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(-) Description

Title :  CRYSTALLOGRAPHIC STRUCTURE OF THE MOUSE SIGN-R1 CRD DOMAIN IN COMPLEX WITH SIALIC ACID
 
Authors :  N. Silva-Martin, S. G. Bartual, J. A. Hermoso
Date :  08 Oct 13  (Deposition) - 15 Oct 14  (Release) - 22 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.19
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  C-Lectin Crd, Sign-R1, Immune System, Capsular Polysaccharide, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Silva-Martin, S. G. Bartual, A. Rodriguez, E. Ramirez, P. Chacon, R. M. Anthony, C. G. Park, J. A. Hermoso
Structural Basis For Selective Recognition Of Endogenous And Microbial Polysaccharides By Macrophage Receptor Sign-R1
Structure V. 22 1595 2014
PubMed-ID: 25450767  |  Reference-DOI: 10.1016/J.STR.2014.09.001

(-) Compounds

Molecule 1 - CD209 ANTIGEN-LIKE PROTEIN B
    Chains: A, B, C, D
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CHO
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Fragment: CRD, RESIDUES 191-325
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: DC-SIGN-RELATED PROTEIN 1, DC-SIGNR1, OTB7, SIGN-R1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 39)

Asymmetric Unit (4, 39)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2CL2Ligand/IonCHLORIDE ION
3SIA3Ligand/IonO-SIALIC ACID
4SO430Ligand/IonSULFATE ION
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3SIA2Ligand/IonO-SIALIC ACID
4SO416Ligand/IonSULFATE ION
Biological Unit 2 (2, 15)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3SIA1Ligand/IonO-SIALIC ACID
4SO414Ligand/IonSULFATE ION

(-) Sites  (39, 39)

Asymmetric Unit (39, 39)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:285 , ASN A:287 , GLU A:292 , ASP A:304 , HOH A:2077BINDING SITE FOR RESIDUE CA A1323
02AC2SOFTWAREGLU A:296 , SER A:305 , LEU A:309 , LYS A:311 , HOH A:2083BINDING SITE FOR RESIDUE SO4 A1324
03AC3SOFTWARELYS A:317 , SER A:318 , HOH A:2099BINDING SITE FOR RESIDUE SO4 A1325
04AC4SOFTWARELEU A:309 , LYS A:310 , HOH A:2090 , HOH A:2100BINDING SITE FOR RESIDUE SO4 A1326
05AC5SOFTWARELYS A:279 , ASN A:287 , ASN A:288 , ILE A:289BINDING SITE FOR RESIDUE SIA A1327
06AC6SOFTWAREARG A:193 , PRO A:196 , TRP A:197 , PRO C:196 , TRP C:197BINDING SITE FOR RESIDUE CL A1328
07AC7SOFTWARESER A:271 , THR A:272BINDING SITE FOR RESIDUE SO4 A1329
08AC8SOFTWARESER A:274 , SER A:275BINDING SITE FOR RESIDUE SO4 A1330
09AC9SOFTWAREASN A:205 , ASN A:234 , LYS A:316BINDING SITE FOR RESIDUE SO4 A1331
10BC1SOFTWARESER A:235 , ASP A:236 , GLU A:237 , ARG A:276BINDING SITE FOR RESIDUE SO4 A1332
11BC2SOFTWARELYS A:211 , LYS A:249 , HOH A:2009 , CYS B:192 , ARG B:193 , LEU B:194 , CYS B:195BINDING SITE FOR RESIDUE SO4 B1324
12BC3SOFTWAREGLU B:285 , ASN B:287 , GLU B:292 , ASP B:304 , SIA B:1329BINDING SITE FOR RESIDUE CA B1325
13BC4SOFTWAREGLU B:296 , LEU B:309 , LYS B:311 , HOH B:2101BINDING SITE FOR RESIDUE SO4 B1326
14BC5SOFTWAREASN B:205 , ASN B:234 , LYS B:316 , HOH B:2014 , SO4 D:1325BINDING SITE FOR RESIDUE SO4 B1327
15BC6SOFTWAREARG A:193 , LEU A:194 , CYS A:195 , HOH A:2015 , LYS B:211 , LYS B:249BINDING SITE FOR RESIDUE SO4 A1333
16BC7SOFTWARELYS B:310 , HOH B:2021BINDING SITE FOR RESIDUE SO4 B1328
17BC8SOFTWAREGLU B:285 , ASN B:287 , ASN B:288 , GLU B:292 , CA B:1325 , HOH B:2112 , HOH B:2115BINDING SITE FOR RESIDUE SIA B1329
18BC9SOFTWARESER B:271 , THR B:272 , HOH B:2118 , LYS C:247BINDING SITE FOR RESIDUE SO4 B1330
19CC1SOFTWARESER B:274 , SER B:275BINDING SITE FOR RESIDUE SO4 B1331
20CC2SOFTWARELYS B:261 , GLU B:262 , HOH B:2120 , HOH B:2121BINDING SITE FOR RESIDUE SO4 B1332
21CC3SOFTWARELYS D:261 , GLU D:262BINDING SITE FOR RESIDUE SO4 B1334
22CC4SOFTWAREGLU C:285 , ASN C:287 , GLU C:292 , ASP C:304 , SIA C:1328BINDING SITE FOR RESIDUE CA C1323
23CC5SOFTWAREGLU C:296 , SER C:305 , LYS C:311 , HOH C:2093 , HOH C:2094 , HOH C:2095 , HOH C:2107BINDING SITE FOR RESIDUE SO4 C1324
24CC6SOFTWARELYS C:317 , SER C:318BINDING SITE FOR RESIDUE SO4 C1325
25CC7SOFTWARELYS C:310BINDING SITE FOR RESIDUE SO4 C1326
26CC8SOFTWAREARG C:193 , LEU C:194 , CYS C:195 , HOH C:2005 , HOH C:2014 , LYS D:211 , LYS D:249BINDING SITE FOR RESIDUE SO4 C1327
27CC9SOFTWAREGLU C:285 , ASN C:287 , ASN C:288 , GLU C:292 , CA C:1323 , HOH C:2107 , HOH C:2109BINDING SITE FOR RESIDUE SIA C1328
28DC1SOFTWAREASN C:288BINDING SITE FOR RESIDUE CL C1329
29DC2SOFTWARETHR C:272 , HOH C:2074 , HOH C:2110BINDING SITE FOR RESIDUE SO4 C1330
30DC3SOFTWARESER C:275 , HOH C:2111BINDING SITE FOR RESIDUE SO4 C1331
31DC4SOFTWARELYS C:260 , LYS C:261 , GLU C:262BINDING SITE FOR RESIDUE SO4 C1332
32DC5SOFTWAREASN C:205 , ASN C:234 , LYS C:316 , HOH C:2038 , HOH C:2113BINDING SITE FOR RESIDUE SO4 C1333
33DC6SOFTWAREGLU D:285 , ASN D:287 , GLU D:292 , ASP D:304 , HOH D:2083BINDING SITE FOR RESIDUE CA D1323
34DC7SOFTWAREGLU D:296 , SER D:305 , LEU D:309 , LYS D:311 , HOH D:2091 , HOH D:2092 , HOH D:2093BINDING SITE FOR RESIDUE SO4 D1324
35DC8SOFTWARESO4 B:1327 , HOH B:2013 , ASN D:205 , ASN D:234 , LYS D:316 , HOH D:2013 , HOH D:2039BINDING SITE FOR RESIDUE SO4 D1325
36DC9SOFTWARELYS D:310BINDING SITE FOR RESIDUE SO4 D1326
37EC1SOFTWARESER D:275BINDING SITE FOR RESIDUE SO4 D1327
38EC2SOFTWARELYS A:247 , SER D:271 , THR D:272 , HOH D:2069BINDING SITE FOR RESIDUE SO4 D1328
39EC3SOFTWARELYS C:211 , LYS C:249 , HOH C:2009 , ARG D:193 , LEU D:194 , CYS D:195BINDING SITE FOR RESIDUE SO4 D1329

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:192 -A:322
2A:195 -A:206
3A:223 -A:315
4A:294 -A:307
5B:192 -B:322
6B:195 -B:206
7B:223 -B:315
8B:294 -B:307
9C:192 -C:322
10C:195 -C:206
11C:223 -C:315
12C:294 -C:307
13D:192 -D:322
14D:195 -D:206
15D:223 -D:315
16D:294 -D:307

(-) 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  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CAJ)

(-) PROSITE Motifs  (2, 8)

Asymmetric Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.C209B_MOUSE202-316
 
 
 		  4A:202-316
B:202-316
C:202-316
D:202-316
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.C209B_MOUSE294-315
 
 
 		  4A:294-315
B:294-315
C:294-315
D:294-315
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.C209B_MOUSE202-316
 
 
 		  2A:202-316
B:202-316
-
-
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.C209B_MOUSE294-315
 
 
 		  2A:294-315
B:294-315
-
-
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.C209B_MOUSE202-316
 
 
 		  2-
-
C:202-316
D:202-316
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.C209B_MOUSE294-315
 
 
 		  2-
-
C:294-315
D:294-315

(-) Exons   (0, 0)

(no "Exon" information available for 4CAJ)

(-) 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:131
 aligned with C209B_MOUSE | Q8CJ91 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:131
                                   201       211       221       231       241       251       261       271       281       291       301       311       321 
          C209B_MOUSE   192 CRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPC 322
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhhhhh.eeeeeeeeee..eeee......hhhhhhh.............eeeee..eeeee......eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------C_TYPE_LECTIN_2  PDB: A:202-316 UniProt: 202-316                                                                   ------ PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1       ------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4caj A 192 CRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPC 322
                                   201       211       221       231       241       251       261       271       281       291       301       311       321 


Chain B from PDB  Type:PROTEIN  Length:133
 aligned with C209B_MOUSE | Q8CJ91 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:133
                                   200       210       220       230       240       250       260       270       280       290       300       310       320   
          C209B_MOUSE   191 LCRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPCT 323
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..eeeee.....hhhhhhhhhhh...ee....hhhhhhhhhhhhhhhh.eeeeee........ee......hhhhhhh.............eeeee..eeeee........eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------C_TYPE_LECTIN_2  PDB: B:202-316 UniProt: 202-316                                                                   ------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1       -------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4caj B 191 LCRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPCT 323
                                   200       210       220       230       240       250       260       270       280       290       300       310       320   


Chain C from PDB  Type:PROTEIN  Length:132
 aligned with C209B_MOUSE | Q8CJ91 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:132
                                   200       210       220       230       240       250       260       270       280       290       300       310       320  
          C209B_MOUSE   191 LCRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPC 322
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eee..eeeee.....hhhhhhhhhhh...ee....hhhhhhhhhhhhhhhh.eeeeee........ee......hhhhhhh.............eeeee..eeeee......eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------C_TYPE_LECTIN_2  PDB: C:202-316 UniProt: 202-316                                                                   ------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1       ------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4caj C 191 LCRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPC 322
                                   200       210       220       230       240       250       260       270       280       290       300       310       320  


Chain D from PDB  Type:PROTEIN  Length:132
 aligned with C209B_MOUSE | Q8CJ91 from UniProtKB/Swiss-Prot  Length:325

    Alignment length:132
                                   200       210       220       230       240       250       260       270       280       290       300       310       320  
          C209B_MOUSE   191 LCRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPC 322
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eee..eeeee.....hhhhhhhhhhhh..ee....hhhhhhhhhhhhhhhh.eeeeee........ee.........hhhh.............eeeee..eeeee........eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------C_TYPE_LECTIN_2  PDB: D:202-316 UniProt: 202-316                                                                   ------ PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1       ------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4caj D 191 LCRLCPWDWTFLLGNCYFFSKSQRNWNDAVTACKEVKAQLVIINSDEEQTFLQQTSKAKGPTWMGLSDLKKEATWLWVDGSTLSSRFQKYWNRGEPNNIGEEDCVEFAGDGWNDSKCELKKFWICKKSATPC 322
                                   200       210       220       230       240       250       260       270       280       290       300       310       320
   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  (0, 0)

(no "SCOP Domain" information available for 4CAJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CAJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CAJ)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (C209B_MOUSE | Q8CJ91)
molecular function
    GO:0001872    (1->3)-beta-D-glucan binding    Interacting selectively and non-covalently with (1->3)-beta-D-glucans.
    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:0030247    polysaccharide binding    Interacting selectively and non-covalently with any polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
biological process
    GO:0016045    detection of bacterium    The series of events in which a stimulus from a bacterium is received and converted into a molecular signal.
    GO:0001879    detection of yeast    The series of events in which a stimulus from a yeast is received and converted into a molecular signal.
    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: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:0050766    positive regulation of phagocytosis    Any process that activates or increases the frequency, rate or extent of phagocytosis.
    GO:0042535    positive regulation of tumor necrosis factor biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of tumor necrosis factor, an inflammatory cytokine produced by macrophages/monocytes during acute inflammation and which is responsible for a diverse range of signaling events within cells, leading to necrosis or apoptosis.
cellular component
    GO:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        C209B_MOUSE | Q8CJ91: 3zhg 4c9f

(-) Related Entries Specified in the PDB File

4c9f STRUCTURE OF SIGN-R1 IN COMPLEX WITH SULFODEXTRAN