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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CARBOHYDRATE RECOGNITION DOMAIN OF HUMAN LANGERIN
 
Authors :  M. Thepaut
Date :  24 Jan 08  (Deposition) - 27 Jan 09  (Release) - 27 Oct 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  C-Type Lectin Domain, Coiled Coil, Glycoprotein, Membrane, Signal-Anchor, Transmembrane, Immune System, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Thepaut, J. Valladeau, A. Nurisso, R. Kahn, B. Arnou, C. Vives, S. Saeland, C. Ebel, C. Monnier, C. Dezutter-Dambuyant, A. Imberty, F. Fieschi
Structural Studies Of Langerin And Birbeck Granule: A Macromolecular Organization Model
Biochemistry V. 48 2684 2009
PubMed-ID: 19175323  |  Reference-DOI: 10.1021/BI802151W
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - C-TYPE LECTIN DOMAIN FAMILY 4 MEMBER K
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30
    Expression System StrainBL21 (DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentCARBOHYDRATE RECOGNITION DOMAIN, UNP RESIDUES 188-328
    GeneCD207
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLANGERIN, CD207 ANTIGEN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A   
Biological Unit 2 (1x) B  
Biological Unit 3 (1x)  C 
Biological Unit 4 (1x)   D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MG6Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:285 , ASN A:287 , GLU A:293 , ASN A:307 , ASP A:308BINDING SITE FOR RESIDUE CA A 1
02AC2SOFTWARETYR A:208 , LEU A:211 , ILE A:212BINDING SITE FOR RESIDUE MG A 2
03AC3SOFTWAREGLU B:285 , ASN B:287 , GLU B:293 , ASN B:307 , ASP B:308BINDING SITE FOR RESIDUE CA B 3
04AC4SOFTWAREGLU B:285 , ASN B:287 , GLU B:293 , ASN B:307 , ASP B:308BINDING SITE FOR RESIDUE MG B 4
05AC5SOFTWARETYR B:208 , SER B:210 , LEU B:211 , ILE B:212BINDING SITE FOR RESIDUE MG B 5
06AC6SOFTWAREGLU C:285 , ASN C:287 , GLU C:293 , ASN C:307 , ASP C:308BINDING SITE FOR RESIDUE CA C 6
07AC7SOFTWAREGLU C:285 , ASN C:287 , GLU C:293 , ASN C:307 , ASP C:308BINDING SITE FOR RESIDUE MG C 7
08AC8SOFTWAREGLN C:197 , TYR C:208 , LEU C:211BINDING SITE FOR RESIDUE MG C 8
09AC9SOFTWAREGLU D:285 , ASN D:287 , GLU D:293 , ASN D:307 , ASP D:308BINDING SITE FOR RESIDUE CA D 9
10BC1SOFTWARETYR D:208 , SER D:210 , LEU D:211 , ILE D:212BINDING SITE FOR RESIDUE MG D 10

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:223 -A:319
2A:295 -A:311
3B:223 -B:319
4B:295 -B:311
5C:223 -C:319
6C:295 -C:311
7D:223 -D:319
8D:295 -D:311

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:285 -Pro A:286
2Glu B:285 -Pro B:286
3Glu C:285 -Pro C:286
4Glu D:285 -Pro D:286

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 20)

Asymmetric Unit (5, 20)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_054782P213SCLC4K_HUMANPolymorphism17006436A/B/C/DP213S
2UniProtVAR_063828W264RCLC4K_HUMANDisease (BIRGD)200837270A/B/C/DW264R
3UniProtVAR_054783V278ACLC4K_HUMANPolymorphism741326A/B/C/DA278A
4UniProtVAR_054784N288DCLC4K_HUMANPolymorphism13383830A/B/C/DN288D
5UniProtVAR_059448A300PCLC4K_HUMANPolymorphism2080391A/B/C/DA300P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_054782P213SCLC4K_HUMANPolymorphism17006436AP213S
2UniProtVAR_063828W264RCLC4K_HUMANDisease (BIRGD)200837270AW264R
3UniProtVAR_054783V278ACLC4K_HUMANPolymorphism741326AA278A
4UniProtVAR_054784N288DCLC4K_HUMANPolymorphism13383830AN288D
5UniProtVAR_059448A300PCLC4K_HUMANPolymorphism2080391AA300P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_054782P213SCLC4K_HUMANPolymorphism17006436BP213S
2UniProtVAR_063828W264RCLC4K_HUMANDisease (BIRGD)200837270BW264R
3UniProtVAR_054783V278ACLC4K_HUMANPolymorphism741326BA278A
4UniProtVAR_054784N288DCLC4K_HUMANPolymorphism13383830BN288D
5UniProtVAR_059448A300PCLC4K_HUMANPolymorphism2080391BA300P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_054782P213SCLC4K_HUMANPolymorphism17006436CP213S
2UniProtVAR_063828W264RCLC4K_HUMANDisease (BIRGD)200837270CW264R
3UniProtVAR_054783V278ACLC4K_HUMANPolymorphism741326CA278A
4UniProtVAR_054784N288DCLC4K_HUMANPolymorphism13383830CN288D
5UniProtVAR_059448A300PCLC4K_HUMANPolymorphism2080391CA300P

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 4 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_054782P213SCLC4K_HUMANPolymorphism17006436DP213S
2UniProtVAR_063828W264RCLC4K_HUMANDisease (BIRGD)200837270DW264R
3UniProtVAR_054783V278ACLC4K_HUMANPolymorphism741326DA278A
4UniProtVAR_054784N288DCLC4K_HUMANPolymorphism13383830DN288D
5UniProtVAR_059448A300PCLC4K_HUMANPolymorphism2080391DA300P

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

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.CLC4K_HUMAN202-320
 
 
 
  4A:202-320
B:202-320
C:202-320
D:202-320
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.CLC4K_HUMAN295-319
 
 
 
  4A:295-319
B:295-319
C:295-319
D:295-319
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.CLC4K_HUMAN202-320
 
 
 
  1A:202-320
-
-
-
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.CLC4K_HUMAN295-319
 
 
 
  1A:295-319
-
-
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.CLC4K_HUMAN202-320
 
 
 
  1-
B:202-320
-
-
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.CLC4K_HUMAN295-319
 
 
 
  1-
B:295-319
-
-
Biological Unit 3 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.CLC4K_HUMAN202-320
 
 
 
  1-
-
C:202-320
-
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.CLC4K_HUMAN295-319
 
 
 
  1-
-
C:295-319
-
Biological Unit 4 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.CLC4K_HUMAN202-320
 
 
 
  1-
-
-
D:202-320
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.CLC4K_HUMAN295-319
 
 
 
  1-
-
-
D:295-319

(-) Exons   (0, 0)

(no "Exon" information available for 3C22)

(-) 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:130
 aligned with CLC4K_HUMAN | Q9UJ71 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:130
                                   205       215       225       235       245       255       265       275       285       295       305       315       325
          CLC4K_HUMAN   196 SQGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSVRFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVP 325
               SCOP domains d3c22a_ A: automated matches                                                                                                       SCOP domains
               CATH domains 3c22A00 A:196-325 Mannose-Binding Protein A, subunit A                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeeeee....eeee......hhhhhhhhh......hhhhh..eeee.......eeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) -----------------S--------------------------------------------------R-------------A---------D-----------P------------------------- SAPs(SNPs)
                PROSITE (1) ------C_TYPE_LECTIN_2  PDB: A:202-320 UniProt: 202-320                                                                       ----- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1          ------ PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c22 A 196 SQGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVP 325
                                   205       215       225       235       245       255       265       275       285       295       305       315       325

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with CLC4K_HUMAN | Q9UJ71 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:128
                                   207       217       227       237       247       257       267       277       287       297       307       317        
          CLC4K_HUMAN   198 GWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSVRFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVP 325
               SCOP domains d3c22b_ B: automated matches                                                                                                     SCOP domains
               CATH domains 3c22B00 B:198-325 Mannose-Binding Protein A, subunit A                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeeeee....eeee......hhhhhhhhh......hhhhh..eeee.......eeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------S--------------------------------------------------R-------------A---------D-----------P------------------------- SAPs(SNPs)
                PROSITE (1) ----C_TYPE_LECTIN_2  PDB: B:202-320 UniProt: 202-320                                                                       ----- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1          ------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c22 B 198 GWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVP 325
                                   207       217       227       237       247       257       267       277       287       297       307       317        

Chain C from PDB  Type:PROTEIN  Length:131
 aligned with CLC4K_HUMAN | Q9UJ71 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:131
                                   204       214       224       234       244       254       264       274       284       294       304       314       324 
          CLC4K_HUMAN   195 VSQGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSVRFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVP 325
               SCOP domains d3c22c_ C: automated matches                                                                                                        SCOP domains
               CATH domains 3c22C00 C:195-325 Mannose-Binding Protein A, subunit A                                                                              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeeeee....eeee......hhhhhhhhh......hhhhh..eeee.......eeee......eeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------S--------------------------------------------------R-------------A---------D-----------P------------------------- SAPs(SNPs)
                PROSITE (1) -------C_TYPE_LECTIN_2  PDB: C:202-320 UniProt: 202-320                                                                       ----- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1          ------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c22 C 195 VSQGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVP 325
                                   204       214       224       234       244       254       264       274       284       294       304       314       324 

Chain D from PDB  Type:PROTEIN  Length:134
 aligned with CLC4K_HUMAN | Q9UJ71 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:134
                                   204       214       224       234       244       254       264       274       284       294       304       314       324    
          CLC4K_HUMAN   195 VSQGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSVRFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVPSEP 328
               SCOP domains d3c22d_ D: automated matches                                                                                                           SCOP domains
               CATH domains 3c22D00 D:195-328 Mannose-Binding Protein A, subunit A                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhh...eeeeeeee....eeee......hhhhhhhhh......hhhhh..eeee.......eeee......eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------S--------------------------------------------------R-------------A---------D-----------P---------------------------- SAPs(SNPs)
                PROSITE (1) -------C_TYPE_LECTIN_2  PDB: D:202-320 UniProt: 202-320                                                                       -------- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1          --------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c22 D 195 VSQGWKYFKGNFYYFSLIPKTWYSAEQFCVSRNSHLTSVTSESEQEFLYKTAGGLIYWIGLTKAGMEGDWSWVDDTPFNKVQSARFWIPGEPNNAGNNEHCGNIKAPSLQAWNDAPCDKTFLFICKRPYVPSEP 328
                                   204       214       224       234       244       254       264       274       284       294       304       314       324    

   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, 4)

Asymmetric Unit

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C22)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (CLC4K_HUMAN | Q9UJ71)
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.
biological process
    GO:0002479    antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.
    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:0006898    receptor-mediated endocytosis    An endocytosis process in which cell surface receptors ensure specificity of transport. A specific receptor on the cell surface binds tightly to the extracellular macromolecule (the ligand) that it recognizes; the plasma-membrane region containing the receptor-ligand complex then undergoes endocytosis, forming a transport vesicle containing the receptor-ligand complex and excluding most other plasma-membrane proteins. Receptor-mediated endocytosis generally occurs via clathrin-coated pits and vesicles.
cellular component
    GO:0030669    clathrin-coated endocytic vesicle membrane    The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0030139    endocytic vesicle    A membrane-bounded intracellular vesicle formed by invagination of the plasma membrane around an extracellular substance. Endocytic vesicles fuse with early endosomes to deliver the cargo for further sorting.
    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
        CLC4K_HUMAN | Q9UJ713kqg 3p5d 3p5e 3p5f 3p5g 3p5h 3p5i 3p7f 3p7g 3p7h 4ak8 4n32 4n33 4n34 4n35 4n36 4n37 4n38

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3C22)