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(-) Description

Title :  L3-12 COMPLEX
 
Authors :  J. Petersen, J. Rossjohn, H. H. Reid, F. Koning
Date :  08 Apr 15  (Deposition) - 03 Jun 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J
Biol. Unit 1:  A,B,G,H,J  (1x)
Biol. Unit 2:  C,D,E,F,I  (1x)
Keywords :  Immune Receptor-Ligand Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Petersen, J. Van Bergen, K. L. Loh, Y. Kooy-Winkelaar, D. X. Beringer, A. Thompson, S. F. Bakker, C. J. Mulder, K. Ladell, J. E. Mclaren, D. A. Price, J. Rossjohn, H. H. Reid, F. Koning
Determinants Of Gliadin-Specific T Cell Selection In Celiac Disease.
J Immunol. V. 194 6112 2015
PubMed-ID: 25948817  |  Reference-DOI: 10.4049/JIMMUNOL.1500161

(-) Compounds

Molecule 1 - MHC CLASS II HLA-DQ-ALPHA CHAIN
    Chains: A, C
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 1-184
    Gene: HLA-DQA1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - MHC CLASS II HLA-DQ-BETA-1
    Chains: B, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Fragment: UNP RESIDUES 1-192
    Gene: HLA-DQB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - T-CELL RECEPTOR, L3-12 ALPHA CHAIN
    Chains: E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - T-CELL RECEPTOR, L3-12 BETA CHAIN
    Chains: F, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 5 - DEAMIDATED DQ8-GLIA-ALPHA1 PEPTIDE
    Chains: I, J
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Organism Common: BREAD WHEAT
    Organism Scientific: TRITICUM AESTIVUM
    Organism Taxid: 4565

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric Unit : ABCDEFGHIJ
Biological Unit 1 (1x): AB    GH J
Biological Unit 2 (1x):   CDEF  I 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1FUC4Ligand/IonALPHA-L-FUCOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2MAN-1Ligand/IonALPHA-D-MANNOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:116 , ASN A:118 , GLU A:166 , TRP A:168binding site for Mono-Saccharide NAG A 1000 bound to ASN A 118
2AC2SOFTWARELYS A:67 , ASN B:19 , THR B:21 , GLU B:22 , GLU H:64binding site for Poly-Saccharide residues NAG B 1000 through MAN B 1005 bound to ASN B 19
3AC3SOFTWAREVAL C:116 , ASN C:118 , GLU C:166 , TRP C:168binding site for Mono-Saccharide NAG C 1000 bound to ASN C 118
4AC4SOFTWAREASN D:19 , GLY D:20 , THR D:21 , GLU D:22binding site for Poly-Saccharide residues NAG D 1000 through FUC D 1003 bound to ASN D 19

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:107 -A:163
2B:15 -B:79
3B:117 -B:173
4C:107 -C:163
5D:15 -D:79
6D:117 -D:173
7E:23 -E:104
8E:151 -E:201
9E:176 -F:184
10F:23 -F:104
11F:158 -F:223
12G:23 -G:104
13G:151 -G:201
14G:176 -H:184
15H:23 -H:104
16H:158 -H:223

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Tyr A:9 -Gly A:9A
2Gly A:17 -Pro A:18
3Phe A:113 -Pro A:114
4Tyr B:123 -Pro B:124
5Tyr C:9 -Gly C:9A
6Gly C:17 -Pro C:18
7Phe C:113 -Pro C:114
8Tyr D:123 -Pro D:124
9Glu D:162 -Met D:163
10Asn E:206 -Asn E:207
11Thr F:7 -Pro F:8
12Tyr F:164 -Pro F:165
13Thr H:7 -Pro H:8
14Tyr H:164 -Pro H:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z7V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z7V)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z7V)

(-) 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:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeeee....eeeeeeee..eeeeeee....eeee.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee.......eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4z7v A   2 VADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEP 180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
                                   9A                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....eeeeeee.....eeeee......eee...ee.....eeeeeee......eeeeee.......eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z7v B   3 SPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSLLVCSVTDFYPAQIKVRWFQEETTGVVSTPLIRNGDWTFQILVMLEMRGDVYTCHVEHPSLQNPIIVEWR 189
                                    12        22        32        42        52        62        72        82        92       102 ||    121       131||     144       154       167       177       187  
                                                                                                                               104|               132|                        163|                      
                                                                                                                                114                136                         167                      


Chain C from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeeee....eeeeeeee..eeeeeee....eeee.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee.......eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4z7v C   2 VADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEP 180
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180
                                   9A                                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....eeeeeee.....eeeee.......ee...ee.....eeeeee...........eeeee.......eeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z7v D   2 DSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSLLVCSVTDFYPAQIKVRWFQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEW 188
                                    11        21        31        41        51        61        71        81        91       101  ||   120       130 ||    143       153       163       173       183     
                                                                                                                                104|               132|                                                    
                                                                                                                                 114                136                                                    


Chain E from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee..eeeeeeee.......eeeeeeee......eeeeee...eee....eeee.....eeeeeeeeehhhhheeeeeeeee...........eeeeee........eeeeeee......eeeeee...............eee...eeeeehhhheeeeeeeeee.....hhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z7v E   2 DAKTTQPNSMESNEEEPVHLPCNHSTISGTDYIHWYRQLPSQGPEYVIHGLTSNVNNRMASLAIAEDRKSSTLILHRATLRDAAVYYCILRDSRAQKLVFGQGTRLTINPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFP 217
                                    11        21        36        46        56 ||   ||76        86        96       106   ||  118       128       138       148       158       168       178       188       198       208         
                                                       30|                    58|  68|                                 110|                                                                                                        
                                                        36                     64   74                                  113                                                                                                        


Chain F from PDB  Type:PROTEIN  Length:243
                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee....eeeeee......eeeeeeee...eeeeeeeee..eeeee......eeeee.....eeeee...hhhhheeeeeeee.........ee...eeeeee.hhhhh...eeeeee.hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z7v F   1 DSGVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGNILERFSAQQFPDLHSELNLSSLELGDSALYFCASSAGTSGEYEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 256
                                    10        20        37        47        57||      71||      83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253   
                                                       29|                   58|       72|     81|                                                                                                                                                                             
                                                        37                    63        74      83                                                                                                                                                                             


Chain G from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeee..eeeeeeee.......eeeeeeee......eeeeee...eee....eeee.....eeeeeeeeehhhhheeeeeeeee...........eeeeee........eeeeeee....eeeeee...............eee...eeeeehhhheeeeeeeeee......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4z7v G   3 AKTTQPNSMESNEEEPVHLPCNHSTISGTDYIHWYRQLPSQGPEYVIHGLTSNVNNRMASLAIAEDRKSSTLILHRATLRDAAVYYCILRDSRAQKLVFGQGTRLTINPNIQNPDPAVYQLRDSKSKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPSP 219
                                    12        22       |37        47        57||   || 77        87        97       107  ||   119       129       139     ||151       161       171       181       191       201       211        
                                                      30|                    58|  68|                                 110|                             145|                                                                       
                                                       36                     64   74                                  113                              148                                                                       


Chain H from PDB  Type:PROTEIN  Length:242
                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeeee....eeeeee......eeeeeeee...eeeeeeeee..eeeee......eeeee.....eeeee...hhhhheeeeeeee.........ee...eeeeee.hhhhh...eeeeee.hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z7v H   2 SGVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGNILERFSAQQFPDLHSELNLSSLELGDSALYFCASSAGTSGEYEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 256
                                    11        21       |38        48        58|       72|      |84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254  
                                                      29|                   58|       72|     81|                                                                                                                                                                             
                                                       37                    63        74      83                                                                                                                                                                             


Chain I from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 4z7v I   1 SGEGSFQPSQENP  13
                                    10   


Chain J from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 4z7v J   1 SGEGSFQPSQENP  13
                                    10
   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  (0, 0)

(no "SCOP Domain" information available for 4Z7V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z7V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z7V)

(-) Gene Ontology  (8, 15)

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  4z7v
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  GDA9_WHEAT | P18573
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 Related Entries

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

UniProtKB/Swiss-Prot
        GDA9_WHEAT | P18573: 2nna 4gg6 4ozf 4ozg 4ozh 4ozi 4z7u 4z7w 5ks9
        O19707_HUMAN | O19707: 5ksa 5ksb
UniProtKB/TrEMBL
        O19707_HUMAN | O19707: 4z7u 4z7w
        Q30069_HUMAN | Q30069: 4z7u 4z7w

(-) Related Entries Specified in the PDB File

4z7u 4z7w