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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF THE CARBOHYDRATE RECOGNITION DOMAIN OF HUMAN DC-SIGN WITH PSEUDO DIMANNOSIDE MIMIC.
 
Authors :  M. Thepaut, I. Suitkeviciute, S. Sattin, J. Reina, A. Bernardi, F. Fies
Date :  10 Sep 10  (Deposition) - 19 Oct 11  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.42
Chains :  Asym./Biol. Unit :  A
Keywords :  Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Thepaut, C. Guzzi, I. Sutkeviciute, S. Sattin, R. Ribeiro-Viana, N. Varga, E. Chabrol, J. Rojo, A. Bernardi, J. Angulo, P. M. Nieto, F. Fieschi
Structure Of A Glycomimetic Ligand In The Carbohydrate Recognition Domain Of C-Type Lectin Dc-Sign. Structural Requirements For Selectivity And Ligand Design.
J. Am. Chem. Soc. V. 135 2518 2013
PubMed-ID: 23360500  |  Reference-DOI: 10.1021/JA3053305

(-) Compounds

Molecule 1 - CD209 ANTIGEN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPASK-IBA7PLUS
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentCARBOHYDRATE RECOGNITION DOMAIN, RESIDUES 254-404
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDC-SIGN, DENDRITIC CELL-SPECIFIC ICAM-3-GRABBING NON-INTEGRIN 1, DC-SIGN1, C-TYPE LECTIN DOMAIN FAMILY 4 MEMBER L, CD209, MDC-SIGN1A TYPE I

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
107B1Ligand/IonDIMETHYL (1S,2S,4S,5S)-4,5-DIHYDROXYCYCLOHEXANE-1,2-DICARBOXYLATE
2CA3Ligand/IonCALCIUM ION
3CL3Ligand/IonCHLORIDE ION
4ETA1Ligand/IonETHANOLAMINE
5MAN1Ligand/IonALPHA-D-MANNOSE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:347 , ASN A:349 , GLU A:354 , ASN A:365 , ASP A:366 , MAN A:1384BINDING SITE FOR RESIDUE CA A1387
2AC2SOFTWAREASP A:320 , GLU A:324 , ASN A:350 , GLU A:354 , ASP A:355 , HOH A:2147BINDING SITE FOR RESIDUE CA A1388
3AC3SOFTWAREGLU A:324 , GLU A:353 , ASP A:355 , HOH A:2066 , HOH A:2131 , HOH A:2135BINDING SITE FOR RESIDUE CA A1389
4AC4SOFTWARECYS A:256 , PHE A:262 , SER A:273 , ARG A:275BINDING SITE FOR RESIDUE CL A1390
5AC5SOFTWAREPHE A:269 , ASN A:272 , SER A:273BINDING SITE FOR RESIDUE CL A1391
6AC6SOFTWARELYS A:285 , GLN A:290 , HOH A:2039 , HOH A:2042BINDING SITE FOR RESIDUE CL A1392
7AC7SOFTWAREARG A:309 , ASN A:311 , GLU A:347 , ASN A:349 , VAL A:351 , GLU A:354 , ASN A:365 , ASP A:366 , CA A:1387 , HOH A:2166 , HOH A:2167BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 1384 TO 1386

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:256 -A:267
2A:284 -A:377
3A:356 -A:369

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:347 -Pro A:348

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_050105A382SCD209_HUMANPolymorphism11465393AA382S

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.CD209_HUMAN263-378  1A:263-378
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.CD209_HUMAN356-377  1A:356-377

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003155991ENSE00001352512chr19:7812464-7812352113CD209_HUMAN1-16160--
1.2cENST000003155992cENSE00001202067chr19:7812251-781219260CD209_HUMAN16-36210--
1.3ENST000003155993ENSE00000671477chr19:7811417-781134672CD209_HUMAN36-60250--
1.4cENST000003155994cENSE00001724938chr19:7810973-7810404570CD209_HUMAN60-2501910--
1.5ENST000003155995ENSE00001689133chr19:7809978-7809827152CD209_HUMAN250-300511A:254-30047
1.6aENST000003155996aENSE00001747548chr19:7809105-7808993113CD209_HUMAN301-338381A:301-33838
1.7ENST000003155997ENSE00001352516chr19:7808126-78048793248CD209_HUMAN338-404671A:338-38447

(-) 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:131
 aligned with CD209_HUMAN | Q9NNX6 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:131
                                   263       273       283       293       303       313       323       333       343       353       363       373       383 
          CD209_HUMAN   254 HPCPWEWTFFQGNCYFMSNSQRNWHDSITACKEVGAQLVVIKSAEEQNFLQLQSSRSNRFTWMGLSDLNQEGTWQWVDGSPLLPSFKQYWNRGEPNNVGEEDCAEFSGNGWNDDKCNLAKFWICKKSAASC 384
               SCOP domains d2xr5a_ A: automated matches                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhhhhh..eeeeeeeeee..eeee......hhhhhhh.............eeeee..eeeee......eeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------S-- SAPs(SNPs)
                PROSITE (1) ---------C_TYPE_LECTIN_2  PDB: A:263-378 UniProt: 263-378                                                                    ------ PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1       ------- PROSITE (2)
           Transcript 1 (1) Exon 1.5  PDB: A:254-300 UniProt: 250-300      Exon 1.6a  PDB: A:301-338             ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------Exon 1.7  PDB: A:338-384 UniProt: 338-404       Transcript 1 (2)
                 2xr5 A 254 HPCPWEWTFFQGNCYFMSNSQRNWHDSITACKEVGAQLVVIKSAEEQNFLQLQSSRSNRFTWMGLSDLNQEGTWQWVDGSPLLPSFKQYWNRGEPNNVGEEDCAEFSGNGWNDDKCNLAKFWICKKSAASC 384
                                   263       273       283       293       303       313       323       333       343       353       363       373       383 

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XR5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2XR5)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CD209_HUMAN | Q9NNX6)
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:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042605    peptide antigen binding    Interacting selectively and non-covalently with an antigen peptide.
    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:0046790    virion binding    Interacting selectively and non-covalently with a virion, either by binding to components of the capsid or the viral envelope.
    GO:0001618    virus receptor activity    Combining with a virus component and mediating entry of the virus into the cell.
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:0019882    antigen processing and presentation    The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0009988    cell-cell recognition    Cell recognition between cells. May involve the formation of specialized cell junctions.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0007157    heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules    The attachment of an adhesion molecule in one cell to a nonidentical adhesion molecule in an adjacent cell.
    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:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0075733    intracellular transport of virus    The directed movement of a virus, or part of a virus, within the host cell.
    GO:0007159    leukocyte cell-cell adhesion    The attachment of a leukocyte to another cell via adhesion molecules.
    GO:0019048    modulation by virus of host morphology or physiology    The process in which a virus effects a change in the structure or processes of its host organism.
    GO:0046968    peptide antigen transport    The directed movement of a peptide antigen into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. The peptide antigen is typically, but not always, processed from an endogenous or exogenous protein.
    GO:0042129    regulation of T cell proliferation    Any process that modulates the frequency, rate or extent of T cell proliferation.
    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.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular 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.
    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
        CD209_HUMAN | Q9NNX61k9i 1sl4 1sl5 2b6b 2it5 2it6 2xr6

(-) Related Entries Specified in the PDB File

1k9i COMPLEX OF DC-SIGN AND GLCNAC2MAN3
1sl4 CRYSTAL STRUCTURE OF DC-SIGN CARBOHYDRATE RECOGNITIONDOMAIN COMPLEXED WITH MAN4
1sl5 CRYSTAL STRUCTURE OF DC-SIGN CARBOHYDRATE RECOGNITIONDOMAIN COMPLEXED WITH LNFP III (DEXTRA L504).
2b6b CRYO EM STRUCTURE OF DENGUE COMPLEXED WITH CRD OF DC -SIGN
2xr6 CRYSTAL STRUCTURE OF THE COMPLEX OF THE CARBOHYDRATE RECOGNITION DOMAIN OF HUMAN DC-SIGN WITH PSEUDO TRIMANNOSIDE MIMIC.