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(-) Description

Title :  CRYSTAL STRUCTURE OF CD23 LECTIN DOMAIN MUTANT S252A
 
Authors :  D. Yuan, B. J. Sutton, B. Dhaliwal
Date :  09 Aug 12  (Deposition) - 26 Jun 13  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
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 :  Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. Yuan, A. H. Keeble, R. G. Hibbert, S. Fabiane, H. J. Gould, J. M. Mcdonnell, A. J. Beavil, B. J. Sutton, B. Dhaliwal
Ca2+-Dependent Structural Changes In The B-Cell Receptor Cd23 Increase Its Affinity For Human Immunoglobulin E.
J. Biol. Chem. V. 288 21667 2013
PubMed-ID: 23775083  |  Reference-DOI: 10.1074/JBC.M113.480657

(-) Compounds

Molecule 1 - LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 156-298
    GeneFCER2, CD23A, CLEC4J, FCE2, IGEBF
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBLAST-2, C-TYPE LECTIN DOMAIN FAMILY 4 MEMBER J, FC-EPSILON- RII, IMMUNOGLOBULIN E-BINDING FACTOR, LYMPHOCYTE IGE RECEPTOR, LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR MEMBRANE-BOUND FORM, LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR SOLUBLE FORM

 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, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:197 , ASP A:283 , HOH A:523BINDING SITE FOR RESIDUE GOL A 301
2AC2SOFTWAREARG A:263 , SER A:265 , ARG A:267 , HOH A:445 , HOH A:467 , LYS C:229 , SER D:254 , GLN D:255BINDING SITE FOR RESIDUE SO4 A 302
3AC3SOFTWAREVAL A:185 , ARG A:224 , HOH A:457 , GOL B:301BINDING SITE FOR RESIDUE SO4 A 303
4AC4SOFTWARESO4 A:303 , VAL B:185 , ARG B:224 , HOH B:426BINDING SITE FOR RESIDUE GOL B 301
5AC5SOFTWAREARG B:263 , SER B:265 , ARG B:267 , HOH B:470 , HOH B:474 , SER C:254 , GLN C:255 , LYS D:229BINDING SITE FOR RESIDUE SO4 B 302
6AC6SOFTWAREPRO A:164 , GLU A:165 , PRO B:164 , GLU B:165BINDING SITE FOR RESIDUE SO4 B 303
7AC7SOFTWARELYS B:182 , HIS B:186 , ALA B:190 , LYS C:182 , HIS C:186 , ALA C:190BINDING SITE FOR RESIDUE GOL C 301
8AC8SOFTWARELYS A:182 , HIS A:186 , ALA A:190 , LYS D:182 , HIS D:186 , ALA D:190 , HOH D:464 , HOH D:468BINDING SITE FOR RESIDUE GOL D 301

(-) SS Bonds  (15, 15)

Asymmetric Unit
No.Residues
1A:160 -A:288
2A:163 -A:174
3A:191 -A:282
4A:259 -A:273
5B:160 -B:288
6B:163 -B:174
7B:191 -B:282
8B:259 -B:273
9C:160 -C:288
10C:163 -C:174
11C:191 -C:282
12C:259 -C:273
13D:163 -D:174
14D:191 -D:282
15D:259 -D:273

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:249 -Pro A:250
2Glu B:249 -Pro B:250
3Glu C:249 -Pro C:250
4Glu D:249 -Pro D:250

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GJ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GJ0)

(-) Exons   (0, 0)

(no "Exon" information available for 4GJ0)

(-) 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:135
                                                                                                                                                                       
               SCOP domains d4gj0a_ A: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhhh....eeeeee........ee........................eeee.....eeee.....eeeeeeeee.eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gj0 A 157 GFVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTARSQGEDCVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPP 291
                                   166       176       186       196       206       216       226       236       246       256       266       276       286     

Chain B from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains d4gj0b_ B: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhhh....eeeeee........ee........................eeee.....eeee.....eeeeeeeee.eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gj0 B 158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTARSQGEDCVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPP 291
                                   167       177       187       197       207       217       227       237       247       257       267       277       287    

Chain C from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains d4gj0c_ C: automated matches                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.....eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhhh....eeeeeee......eee........................eeee.....eeee.....eeeeeeeee.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gj0 C 159 VCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTARSQGEDCVMMRGSGRWNDAFCDRKLGAWVCDRLATCTP 290
                                   168       178       188       198       208       218       228       238       248       258       268       278       288  

Chain D from PDB  Type:PROTEIN  Length:130
                                                                                                                                                                  
               SCOP domains d4gj0d_ D: automated matches                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..eeeeeeeeeehhhhhhhhhhh...ee....hhhhhhhhhhhh....eeeeeee......eee........................eeee.....eeee.....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gj0 D 159 VCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTARSQGEDCVMMRGSGRWNDAFCDRKLGAWVCDRLATC 288
                                   168       178       188       198       208       218       228       238       248       258       268       278       288

   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  (0, 0)

(no "CATH Domain" information available for 4GJ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GJ0)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        FCER2_HUMAN | P067341hli 1kje 1t8c 1t8d 2h2r 2h2t 4ezm 4g96 4g9a 4gi0 4gjx 4gk1 4gko 4j6j 4j6k 4j6l 4j6m 4j6n 4j6p 4j6q 4ki1 5lgk

(-) Related Entries Specified in the PDB File

1t8c
1t8d
2h2r
2h2t
4ezm
4g96 WILD TYPE CD23
4g9a WILD TYPE CD23
4gi0 CD23 MUTANT E249A
4gjx CD23 MUTANT D258A
4gk1 CD23 MUTANT D270A
4gko