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(-) Description

Title :  BEL602-DQ8.5-GLIA-GAMMA1 COMPLEX
 
Authors :  J. Petersen, J. Rossjohn, H. H. Reid
Date :  08 Jul 16  (Deposition) - 21 Sep 16  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D,J
Keywords :  Celiac Disease T Cell Receptor Peptide Mhc Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Petersen, Y. Kooy-Winkelaar, K. L. Loh, M. Tran, J. Van Bergen, F. Koning, J. Rossjohn, H. H. Reid
Diverse T Cell Receptor Gene Usage In Hla-Dq8-Associated Celiac Disease Converges Into A Consensus Binding Solution.
Structure V. 24 1643 2016
PubMed-ID: 27568928  |  Reference-DOI: 10.1016/J.STR.2016.07.010

(-) Compounds

Molecule 1 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DQ ALPHA 1 CHAIN
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: HLA-DQA1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DC-1 ALPHA CHAIN,DC-ALPHA,HLA-DCA,MHC CLASS II DQA1
 
Molecule 2 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DQ BETA 1 CHAIN
    Chains: B
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: HLA-DQB1
    Organism Common: HUMAN
    Organism Scientific: TRITICUM AESTIVUM, HOMO SAPIENS
    Organism Taxid: 4565, 9606
 
Molecule 3 - BEL602 ALPHA TRAV20*01
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - BEL602 BETA TRBV9*01
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 5 - DQ8.5-GLIA-GAMMA1 PEPTIDE
    Chains: J
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Organism Scientific: TRITICUM AESTIVUM
    Organism Taxid: 4565

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDJ

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:44 , HOH A:336 , HOH A:387 , HOH A:424 , HOH A:445binding site for residue CA A 202
2AC2SOFTWAREASN A:118 , HOH A:361binding site for Mono-Saccharide NAG A 201 bound to ASN A 118

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:107 -A:163
2B:15 -B:79
3B:117 -B:173
4C:29 -C:104
5C:151 -C:201
6C:176 -D:184
7D:23 -D:104
8D:158 -D:223

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological 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
5Ser C:13 -Pro C:14
6Lys C:144 -Ser C:145
7Ser C:146 -Asp C:147
8Ile C:210 -Pro C:211
9Thr D:7 -Pro D:8
10Phe D:164 -Pro D:165

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KSA)

(-) 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:182
                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeeeee..eeeeeee....eeee.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ksa A   0 DIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWSLPVLRQFRFDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHWEPE 181
                                     9|       18        28        38        48 ||     59        69        79        89        99       109       119       129       139       149       159       169       179  
                                     9A                                       50|                                                                                                                                 
                                                                               52                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee......eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ksa B   2 DSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEWRAQ 191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191


Chain C from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....eeeeeeeee......eeeeee.....eeee..eeeee...eeeeee...hhhhheeeeeeeee.......ee...eeeeee........eeeee........eeeeee...............eee...eeeeehhhheeeeeeeeee.................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ksa C   7 EDQVTQSPEALRLQEGESSSLNCSYTVSGLRGLFWYRQDPGKGPEFLFTLYSAGEEKEKERLKATLTKKESFLHITAPKPEDSATYLCAVQFMDSNYQLIWGAGTKLIIKPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPE 212
                                    16        26        36        46        56  ||    74       |86        96       106       116|      127       137       147       157       167       177       187       197       207     
                                                                               59|   68|      82|                            116|                                                                                              
                                                                                63    74       85                             118                                                                                              


Chain D 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...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ksa D   3 GVTQTPKHLITATGQRVTLRCSPRSGDLSVYWYQQSLDQGLQFLIQYYNGEERAKGNILERFSAQQFPDLHSELNLSSLELGDSALYFCASSVAGTPSYEQYFGPGTRLTVTEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 257
                                    12        22      ||39        49        63        74      ||85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255  
                                                     29|                   58|       72|     81|                                                                                                                                                                              
                                                      37                    63        74      83                                                                                                                                                                              


Chain J from PDB  Type:PROTEIN  Length:11
                                           
               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
                 5ksa J  -1 QPQQSFPEQEA  10
                            ||       9 
                           -1|         
                             1
   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 5KSA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (31, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DQA1_HUMAN | P01909: 1jk8 1nbn 1s9v 1uvq 2nna 4gg6 4ozf 4ozg 4ozh 4ozi 5ksb 5ksu 5ksv
        GDB0_WHEAT | P08079: 5ksb
        O19707_HUMAN | O19707: 5ksb
        TCA_HUMAN | P01848: 1ao7 1bd2 1fyt 1j8h 1kgc 1mi5 1oga 1qrn 1qsf 1ymm 1zgl 2ak4 2bnq 2bnr 2bnu 2cdf 2cdg 2esv 2eyr 2eys 2eyt 2f53 2f54 2gj6 2ial 2iam 2ian 2nx5 2p5e 2p5w 2po6 2pye 2pyf 2vlj 2vlk 2vlm 2vlr 2xn9 2xna 3arb 3ard 3are 3arf 3arg 3d39 3dx9 3dxa 3ffc 3gsn 3he7 3hg1 3kpr 3kps 3kxf 3o4l 3o6f 3o8x 3o9w 3pwp 3qdg 3qdj 3qdm 3qeq 3qeu 3qib 3qjf 3qux 3scm 3sda 3sdc 3sdd 3sdx 3sjv 3skn 3t0e 3tn0 3tvm 4apq 4c56 4g8e 4g8f 4irs 4jfd 4jfe 4jff 4jfh 4jrx 4jry 4mvb 4mxq 4n0c 4n5e 4nhu 4onh 4p4k 4prh 4pri 4prp 4udt 4udu 4ww1 4ww2 4wwk 4x6b 4x6c 4x6d 4y16 4y2d 4y4f 4y4h 4y4k 4zdh 4zez 5brz 5bs0 5c07 5c08 5c09 5c0a 5c0b 5c0c 5eu6 5fk9 5fka 5hhm 5hho 5hyj 5ks9 5ksb
        TRBC2_HUMAN | A0A5B9: 1ao7 1bd2 2eyr 2eys 2eyt 3kxf 3o6f 3o8x 3o9w 3qux 3t0e 3ta3 3tvm 4c56 4mvb 4mxq 4n0c 4n5e 4nhu 4onh 4p4k 4udt 4udu 4ww1 4ww2 4wwk 4y16 4y2d 4y4f 4y4h 4y4k 4zak 4zez 5brz 5bs0 5c07 5c08 5c09 5c0a 5c0b 5c0c 5eu6 5fk9 5fka 5hhm 5hho 5hyj 5ks9 5ksb
UniProtKB/TrEMBL
        A0A0B4J274_H | A0A0B4J274: 5ks9 5ksb
        A0A0U5Q247_H | A0A0U5Q247: 5ks9 5ksb
        A0A580_HUMAN | A0A580: 5ks9 5ksb
        O19707_HUMAN | O19707: 4z7u 4z7v 4z7w

(-) Related Entries Specified in the PDB File

5ks9 5ksb