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(-) Description

Title :  T316 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 :  2.89
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, T316 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, T316 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 - DQ8-GLIA-ALPHA1
    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  (4, 15)

Asymmetric Unit (4, 15)
No.NameCountTypeFull Name
1FUC4Ligand/IonALPHA-L-FUCOSE
2MAN4Ligand/IonALPHA-D-MANNOSE
3NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO41Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU F:178 , VAL F:179 , HIS F:180 , SER F:181binding site for residue SO4 F 301
2AC2SOFTWAREASN A:78 , HOH A:309 , TYR D:60 , GLN D:64 , GLY F:3 , ASP F:26 , MET F:27 , HIS F:29 , ARG F:85 , PHE F:117binding site for Poly-Saccharide residues NAG A 201 through MAN A 206 bound to ASN A 78
3AC3SOFTWAREASN A:118 , GLU A:166 , TRP A:168binding site for Mono-Saccharide NAG A 207 bound to ASN A 118
4AC4SOFTWAREGLN B:64 , GLU B:66 , ASN C:78 , HOH C:308 , GLY H:3 , ASP H:26 , MET H:27 , ARG H:85 , GLU H:108 , GLN J:14binding site for Poly-Saccharide residues NAG C 201 through MAN C 206 bound to ASN C 78
5AC5SOFTWAREASN C:118 , GLU C:166 , TRP C:168binding site for Mono-Saccharide NAG C 207 bound to ASN C 118

(-) 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  (15, 15)

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
9Asp E:174 -Lys E:175
10Thr F:7 -Pro F:8
11Tyr F:164 -Pro F:165
12Asp G:174 -Lys G:175
13Asp G:184 -Phe G:185
14Thr H:7 -Pro H:8
15Tyr H:164 -Pro H:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z7W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z7W)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z7W)

(-) 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:181
                                                                                                                                                                                                                     
               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
                 4z7w A   1 IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEP 180
                                    9A        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179 
                                    9A                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee...eeeeeeeee.....eeeeee........eee...ee.....eeeeeeee........eeeeee.......eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4z7w B   3 SPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEWR 189
                                    12        22        32        42        52        62        72        82        92       102 ||    119       129       139       149       159       169       179       189
                                                                                                                               104|                                                                             
                                                                                                                                112                                                                             


Chain C from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               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
                 4z7w C   1 IVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEP 180
                                    9A        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179 
                                    9A                                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee...eeeeeeeee.....eeeeee........eee...ee.....eeeeeeee........eeeeee.......eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4z7w D   3 SPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEWR 189
                                    12        22        32        42        52        62        72        82        92       102 ||    119       129       139       149       159       169       179       189
                                                                                                                               104|                                                                             
                                                                                                                                112                                                                             


Chain E from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeeee....eee..ee.....eeeeeeee.....eeeeeee.....eee.hhh.eeeee....eeeeee...hhhhh.eeeeeeee..eeeeee...eeeeee........eeee...........eeee................eee...ee...........eeee...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z7w E   2 QSVTQPDIHITVSEGASLELRCNYSYGATPYLFWYVQSPGQGLQLLLKYFSGDTLVQGIKGFEAEFKRSQSSFNLRKPSVHWSDAAEYFCAVGETGANNLFFGTGTRLTVIPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTF 215
                                    11        21       |37        47        57 ||     74        84        94       104     ||116       126       136       146       156       166       176       186       196       206         
                                                      29|                     59|    68|                                 110|                                                                                                      
                                                       36                      62     74                                  113                                                                                                      


Chain F from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee.......eee.....eeeeee...hhhhh.eeeeeee........ee...eeeeee.........eeeee..hhhhhhhh.eeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee...................eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z7w F   3 GVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKGEVPNGYNVSRLNKREFSLRLESAAPSQTSVYFCASSEARRYNEQFFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 257
                                    12        22      ||39        49        63        74      ||85        95       105    || 116       126       136       146       156       166       176       186       196       206       216       226       236       246       256 
                                                     29|                   58|       72|     81|                        110|                                                                                                                                                 
                                                      37                    63        74      83                         112                                                                                                                                                 


Chain G from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeeee....eee..ee.....eeeeeeee.....eeeeeee.....eee.hhh.eeeee....eeeeee...hhhhh.eeeeeeee..eeeeee...eeeeee........eeee.........eeeeee................eee..........eeeeee.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z7w G   2 QSVTQPDIHITVSEGASLELRCNYSYGATPYLFWYVQSPGQGLQLLLKYFSGDTLVQGIKGFEAEFKRSQSSFNLRKPSVHWSDAAEYFCAVGETGANNLFFGTGTRLTVIPYIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCSMDFKSNSAVAWSNKSDFACANNSIIPEDTF 215
                                    11        21       |37        47        57 ||     74        84        94       104     ||116       126       136       146       156       166       176|      191       201||     214 
                                                      29|                     59|    68|                                 110|                                                            176|                 202|         
                                                       36                      62     74                                  113                                                             182                  206         


Chain H from PDB  Type:PROTEIN  Length:239
                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeee....eeeeeee.....eeeeeeee...eeeeeeee......ee.......eee.....eeeeee...hhhhh.eeeeeee........ee...eeeeee................hhhhhhhh.eeeeeeeeeee....eeeeeee..eee...eee.............eeeeeeeeeehhhhhh...eeeeeeee....................eeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z7w H   3 GVTQTPKFQVLKTGQSMTLQCAQDMNHNSMYWYRQDPGMGLRLIYYSASEGTTDKGEVPNGYNVSRLNKREFSLRLESAAPSQTSVYFCASSEARRYNEQFFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 257
                                    12        22      ||39        49        63        74      ||85        95       105    || 116       126       136       146       156       166       176       186  ||   198       208       218       228       238       248         
                                                     29|                   58|       72|     81|                        110|                                                                          189|                                                                 
                                                      37                    63        74      83                         112                                                                           192                                                                 


Chain I from PDB  Type:PROTEIN  Length:15
                                               
               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
                 4z7w I   0 PSGEGSFQPSQENPQ  14
                                     9     


Chain J from PDB  Type:PROTEIN  Length:15
                                               
               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
                 4z7w J   0 PSGEGSFQPSQENPQ  14
                                     9
   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 4Z7W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z7W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z7W)

(-) Gene Ontology  (8, 15)

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

UniProtKB/Swiss-Prot
        GDA9_WHEAT | P18573: 2nna 4gg6 4ozf 4ozg 4ozh 4ozi 4z7u 4z7v 5ks9
        O19707_HUMAN | O19707: 5ksa 5ksb
UniProtKB/TrEMBL
        O19707_HUMAN | O19707: 4z7u 4z7v
        Q30069_HUMAN | Q30069: 4z7u 4z7v

(-) Related Entries Specified in the PDB File

4z7u 4z7v