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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN IGE-FC BOUND TO ITS B CELL RECEPTOR DERCD23
 
Authors :  B. Dhaliwal, M. O. Y. Pang, B. J. Sutton
Date :  07 Jul 16  (Deposition) - 05 Apr 17  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,E  (1x)
Biol. Unit 2:  C,D,F  (1x)
Keywords :  Immunoglobulin Fold Lectin, Antibody Receptor, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Dhaliwal, M. O. Pang, A. H. Keeble, L. K. James, H. J. Gould, J. M. Mcdonnell, B. J. Sutton, A. J. Beavil
Ige Binds Asymmetrically To Its B Cell Receptor Cd23.
Sci Rep V. 7 45533 2017
PubMed-ID: 28361904  |  Reference-DOI: 10.1038/SREP45533

(-) Compounds

Molecule 1 - IG EPSILON CHAIN C REGION
    Chains: A, B, C, D
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Common: MOUSE
    Expression System Taxid: 10090
    Gene: IGHE
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - LOW AFFINITY IMMUNOGLOBULIN EPSILON FC RECEPTOR
    Chains: E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB  E 
Biological Unit 2 (1x):   CD F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:392 , ASN A:394binding site for Mono-Saccharide NAG A 601 bound to ASN A 394
2AC2SOFTWAREASP B:271 , LYS B:326 , LEU B:359 , GLN B:392 , ASN B:394 , THR B:396 , THR B:398binding site for Poly-Saccharide residues NAG B 601 through BMA B 603 bound to ASN B 394
3AC3SOFTWAREGLN C:392 , ASN C:394binding site for Mono-Saccharide NAG C 601 bound to ASN C 394
4AC4SOFTWAREASP D:271 , ASP D:307 , ARG D:308 , THR D:309 , LYS D:326 , LEU D:359 , GLN D:392 , ASN D:394 , THR D:398binding site for Poly-Saccharide residues NAG D 601 through BMA D 603 bound to ASN D 394

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1C:464 -C:524
2E:191 -E:282
3F:191 -F:282

(-) Cis Peptide Bonds  (8, 8)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LGK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LGK)

(-) Exons   (0, 0)

(no "Exon" information available for 5LGK)

(-) 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:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..........eee...eeee.....eeeeee.....hhh.eeeeeeee..eeeeeeeeeeehhhhh....eeeeee........ee..........eeeeee..hhhhhhh....eeeeeeee........eeeeee.........eeeeee.....eeeeeeee.hhhhhhhh..eeeeee.......ee.............eeeeee..........eeeeeeee.......eeeeee..ee......ee...ee.....eeeeeeeeehhhhhhhh...eeeee.........eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lgk A 234 VKILQSSCDGGGHFPPTIQLCLVSGYTPGTIQITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVQLTWSRASGKPVQHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRA 540
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       


Chain B from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..........eee...eeee.....eeeeee.....hhh.eeeeeeee..eeeeeeeeeeehhhhh....eeeeee........ee...........eeeee..hhhhhhh....eeeeeee.......eeeeee.........eeeeee.....eeeeeeee.hhhhhhhh..eeeeee.......ee.............eeeeee..........eeeeeeee.......eeeeee..ee......ee...ee.....eeeeeeeeehhhhhhhh...eeeee.........eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lgk B 235 KILQSSCDGGGHFPPTIQLCLVSGYTPGTIQITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDPSKGTVQLTWSRASGKPVQHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRA 540
                                   244       254       264       274       284       294       304       314       324       334       344       354       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536    
                                                                                                                                                         362|                                                                                                                                                                               
                                                                                                                                                          365                                                                                                                                                                               


Chain C from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee..........eee...eeee.....eeeeee.....hhh.eeeeeeee..eeeeeeeeeeehhhhh....eeeeeee..eee..ee..........eeeeee..hhhhhhh....eeeeeeee.........eeeee.........eeeeee.....eeeeeeee.hhhhhhhh..eeeee........ee.............eeeeee..........eeeeeeee.......eeeeee..ee.....eee...ee.....eeeeeeeeehhhhhhhh...eeeee.........eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lgk C 235 KILQSSCDGGGHFPPTIQLCLVSGYTPGTIQITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVQLTWSRASGKPVQHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRA 540
                                   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534      


Chain D from PDB  Type:PROTEIN  Length:304
                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..........eee...eeee.....eeeeee.....hhh.eeeeeeee..eeeeeeeeeeehhhhh....eeeeee........ee...........eeeee..hhhhhhh....eeeeeeee......eeeeee.........eeeeee.....eeeeeeee.hhhhhhhh..eeeeee.......ee.............eeeeee..........eeeeeeee.......eeeeee..ee......ee...ee.....eeeeeeeeehhhhhhhh...eeeee.........eee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lgk D 235 KILQSSCDGGGHFPPTIQLCLVSGYTPGTIQITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDPSKGTVQLTWSRASGKPVQHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRA 540
                                   244       254       264       274       284       294       304       314       324       334       344       354       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536    
                                                                                                                                                         362|                                                                                                                                                                               
                                                                                                                                                          365                                                                                                                                                                               


Chain E from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhh.....eeeeee........ee..........eeee.....eeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 5lgk E 166 KWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSDCVMMRGSGRWNDAFCDRKLGAWVCDR 284
                                   175       185       195       205       215       225       235       259       269       279     
                                                                                                       243|                          
                                                                                                        258                          


Chain F from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeeeeeeeeehhhhhhhhhhhh..ee....hhhhhhhhhhh.....eeeeee........ee..........eeee.....eeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 5lgk F 165 EKWINFQRKCYYFGKGTKQWVHARYACDDMEGQLVSIHSPEEQDFLTKHASHTGSWIGLRNLDLKGEFIWVDGSHVDYSDCVMMRGSGRWNDAFCDRKLGAWVCDR 284
                                   174       184       194       204       214       224       234       258       268       278      
                                                                                                        243|                          
                                                                                                         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 5LGK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LGK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LGK)

(-) Gene Ontology  (30, 32)

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  5lgk
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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 4ki1
        IGHE_HUMAN | P01854: 1f6a 1fp5 1g84 1ige 1o0v 2ige 2wqr 2y7q 3h9y 3h9z 3ha0 4ezm 4gko 4grg 4gt7 4j4p 4ki1 5anm 5hys 5lgj

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LGK)