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(-) Description

Title :  CRYSTAL STRUCTURE OF CD23 LECTIN DOMAIN MUTANT D270A
 
Authors :  D. Yuan, B. J. Sutton, B. Dhaliwal
Date :  10 Aug 12  (Deposition) - 26 Jun 13  (Release) - 14 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym. Unit :  A,B,C,D,E,F,G
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  G  (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
    Chains: A, B, C, D, E, F, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 156-298
    Gene: FCER2, CD23A, CLEC4J, FCE2, IGEBF
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BLAST-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

  1234567
Asymmetric Unit : ABCDEFG
Biological Unit 1 (1x): A      
Biological Unit 2 (1x):  B     
Biological Unit 3 (1x):   C    
Biological Unit 4 (1x):    D   
Biological Unit 5 (1x):     E  
Biological Unit 6 (1x):      F 
Biological Unit 7 (1x):       G

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 37)

Asymmetric Unit (2, 37)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
2SO425Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO45Ligand/IonSULFATE ION
Biological Unit 3 (2, 6)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
Biological Unit 4 (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION
Biological Unit 5 (2, 5)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
Biological Unit 6 (2, 9)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO46Ligand/IonSULFATE ION
Biological Unit 7 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION

(-) Sites  (37, 37)

Asymmetric Unit (37, 37)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:263 , GLY A:264 , SER A:265BINDING SITE FOR RESIDUE GOL A 301
02AC2SOFTWARELYS A:179 , SER A:215 , HIS A:216BINDING SITE FOR RESIDUE GOL A 302
03AC3SOFTWARETHR A:181 , GLN A:183 , HIS A:186 , LYS A:276BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREARG A:172 , LYS A:173 , HIS A:202 , GLU A:206 , HOH A:425BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWAREASN A:225 , LEU A:228 , ARG A:253 , GLN A:255 , GLY A:256 , ASP A:258 , HOH A:435 , ARG B:224BINDING SITE FOR RESIDUE SO4 A 305
06AC6SOFTWAREHIS A:186 , ARG B:172 , LEU B:285 , HOH B:458BINDING SITE FOR RESIDUE GOL B 301
07AC7SOFTWAREARG A:224 , LEU A:226 , ARG B:188 , ASP B:192 , GLN B:197 , VAL B:235 , HOH B:423 , HOH B:435BINDING SITE FOR RESIDUE SO4 B 302
08AC8SOFTWAREARG B:172 , LYS B:173 , HIS B:202 , GLU B:206 , HOH B:477BINDING SITE FOR RESIDUE SO4 B 303
09AC9SOFTWAREARG B:263 , ASN B:269 , ARG B:275 , HOH B:461 , HIS E:216BINDING SITE FOR RESIDUE SO4 B 304
10BC1SOFTWAREARG B:263 , SER B:265 , ARG B:267 , HOH B:452 , SER E:215 , HIS E:216 , THR E:217BINDING SITE FOR RESIDUE SO4 B 305
11BC2SOFTWARELYS B:229 , GLU B:231 , ILE B:233 , HIS B:239 , ASN D:225 , ARG D:253 , GLN D:255 , GLY D:256 , ASP D:258 , HOH D:455BINDING SITE FOR RESIDUE SO4 B 306
12BC3SOFTWARECYS C:163 , ILE C:168 , ASN C:169 , HOH C:476BINDING SITE FOR RESIDUE GOL C 301
13BC4SOFTWAREARG C:263 , GLY C:264 , SER C:265 , ARG C:267 , HOH C:462BINDING SITE FOR RESIDUE GOL C 302
14BC5SOFTWAREASN C:225 , LEU C:228 , ARG C:253 , GLY C:256 , ASP C:258 , HOH C:415 , HOH C:425 , HOH C:441 , HOH C:461 , ARG E:224BINDING SITE FOR RESIDUE SO4 C 303
15BC6SOFTWAREARG C:172 , LYS C:173 , HIS C:202 , GLU C:206 , HOH C:418BINDING SITE FOR RESIDUE SO4 C 304
16BC7SOFTWAREARG C:284 , HOH C:416 , HOH C:464 , ARG D:267BINDING SITE FOR RESIDUE SO4 C 305
17BC8SOFTWAREGLN C:183 , HIS C:186 , LYS C:276BINDING SITE FOR RESIDUE SO4 C 306
18BC9SOFTWAREARG D:263 , GLY D:264 , SER D:265BINDING SITE FOR RESIDUE GOL D 301
19CC1SOFTWAREGLU D:257 , ASN D:269 , ALA D:270 , ARG D:275 , HOH D:460BINDING SITE FOR RESIDUE GOL D 302
20CC2SOFTWAREARG D:188 , ARG D:224 , HOH D:445BINDING SITE FOR RESIDUE SO4 D 303
21CC3SOFTWAREARG D:188 , ASP D:192 , GLN D:197 , HOH D:419 , ARG F:172BINDING SITE FOR RESIDUE SO4 D 304
22CC4SOFTWAREHIS C:186 , ARG E:172 , LEU E:285BINDING SITE FOR RESIDUE SO4 E 301
23CC5SOFTWAREASN E:225 , ASP E:227 , ARG E:253 , GLN E:255 , GLY E:256 , ASP E:258BINDING SITE FOR RESIDUE GOL E 302
24CC6SOFTWAREARG E:172 , LYS E:173 , HIS E:202 , GLU E:206 , HOH E:449BINDING SITE FOR RESIDUE SO4 E 303
25CC7SOFTWAREARG E:263 , SER E:265 , ARG E:267 , HOH E:423BINDING SITE FOR RESIDUE SO4 E 304
26CC8SOFTWAREARG C:224 , LEU C:226 , ARG E:188 , ASP E:192 , GLN E:197 , VAL E:235 , HOH E:420 , HOH E:455BINDING SITE FOR RESIDUE SO4 E 305
27CC9SOFTWAREPRO C:247 , ASP D:193 , VAL F:159 , THR F:289 , PRO F:290BINDING SITE FOR RESIDUE GOL F 301
28DC1SOFTWAREARG F:263 , GLY F:264 , SER F:265BINDING SITE FOR RESIDUE GOL F 302
29DC2SOFTWAREARG C:275 , ARG F:275 , LYS F:276BINDING SITE FOR RESIDUE GOL F 303
30DC3SOFTWARELYS E:229 , GLU E:231 , HIS E:239 , ASN F:225 , ARG F:253 , GLN F:255 , GLY F:256 , ASP F:258 , HOH F:429BINDING SITE FOR RESIDUE SO4 F 304
31DC4SOFTWAREARG D:172 , ARG F:188 , ASP F:192 , GLN F:197 , VAL F:235 , HOH F:420 , HOH F:431BINDING SITE FOR RESIDUE SO4 F 305
32DC5SOFTWAREARG A:284 , ARG F:267BINDING SITE FOR RESIDUE SO4 F 306
33DC6SOFTWARELYS F:182 , GLN F:183 , HIS F:186 , LYS F:276 , HOH F:463BINDING SITE FOR RESIDUE SO4 F 307
34DC7SOFTWARELYS B:166 , LYS F:179 , HIS F:216 , HOH F:451BINDING SITE FOR RESIDUE SO4 F 308
35DC8SOFTWAREGLU A:195 , ARG F:267 , HOH F:417 , HOH F:457BINDING SITE FOR RESIDUE SO4 F 309
36DC9SOFTWAREARG G:188 , ARG G:224 , LEU G:226 , ASP G:227BINDING SITE FOR RESIDUE GOL G 301
37EC1SOFTWARELEU G:228 , ARG G:253 , GLN G:255 , GLY G:256 , ASP G:258BINDING SITE FOR RESIDUE SO4 G 302

(-) SS Bonds  (28, 28)

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:160 -D:288
14D:163 -D:174
15D:191 -D:282
16D:259 -D:273
17E:160 -E:288
18E:163 -E:174
19E:191 -E:282
20E:259 -E:273
21F:160 -F:288
22F:163 -F:174
23F:191 -F:282
24F:259 -F:273
25G:160 -G:288
26G:163 -G:174
27G:191 -G:282
28G:259 -G:273

(-) Cis Peptide Bonds  (8, 8)

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
5Glu E:249 -Pro E:250
6Glu F:249 -Pro F:250
7Glu G:249 -Pro G:250
8Gln G:255 -Gly G:256

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GK1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GK1)

(-) Exons   (0, 0)

(no "Exon" information available for 4GK1)

(-) 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:134
                                                                                                                                                                      
               SCOP domains d4gk1a_ A: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeeee......eee........................eeee.....eeee.....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gk1 A 156 SGFVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNAAFCDRKLGAWVCDRLATCT 289
                                   165       175       185       195       205       215       225       235       245       255       265       275       285    


Chain B from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains d4gk1b_ B: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.........eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeeeee....eeee.......ee...............eeee.....eeee.....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gk1 B 156 SGFVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNAAFCDRKLGAWVCDRLATC 288
                                   165       175       185       195       205       215       225       235       245       255       265       275       285   


Chain C from PDB  Type:PROTEIN  Length:135
                                                                                                                                                                       
               SCOP domains d4gk1c_ C: automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.........eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeeee......eee.......ee...............eeee.....eeee.....eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gk1 C 156 SGFVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNAAFCDRKLGAWVCDRLATCTP 290
                                   165       175       185       195       205       215       225       235       245       255       265       275       285     


Chain D from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains d4gk1d_ D: automated matches                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeee........ee........................eeee.....eeee.....eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gk1 D 159 VCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNAAFCDRKLGAWVCDRLATCTP 290
                                   168       178       188       198       208       218       228       238       248       258       268       278       288  


Chain E from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains d4gk1e_ E: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeeee......eee........................eeee.....eeee.....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gk1 E 156 SGFVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNAAFCDRKLGAWVCDRLATCT 289
                                   165       175       185       195       205       215       225       235       245       255       265       275       285    


Chain F from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains d4gk1f_ F: automated matches                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeee........ee........................eeee.....eeee.....eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gk1 F 159 VCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNAAFCDRKLGAWVCDRLATCTPP 291
                                   168       178       188       198       208       218       228       238       248       258       268       278       288   


Chain G from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains d4gk1g_ G: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeeee.hhh..eee........................eeee.....eeee.....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gk1 G 160 CNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQGEDCVMMRGSGRWNAAFCDRKLGAWVCDRLATC 288
                                   169       179       189       199       209       219       229       239       249       259       269       279
   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, 7)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GK1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GK1)

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gln G:255 - Gly G:256   [ RasMol ]  
    Glu A:249 - Pro A:250   [ RasMol ]  
    Glu B:249 - Pro B:250   [ RasMol ]  
    Glu C:249 - Pro C:250   [ RasMol ]  
    Glu D:249 - Pro D:250   [ RasMol ]  
    Glu E:249 - Pro E:250   [ RasMol ]  
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  4gk1
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  FCER2_HUMAN | P06734
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  FCER2_HUMAN | P06734
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 Related Entries

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

UniProtKB/Swiss-Prot
        FCER2_HUMAN | P06734: 1hli 1kje 1t8c 1t8d 2h2r 2h2t 4ezm 4g96 4g9a 4gi0 4gj0 4gjx 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 DERCD23
4g9a WILD TYPE DERCD23
4gi0 DERCD23 MUTANT E249A
4gj0 DERCD23 MUTANT S252A
4gjx DERCD23 MUTANT D258A
4gko