPQESLLHNCVWIHGSEVYNQICNTSSYSICEKEL-   -
               SCOP domains d2bpea_ A: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.eeeeeeeeeeehhhhhhhhhhhh..eee...hhhhhhhhhhhhh.....eeeeeeee..........................hhhhh..eeeeee..eeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------C_TYPE_LECTIN_2  PDB: A:126-241 UniProt: 126-241                                                                    ---- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bpe A 117 QSCLPNWIMHGKSCYLFSFSGNSWYGSKRHCSQLGAHLLKIDNSKEFEFIESQTSSHRINAFWIGLSRNQSEGPWFWEDGSAFFPNSFQVRNAVPQESLLHNCVWIHGSEVYNQICNTSSYSICEKELK 245
                                   126       136       146       156       166       176       186       196       206       216       226       236         


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with CLC7A_MOUSE | Q6QLQ4 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:129
                                                                                                                                                         244 
                                   126       136       146       156       166       176       186       196       206       216       226       236       | 
          CLC7A_MOUSE   117 QPCLPNWIMHGKSCYLFSFSGNSWYGSKRHCSQLGAHLLKIDNSKEFEFIESQTSSHRINAFWIGLSRNQSEGPWFWEDGSAFFPNSFQVRNTAPQESLLHNCVWIHGSEVYNQICNTSSYSICEKEL-   -
               SCOP domains d2bpeb_ B: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee.eeeeeeeeeeehhhhhhhhhhhh..eee...hhhhhhhhhhhhh.....eeeeeeee.........................hhhhhh..eeeeee..eeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------C_TYPE_LECTIN_2  PDB: B:126-241 UniProt: 126-241                                                                    ---- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bpe B 117 QSCLPNWIMHGKSCYLFSFSGNSWYGSKRHCSQLGAHLLKIDNSKEFEFIESQTSSHRINAFWIGLSRNQSEGPWFWEDGSAFFPNSFQVRNAVPQESLLHNCVWIHGSEVYNQICNTSSYSICEKELK 245
                                   126       136       146       156       166       176       186       196       206       216       226       236
   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 2BPE)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CLC7A_MOUSE | Q6QLQ4)
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.
    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:0008329    signaling pattern recognition receptor activity    Combining with a pathogen-associated molecular pattern (PAMP), a structure conserved among microbial species, or damage-associated molecular pattern (DAMP), an endogenous molecule released from damaged cells), and transmitting a signal to initiate a change in cell activity.
biological process
    GO:0008037    cell recognition    The process in which a cell in an organism interprets its surroundings.
    GO:0071226    cellular response to molecule of fungal origin    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of fungal origin such as chito-octamer oligosaccharide.
    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:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0002366    leukocyte activation involved in immune response    A change in morphology and behavior of a leukocyte resulting from exposure to a specific antigen, mitogen, cytokine, cellular ligand, or soluble factor, leading to the initiation or perpetuation of an immune response.
    GO:0002221    pattern recognition receptor signaling pathway    Any series of molecular signals generated as a consequence of a pattern recognition receptor (PRR) binding to one of its physiological ligands. PRRs bind pathogen-associated molecular pattern (PAMPs), structures conserved among microbial species, or damage-associated molecular pattern (DAMPs), endogenous molecules released from damaged cells.
    GO:0006910    phagocytosis, recognition    The initial step in phagocytosis involving adhesion to bacteria, immune complexes and other particulate matter, or an apoptotic cell and based on recognition of factors such as bacterial cell wall components, opsonins like complement and antibody or protein receptors and lipids like phosphatidyl serine, and leading to intracellular signaling in the phagocytosing cell.
    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:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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
        CLC7A_MOUSE | Q6QLQ4: 2bpd 2bph 2cl8

(-) Related Entries Specified in the PDB File

2bpd STRUCTURE OF MURINE DECTIN-1
2bph STRUCTURE OF MURINE DECTIN-1