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(-) Description

Title :  AN ENGINEERED DISULFIDE BOND REVERSIBLY TRAPS THE IGE-FC3-4 IN A CLOSED, NON-RECEPTOR BINDING CONFORMATION
 
Authors :  B. A. Wurzburg, B. K. Kim, T. S. Jardetzky
Date :  28 Aug 12  (Deposition) - 12 Sep 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Immunoglobulin, Antibody, Ige, Fc Fragment, Immune System, Fc Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. A. Wurzburg, B. Kim, S. S. Tarchevskaya, A. Eggel, M. Vogel, T. S. Jardetzky
An Engineered Disulfide Bond Reversibly Traps The Ige-Fc3-4 In A Closed, Nonreceptor Binding Conformation.
J. Biol. Chem. V. 287 36251 2012
PubMed-ID: 22948141  |  Reference-DOI: 10.1074/JBC.M112.407502

(-) Compounds

Molecule 1 - IG EPSILON CHAIN C REGION
    Chains: A, B, C, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: IGE FC CEPSILON3-CEPSILON4 FRAGMENT (UNP RESIDUES 210-426)
    Gene: IGHE
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 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  (3, 19)

Asymmetric Unit (3, 19)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2MAN7Ligand/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, 9)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2MAN3Ligand/IonALPHA-D-MANNOSE
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:361 , ASP A:362 , GLN A:392 , ASN A:394 , THR A:396 , NAG A:602BINDING SITE FOR RESIDUE NAG A 601
02AC2SOFTWARETYR A:339 , LEU A:359 , VAL A:361 , NAG A:601 , BMA A:603BINDING SITE FOR RESIDUE NAG A 602
03AC3SOFTWARENAG A:602 , MAN A:604 , MAN A:605BINDING SITE FOR RESIDUE BMA A 603
04AC4SOFTWAREGLN A:494 , BMA A:603BINDING SITE FOR RESIDUE MAN A 604
05AC5SOFTWAREBMA A:603 , HOH A:721 , HOH A:722BINDING SITE FOR RESIDUE MAN A 605
06AC6SOFTWAREGLN B:392 , ASN B:394 , NAG B:602BINDING SITE FOR RESIDUE NAG B 601
07AC7SOFTWARETYR B:339 , LEU B:359 , NAG B:601 , BMA B:603BINDING SITE FOR RESIDUE NAG B 602
08AC8SOFTWARENAG B:602 , MAN B:604 , MAN B:605BINDING SITE FOR RESIDUE BMA B 603
09AC9SOFTWAREGLN B:494 , BMA B:603BINDING SITE FOR RESIDUE MAN B 604
10BC1SOFTWAREBMA B:603 , HOH B:718BINDING SITE FOR RESIDUE MAN B 605
11BC2SOFTWAREVAL C:361 , ASP C:362 , GLN C:392 , ASN C:394 , THR C:396 , NAG C:602BINDING SITE FOR RESIDUE NAG C 601
12BC3SOFTWARESER C:337 , TYR C:339 , LEU C:359 , VAL C:361 , THR C:398 , NAG C:601 , BMA C:603BINDING SITE FOR RESIDUE NAG C 602
13BC4SOFTWARETYR C:339 , NAG C:602 , MAN C:604 , MAN C:605BINDING SITE FOR RESIDUE BMA C 603
14BC5SOFTWAREGLN C:494 , BMA C:603BINDING SITE FOR RESIDUE MAN C 604
15BC6SOFTWAREBMA C:603BINDING SITE FOR RESIDUE MAN C 605
16BC7SOFTWAREVAL D:361 , ASP D:362 , GLN D:392 , ASN D:394 , NAG D:602BINDING SITE FOR RESIDUE NAG D 601
17BC8SOFTWARETYR D:339 , LEU D:359 , VAL D:361 , NAG D:601 , BMA D:603BINDING SITE FOR RESIDUE NAG D 602
18BC9SOFTWARENAG D:602 , MAN D:604BINDING SITE FOR RESIDUE BMA D 603
19CC1SOFTWAREGLN D:494 , BMA D:603BINDING SITE FOR RESIDUE MAN D 604

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1A:335 -B:335
2A:358 -A:418
3A:464 -A:524
4B:358 -B:418
5B:464 -B:524
6C:335 -D:335
7C:358 -C:418
8C:464 -C:524
9D:358 -D:418
10D:464 -D:524

(-) 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 4GT7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GT7)

(-) Exons   (0, 0)

(no "Exon" information available for 4GT7)

(-) 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:212
                                                                                                                                                                                                                                                    
               SCOP domains d4gt7a1 A:334-438 automated matches                                                                      d4gt7a2 A:439-545 automated matches                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhh....eeeeeeeee.......eeeeee.........eeeeee.....eeeeeeee.hhhhhhh..eeeeeee.......eeeeee.........eeeeee.........eeeeeeeeeee.....eeeeee..ee.hhh.eee...ee.....eeeeeeeeeehhhhhhh..eeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gt7 A 334 RCVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNP 545
                                   343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543  


Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d4gt7b1 B:333-438 automated matches                                                                       d4gt7b2 B:439-545 automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhh....eeeeeeeee.......eeeeee.........eeeeee.....eeeeeeee.hhhhhhh..eeeeeee.......eeeeee.........eeeeee.........eeeeeeeeeee.....eeeeee..ee.hhh.eee...ee.....eeeeeeeeeehhhhhhh..eeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gt7 B 333 PRCVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNP 545
                                   342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542   


Chain C from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d4gt7c1 C:332-438 automated matches                                                                        d4gt7c2 C:439-545 automated matches                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee..hhhhhhh....eeeeeeeee.......eeeeee.........eeeeee.....eeeeeeee.hhhhhhh..eeeeeee.......eeeeee.........eeeeee.........eeeeeeeeeee.....eeeeee..ee.hhh.eee...ee.....eeeeeeeeeehhhhhhh..eeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gt7 C 332 NPRCVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNP 545
                                   341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541    


Chain D from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d4gt7d1 D:333-438 automated matches                                                                       d4gt7d2 D:439-545 automated matches                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..hhhhhhh....eeeeeeeee.......eeeeee.........eeeeee.....eeeeeeee.hhhhhhh..eeeeeee.......eeeeee.........eeeeee.........eeeeeeeeeee.....eeeeee..ee.hhh.eee...ee.....eeeeeeeeeehhhhhhh..eeeeee........eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gt7 D 333 PRCVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVNLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVNP 545
                                   342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542
   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, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GT7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GT7)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4GT7)