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(-) Description

Title :  JR5.1 PROTEIN COMPLEX
 
Authors :  J. Petersen, H. H. Reid, J. Rossjohn
Date :  15 Feb 14  (Deposition) - 16 Apr 14  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,G,H,J
Keywords :  Immune Receptor-Ligand Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Petersen, V. Montserrat, J. R. Mujico, K. L. Loh, D. X. Beringer, M. Van Lummel, A. Thompson, M. L. Mearin, J. Schweizer, Y. Kooy-Winkelaar, J. Van Bergen, J. W. Drijfhout, W. T. Kan, N. L. La Gruta, R. P. Anderson, H. H. Reid, F. Koning, J. Rossjohn
T-Cell Receptor Recognition Of Hla-Dq2-Gliadin Complexes Associated With Celiac Disease.
Nat. Struct. Mol. Biol. V. 21 480 2014
PubMed-ID: 24777060  |  Reference-DOI: 10.1038/NSMB.2817

(-) Compounds

Molecule 1 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DQ ALPHA 1 CHAIN
    Chains: A
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HI5
    Expression System Common: CABBAGE LOOPER
    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 Cell Line: HI5
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Gene: HLA-DQB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MHC CLASS II ANTIGEN
 
Molecule 3 - T-CELL RECEPTOR, JR5.1 ALPHA CHAIN
    Chains: G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 4 - T-CELL RECEPTOR, JR5.1 BETA CHAIN
    Chains: H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 5 - DEAMIDATED GLIADIN-ALPHA2 PEPTIDE
    Chains: J
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HI5
    Expression System Common: CABBAGE LOOPER
    Expression System Taxid: 7111
    Mutation: YES
    Organism Common: BREAD WHEAT
    Organism Scientific: TRITICUM AESTIVUM
    Organism Taxid: 4565

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABGHJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:78binding site for Mono-Saccharide NAG A 1001 bound to ASN A 78
2AC2SOFTWAREVAL A:116 , ASN A:118 , GLU A:166 , TRP A:168binding site for Mono-Saccharide NAG A 1000 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
4G:23 -G:104
5G:151 -G:201
6G:176 -H:184
7H:23 -H:104
8H:158 -H:223

(-) Cis Peptide Bonds  (14, 14)

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:32 -Asn B:33
5Tyr B:123 -Pro B:124
6His G:46 -Ser G:47
7Asp G:147 -Lys G:148
8Ser G:208 -Ile G:209
9Ser H:7 -Pro H:8
10Leu H:46 -Gly H:47
11Gly H:83 -Gly H:84
12Tyr H:164 -Pro H:165
13Ala J:2 -Pro J:3
14Pro J:12 -Gly J:13

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OZF)

(-) 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:181
                                                                                                                                                                                                                     
               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
                 4ozf A   1 IVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHWEPE 181
                                    9A        19        29        39        49  ||    60        70        80        90       100       110       120       130       140       150       160       170       180 
                                    9A                                         52|                                                                                                                               
                                                                                54                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeeeeee....eeeeee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh....eeeeeee..eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee.......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ozf B   3 SPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRA 190
                                    12        22        32        42        52        62        72        82        92       102 ||    119       129       139       149       159       169       179       189 
                                                                                                                               104|                                                                              
                                                                                                                                112                                                                              


Chain G from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee....eeeeee........eeeeeee......eeeeee....ee....eeee.....eeeeee...hhhhheeeeeeee...........eeeeee........eeeeeee....eeeee...............eeeeeeeeee.hhhh.eeeeeeeee...................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ozf G   2 MKTTQPPSMDCAEGRAANLPCNHSTISGNEYVYWYRQIHSQGPQYIIHGLKNNETNEMASLIITEDRKSSTLILPHATLRDTAVYYCIAFQGAQKLVFGQGTRLTINPNIQNPDPAVYQLRDSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDACANAFNNSIIPEDTFFP 217
                                ||  12        22       |37        47        57||   || 77        87        97       107 ||    120       130       140  ||   153       163       173       183       193    || 204       214   
                                6|                    30|                    58|  68|                                109|                           143|                                                198|                 
                                 8                     36                     64   74                                 113                            147                                                 200                 


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......eeeeeee.....eeeeeeee..eeee........eeee......eeeee...hhhhheeeeeeee.........ee...eeeeee.........eeeeee.hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ozf H   3 GVSQSPSNKVTEKGKDVELRCDPISGHTALYWYRQSLGQGLEFLIYFQGNSAPDKSGLPSDRFSAERTGGSVSTLTIQRTQQEDSAVYLCASSFRALAADTQYFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 256
                                    12        22      ||39        49        63        73       |84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254  
                                                     29|                   58|                81|                                                                                                                                                                             
                                                      37                    63                 83                                                                                                                                                                             


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
                 4ozf J   2 APQPELPYPQPGS  14
                                    11
   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 4OZF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 77)

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 4ozg 4ozh 4ozi 5ksa 5ksb 5ksu 5ksv
        DQB1_HUMAN | P01920: 1jk8 1nbn 1s9v 1uvq 2nna 4gg6 4ozg 4ozh 4ozi
        GDA9_WHEAT | P18573: 2nna 4gg6 4ozg 4ozh 4ozi 4z7u 4z7v 4z7w 5ks9
        Q5Y7D3_HUMAN | Q5Y7D3: 4d8p
        TRBC1_HUMAN | P01850: 1ao7 1fyt 1j8h 1kgc 1ktk 1mi5 1oga 1ymm 1zgl 2ak4 2axh 2bnq 2bnr 2bnu 2cde 2cdf 2cdg 2esv 2f53 2f54 2gj6 2ial 2iam 2ian 2nts 2nw2 2nx5 2p5e 2p5w 2po6 2pye 2pyf 2vlj 2vlk 2vlm 2vlr 2xn9 2xna 3arb 3ard 3are 3arf 3arg 3d39 3d3v 3dx9 3dxa 3ffc 3he6 3hg1 3kpr 3kps 3o4l 3tn0 4g8e 4g8f 4gg6 4gg8 4iiq 4jfd 4jfe 4jff 4jfh 4jrx 4jry 4l4t 4l4v 4l9l 4lcc 4lcw 4mji 4mnq 4nqc 4nqd 4nqe 4ozg 4ozh 4ozi 4p46 4prh 4pri 4prp 4x6b 4x6c 4x6d 4zdh
UniProtKB/TrEMBL
        Q2YD82_HUMAN | Q2YD82: 4ozg 4ozh 4ozi
        Q5Y7D3_HUMAN | Q5Y7D3: 4ozg 4ozh 4ozi 5ksu 5ksv

(-) Related Entries Specified in the PDB File

4ozg 4ozh 4ozi