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(-) Description

Title :  THE COMPLEX OF HUMAN IGE-FC WITH TWO BOUND FAB FRAGMENTS
 
Authors :  N. Drinkwater, B. J. Sutton
Date :  07 Feb 13  (Deposition) - 12 Mar 14  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.91
Chains :  Asym./Biol. Unit :  A,B,C,D,H,L
Keywords :  Ig Like Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Drinkwater, B. P. Cossins, A. H. Keeble, M. Wright, K. Cain, H. Hailu A. Oxbrow, J. Delgado, L. K. Shuttleworth, M. W. Kao, J. M. Mcdonnell, A. J. Beavil, A. J. Henry, B. J. Sutton
Human Immunoglobulin E Flexes Between Acutely Bent And Extended Conformations.
Nat. Struct. Mol. Biol. V. 21 397 2014
PubMed-ID: 24632569  |  Reference-DOI: 10.1038/NSMB.2795

(-) Compounds

Molecule 1 - IG EPSILON CHAIN C REGION
    Chains: A, B
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Strain: NSO CELL LINE
    Expression System Taxid: 10090
    Gene: IGHE
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - IMMUNOGLOBULIN G FAB FRAGMENT HEAVY CHAIN
    Chains: H, C
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Strain: CHO CELL LINE
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - IMMUNOGLOBULIN G FAB FRAGMENT LIGHT CHAIN
    Chains: L, D
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Strain: CHO CELL LINE
    Expression System Taxid: 10029
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1BMA6Ligand/IonBETA-D-MANNOSE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:362 , GLN A:392 , ASN A:394 , THR A:396 , NAG A:602 , TYR H:129BINDING SITE FOR RESIDUE NAG A 601
02AC2SOFTWARETYR A:339 , VAL A:361 , THR A:398 , NAG A:601 , BMA A:603BINDING SITE FOR RESIDUE NAG A 602
03AC3SOFTWARETYR A:339 , LEU A:359 , NAG A:602 , BMA A:604 , BMA A:605BINDING SITE FOR RESIDUE BMA A 603
04AC4SOFTWAREBMA A:603BINDING SITE FOR RESIDUE BMA A 604
05AC5SOFTWAREBMA A:603 , BMA B:605BINDING SITE FOR RESIDUE BMA A 605
06AC6SOFTWAREASP B:362 , GLN B:392 , ASN B:394 , THR B:396 , NAG B:602 , TYR C:129BINDING SITE FOR RESIDUE NAG B 601
07AC7SOFTWARETYR B:339 , LEU B:359 , VAL B:361 , THR B:398 , NAG B:601 , BMA B:603BINDING SITE FOR RESIDUE NAG B 602
08AC8SOFTWARENAG B:602 , BMA B:604 , BMA B:605BINDING SITE FOR RESIDUE BMA B 603
09AC9SOFTWARESER B:341 , BMA B:603BINDING SITE FOR RESIDUE BMA B 604
10BC1SOFTWAREBMA A:605 , BMA B:603 , TYR H:126BINDING SITE FOR RESIDUE BMA B 605

(-) SS Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1A:241 -B:328
2A:254 -A:312
3A:328 -B:241
4A:358 -A:418
5A:464 -A:524
6B:254 -B:312
7B:358 -B:418
8B:464 -B:524
9C:41 -C:118
10C:173 -C:229
11D:41 -D:108
12D:157 -D:216
13H:41 -H:118
14H:173 -H:229
15L:41 -L:108
16L:157 -L:216

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Arg A:334 -Gly A:335
2Met A:470 -Pro A:471
3Ser A:532 -Pro A:533
4Arg B:334 -Gly B:335
5Met B:470 -Pro B:471
6Ser B:532 -Pro B:533
7Val H:84 -Ser H:85
8Phe H:179 -Pro H:180
9Val C:84 -Ser C:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J4P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J4P)

(-) Exons   (0, 0)

(no "Exon" information available for 4J4P)

(-) Sequences/Alignments

Asymmetric/Biological 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:315
                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee..........eeeeeeeee.......eeeeee..ee.hhh.eeeeeeee..eeeeeeeeeeehhhhh....eeeeeee..eeeeeee...........eeee...hhhhhhh....eeeeeeeee.......eeeeee.........eeeeee.....eeeeeeee...........eeeeee.......eeeee..........eee............eeeeeeeeeee.....eeeeee..ee......ee...ee.....eeeeeeeeeehhhhh....eeeeee........eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4j4p A  230 TPPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTIQITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVQLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSV  543
                                   239       249    |  258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538     
                                                 253A                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:317
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee..........eeeeeeeeeee.....eeeeee..ee.hhh.eeeeee.....eeeeeeeeeehhhhhh...eeeeeee..eeeeeee...........eeee...hhhhhhh....eeeeeeeee.......eeeeee.........eeeeee.....eeeeeeee.hhhhhhh...eeeeee.......eeeee..........eeee..............eeeeeeee....eeeeee...........ee...ee.....eeeeeee..hhhhhhhh..eeeeeee.......ee..ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4j4p B  229 FTPPTVKILQSSCDGGGHFPPTIQLLCLVSGYTPGTIQITWLEDGQVMDVDLSTASTTQEGELASTQSELTLSQKHWLSDRTYTCQVTYQGHTFEDSTKKCADSNPRGVSAYLSRPSPFDLFIRKSPTITCLVVDLAPSKGTVQLTWSRASGKPVNHSTRKEEKQRNGTLTVTSTLPVGTRDWIEGETYQCRVTHPHLPRALMRSTTKTSGPRAAPEVYAFATPEWPGSRDKRTLACLIQNFMPEDISVQWLHNEVQLPDARHSTTQPRKTKGSGFFVFSRLEVTRAEWEQKDEFICRAVHEAASPSQTVQRAVSVN  544
                                   238       248     | 257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       
                                                  253A                                                                                                                                                                                                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:222
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee.....ee.....eeeeeeee........eeeeeeeee...eeeeeeeeee...eeeee.......eeeeee....eeeeee...hhhhheeeeeeeeee.......eeeeee...eeeee........eeee......eee.eeeeee.....eeee........eee...ee.....eeeeeeeee.........eeeeeee....ee..eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4j4p C   20 QVQLQQSGPGLVKPSQTLSLTCGISGDSVSSNSAAWNWLRQSPSRGLEWLGRTYYRSKWYNDYAVSMKSRITINPDTSRNQFSLQLNSVTPEDTAVYYCARDGEISYDYYYYGMDVWGRGTLVTVSSASTKGPSVFPLAPGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  247
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159|      175       185       195       205       215       225       235       245  
                                                                                                                                                                     159|                                                                                 
                                                                                                                                                                      166                                                                                 


Chain D from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains d4j4pd1 D:19-130 automated matches                                                                              d4j4pd2 D:131-233 automated matches                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.....eeeeee..........eeeeee......eeee.............eeeeee..eeeeee........eeeeeeeee....eeee...eeeee........eeeee...........eeeeeeee...........ee..ee....eee...........eeeeeeeehhhhhh....ee.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4j4p D   19 AQSVLTQPPSASGTPGQRVTISCSGSSSNIGNNGVNWYQQVPGKPPKLLIYYDDLLPSGVSDRFSGSKSGTSASLAISGLQSEDEADYYCEAWDDSLDGVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE  233
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228     


Chain H from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeeeee...eeeeeeeeee...eeeee..hhhh.eeeeee....eeeeee...hhhhheeeeeeee...........eeee...eeeee........eeeee......eeeeeeeee.....eeee........eee...ee.....eeeeeeee...........eeeeehhhhh...eee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4j4p H   20 QVQLQQSGPGLVKPSQTLSLTCGISGDSVSSNSAAWNWLRQSPSRGLEWLGRTYYRSKWYNDYAVSMKSRITINPDTSRNQFSLQLNSVTPEDTAVYYCARDGEISYDYYYYGMDVWGRGTLVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC  249
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159||     175       185       195       205       215       225       235       245    
                                                                                                                                                                      160|                                                                                  
                                                                                                                                                                       167                                                                                  


Chain L from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                        
               SCOP domains d4j4pl1 L:19-130 automated matches                                                                              d4j4pl2 L:131-233 automated matches                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee....eeeeeee..........eeeeee......eeee.............eeeeee..eeeeeee.......eeeeeeeee....eeee...eeeee.........eeee...........eeeeeeeeee....eeeeeee..ee....eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4j4p L   19 AQSVLTQPPSASGTPGQRVTISCSGSSSNIGNNGVNWYQQVPGKPPKLLIYYDDLLPSGVSDRFSGSKSGTSASLAISGLQSEDEADYYCEAWDDSLDGVVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTE  233
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228
   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  (2, 4)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J4P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J4P)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:334 - Gly A:335   [ RasMol ]  
    Arg B:334 - Gly B:335   [ RasMol ]  
    Met A:470 - Pro A:471   [ RasMol ]  
    Met B:470 - Pro B:471   [ RasMol ]  
    Phe H:179 - Pro H:180   [ RasMol ]  
    Ser A:532 - Pro A:533   [ RasMol ]  
    Ser B:532 - Pro B:533   [ RasMol ]  
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  4j4p
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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 4gt7 4ki1 5anm 5hys 5lgj 5lgk

(-) Related Entries Specified in the PDB File

1lso 2wqr 2y7q