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(-) Description

Title :  PRIMITIVE TRICLINIC CRYSTAL FORM OF THE HUMAN IGE-FC(EPSILON)3-4 BOUND TO ITS B CELL RECEPTOR DERCD23
 
Authors :  B. Dhaliwal, M. O. Y. Pang, B. J. Sutton, A. J. Beavil
Date :  01 May 13  (Deposition) - 05 Mar 14  (Release) - 24 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
Keywords :  Immunoglobulin Fold, Lectin, Antibody Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Dhaliwal, M. O. Pang, D. Yuan, A. J. Beavil, B. J. Sutton
A Range Of C3-C4 Interdomain Angles In Ige Fc Accommodate Binding To Its Receptor Cd23.
Acta Crystallogr F Struct V. 70 305 2014 Biol Commun
PubMed-ID: 24598915  |  Reference-DOI: 10.1107/S2053230X14003355

(-) Compounds

Molecule 1 - IG EPSILON CHAIN C REGION
    Chains: A, B, C, D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293
    Expression System Taxid: 9606
    Fragment: HUMAN IGE-FC(EPSILON)3-4, UNP RESIDUES 209-428
    Gene: IGHE
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR
    Chains: E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: HUMAN DERCD23, UNP RESIDUES 156-298
    Gene: FCER2, CD23A, CLEC4J, FCE2, IGEBF
    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

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB  EF  
Biological Unit 2 (1x):   CD  GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 20)

Asymmetric Unit (3, 20)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2MAN8Ligand/IonALPHA-D-MANNOSE
3NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2MAN4Ligand/IonALPHA-D-MANNOSE
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 10)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2MAN4Ligand/IonALPHA-D-MANNOSE
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:339 , LEU A:359 , GLN A:392 , ASN A:394 , THR A:396 , THR A:398BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 394 RESIDUES 601 TO 605
2AC2SOFTWARETYR B:339 , LEU B:359 , GLN B:392 , ASN B:394 , THR B:396 , THR B:398BINDING SITE FOR CHAIN B OF SUGAR BOUND TO ASN B 394 RESIDUES 601 TO 605
3AC3SOFTWARETYR C:339 , LEU C:359 , GLN C:392 , ASN C:394 , THR C:396 , THR C:398 , GLN C:494BINDING SITE FOR CHAIN C OF SUGAR BOUND TO ASN C 394 RESIDUES 601 TO 605
4AC4SOFTWARETYR D:339 , LEU D:359 , GLN D:392 , ASN D:394 , THR D:396 , THR D:398 , GLN D:494BINDING SITE FOR CHAIN D OF SUGAR BOUND TO ASN D 394 RESIDUES 601 TO 605

(-) SS Bonds  (18, 18)

Asymmetric Unit
No.Residues
1A:358 -A:418
2A:464 -A:524
3B:358 -B:418
4B:464 -B:524
5C:464 -C:524
6D:358 -D:418
7D:464 -D:524
8E:160 -E:288
9E:191 -E:282
10E:259 -E:273
11F:160 -F:288
12F:163 -F:174
13F:191 -F:282
14F:259 -F:273
15G:160 -G:288
16G:163 -G:174
17H:191 -H:282
18H:259 -H:273

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Met A:470 -Pro A:471
2Ser A:532 -Pro A:533
3Met B:470 -Pro B:471
4Ser B:532 -Pro B:533
5Met C:470 -Pro C:471
6Ser C:532 -Pro C:533
7Met D:470 -Pro D:471
8Ser D:532 -Pro D:533
9Glu E:249 -Pro E:250
10Glu F:249 -Pro F:250
11Glu G:249 -Pro G:250
12Glu H:249 -Pro H:250

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4KI1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4KI1)

(-) Exons   (0, 0)

(no "Exon" information available for 4KI1)

(-) 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:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhh....eeeeeeee......eeeeee.........eeeeee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeeee.........eeeeeeeeeee.....eeeeee..ee.hhh.eee...ee.....eeeeeeeeeehhhhhhh..eeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ki1 A 336 VSAYLSRPSPFDLFIRKSPTITCLVVDPSKGTVQLTWSRASGKPVQHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNP 545
                                   345       355      |367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537        
                                                    362|                                                                                                                                                                                    
                                                     365                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhh....eeeeeeee.........eeeee.........eeeeee.....eeeeeeee.hhhhhhh...eeeee........eeeee..........eeeeee.........eeeeeeeee.......eeeeee..ee.hhh.eee...ee.....eeeeeeeeeehhhhhhh..eeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ki1 B 335 GVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVQLTWSRASGKPVQHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNP 545
                                   344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544 


Chain C from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhh....eeeeeeee.........eeeee.........eeeeee.....eeeeeeee.hhhhhhh...eeeee........eeeee..........eeeeee.........eeeeeeeee.......eeeeee..ee.hhh.eee...ee.....eeeeeeeeeehhhhhhh..eeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ki1 C 335 GVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVQLTWSRASGKPVQHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNP 545
                                   344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544 


Chain D from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhhhh....eeeeeeee......eeeeee.........eeeeee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeeeee.........eeeeeeeee.......eeeeee..ee.hhh.eee...ee.....eeeeeeeeeehhhhhhh..eeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ki1 D 336 VSAYLSRPSPFDLFIRKSPTITCLVVDPSKGTVQLTWSRASGKPVQHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNP 545
                                   345       355      |367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537        
                                                    362|                                                                                                                                                                                    
                                                     365                                                                                                                                                                                    


Chain E from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.....eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeee........ee......................eeee.....eeee.....eeeeeeeee.eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ki1 E 158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQDCVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPP 291
                                   167       177       187       197       207       217       227       237       247       259       269       279       289  
                                                                                                                           255|                                 
                                                                                                                            258                                 


Chain F from PDB  Type:PROTEIN  Length:131
                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeee........ee......................eeee.....eeee.....eeeeeeeee.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ki1 F 158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQDCVMMRGSGRWNDAFCDRKLGAWVCDRLATCTP 290
                                   167       177       187       197       207       217       227       237       247       259       269       279       289 
                                                                                                                           255|                                
                                                                                                                            258                                


Chain G from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....ee..ee........ee......................eeee.....eeee.....eeeeeeeee.eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ki1 G 158 FVCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQDCVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPPA 292
                                   167       177       187       197       207       217       227       237       247       259       269       279       289   
                                                                                                                           255|                                  
                                                                                                                            258                                  


Chain H from PDB  Type:PROTEIN  Length:132
                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee.....eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhhh....eeeeeee......eee......................eeee.....eeee.....eeeeeeeee.ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ki1 H 159 VCNTCPEKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSNWAPGEPTSRSQDCVMMRGSGRWNDAFCDRKLGAWVCDRLATCTPPA 292
                                   168       178       188       198       208       218       228       238       248      |260       270       280       290  
                                                                                                                          255|                                  
                                                                                                                           258
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  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 4KI1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4KI1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4KI1)

(-) Gene Ontology  (30, 32)

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  FCER2_HUMAN | P06734
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  IGHE_HUMAN | P01854
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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 4gk1 4gko 4j6j 4j6k 4j6l 4j6m 4j6n 4j6p 4j6q 5lgk
        IGHE_HUMAN | P01854: 1f6a 1fp5 1g84 1ige 1o0v 2ige 2wqr 2y7q 3h9y 3h9z 3ha0 4ezm 4gko 4grg 4gt7 4j4p 5anm 5hys 5lgj 5lgk

(-) Related Entries Specified in the PDB File

4ezm