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(-) Description

Title :  STRUCTURAL AND FUNCTIONAL STUDIES OF THE TRANS-ENCODED HLA-DQ2.3 (DQA1*03:01/DQB1*02:01) MOLECULE
 
Authors :  C. -Y. Kim, K. Hotta, I. I. Mathews, X. Chen
Date :  11 Jan 12  (Deposition) - 14 Mar 12  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Class Ii Mhc, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Tollefsen, K. Hotta, X. Chen, B. Simonsen, K. Swaminathan, I. I. Mathews, L. M. Sollid, C. -Y. Kim
Structural And Functional Studies Of Trans-Encoded Hla-Dq2. (Dqa1*03:01/Dqb1*02:01) Protein Molecule
J. Biol. Chem. V. 287 13611 2012
PubMed-ID: 22362761  |  Reference-DOI: 10.1074/JBC.M111.320374

(-) Compounds

Molecule 1 - HLA-DQA1 PROTEIN
    Chains: A, C
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Cell: SCHNEIDER 2(S2)
    Expression System Plasmid: PRMHA3
    Expression System Taxid: 7227
    Expression System Vector Type: BACULOVIRUS
    Fragment: UNP RESIDUES 24-217
    Gene: HLA-DQA1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MHC CLASS II ANTIGEN
 
Molecule 2 - PEPTIDE FROM GAMMA-GLIADIN,HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DQ BETA 1 CHAIN
    Chains: B, D
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Cell: SCHNEIDER 2(S2)
    Expression System Plasmid: PRMHA3
    Expression System Taxid: 7227
    Expression System Vector Type: BACULOVIRUS
    Gene: HLA-DQB1
    Mutation: YES
    Organism Common: WHEAT, HUMAN
    Organism Scientific: TRITICUM AESTIVUM, HOMO SAPIENS
    Organism Taxid: 4565, 9606
    Other Details: CHIMERA PROTEIN OF PEPTIDE FROM GAMMA-GLIADIN (RESIDUES 68-81 IN UNIPROT Q94G94), LINKER, MHC CLASS II ANTIGEN (RESIDUES 33-230 IN UNIPROT Q5Y7D3)
    Synonym: MHC CLASS II ANTIGEN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:110 , LYS A:140 , ARG B:149BINDING SITE FOR RESIDUE GOL A 301
2AC2SOFTWAREILE A:1 , ARG B:29 , ARG B:39BINDING SITE FOR RESIDUE GOL B 301

(-) SS Bonds  (6, 6)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:17 -Pro A:18
2Phe A:113 -Pro A:114
3Tyr B:123 -Pro B:124
4Gly C:17 -Pro C:18
5Phe C:113 -Pro C:114
6Tyr D:123 -Pro D:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4D8P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4D8P)

(-) Exons   (4, 8)

Asymmetric Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003832471aENSE00001824118HSCHR6_MHC_QBL:32563145-32562981165Q5Y7D3_HUMAN1-37372B:-29-5 (gaps)
D:-29-5 (gaps)		28
28
1.2ENST000003832472ENSE00001798583HSCHR6_MHC_QBL:32561542-32561273270Q5Y7D3_HUMAN37-127912B:5-95
D:5-95		91
91
1.3aENST000003832473aENSE00001697940HSCHR6_MHC_QBL:32558383-32558102282Q5Y7D3_HUMAN127-221952B:95-189 (gaps)
D:95-189 (gaps)		95
95
1.5ENST000003832475ENSE00001604952HSCHR6_MHC_QBL:32557585-32557475111Q5Y7D3_HUMAN221-258382B:189-190
D:189-190		2
2
1.6cENST000003832476cENSE00001809476HSCHR6_MHC_QBL:32556354-32555534821Q5Y7D3_HUMAN258-26140--

(-) 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:184
 aligned with L8E864_HUMAN | L8E864 from UniProtKB/TrEMBL  Length:255

    Alignment length:184
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204    
         L8E864_HUMAN    25 DIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEPEI 208
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeeeee...eeeeee....eeee...........hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee.......eeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d8p A  1B DIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEPEI 182
                            |        9|       18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178    
                            |        9A                                                                                                                                                                             
                           1B                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:193
 aligned with Q5Y7D3_HUMAN | Q5Y7D3 from UniProtKB/TrEMBL  Length:261

    Alignment length:213
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219   
         Q5Y7D3_HUMAN    10 PGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRA 222
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .----------...........--......eeeeeeeeeee....eeee..eeee..eeeeee......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee.--------.eeeeeeeee.....eeeeee...ee....ee...ee.....eeeeeeee.......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a UniProt: 1-37     -----------------------------------------------------------------------------------------Exon 1.3a  PDB: B:95-189 (gaps) UniProt: 127-221                                               - Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.2  PDB: B:5-95 UniProt: 37-127                                                      ---------------------------------------------------------------------------------------------1. Transcript 1 (2)
                 4d8p B -29 P----------QPEQPEQPFPQ--PSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPS--------NLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRA 190
                            |        - |     -20 |  ||   7        17        27        37        47        57        67        77        87        97      |  -     | 117       127       137       147       157       167       177       187   
                          -29        -28       -18  ||                                                                                                  104      113                                                                             
                                                  -17|                                                                                                                                                                                           
                                                     3                                                                                                                                                                                           


Chain C from PDB  Type:PROTEIN  Length:183
 aligned with L8E864_HUMAN | L8E864 from UniProtKB/TrEMBL  Length:255

    Alignment length:183
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204   
         L8E864_HUMAN    25 DIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEPE 207
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeeeee...eeeeee....eeee...........hhhhhhhhhhhhhhhhhhhhhhh.............eee.........eeeeeeeeee.....eeeeee..ee....eee...eee...eeeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4d8p C  1B DIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEPE 181
                            |        9|       18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178   
                           1B        9A                                                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:193
 aligned with Q5Y7D3_HUMAN | Q5Y7D3 from UniProtKB/TrEMBL  Length:261

    Alignment length:213
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219   
         Q5Y7D3_HUMAN    10 PGGLRAATVTLMLSMLSTPVAEGRDSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRA 222
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .----------...........--......eeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eee.--------.eeeeeeeee.....eeeeee.........ee...ee.....eeeeeeee.......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a UniProt: 1-37     -----------------------------------------------------------------------------------------Exon 1.3a  PDB: D:95-189 (gaps) UniProt: 127-221                                               - Transcript 1 (1)
           Transcript 1 (2) ---------------------------Exon 1.2  PDB: D:5-95 UniProt: 37-127                                                      ---------------------------------------------------------------------------------------------1. Transcript 1 (2)
                 4d8p D -29 P----------QPEQPEQPFPQ--PSPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPS--------NLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRA 190
                            |        - |     -20 |  ||   7        17        27        37        47        57        67        77        87        97      |  -     | 117       127       137       147       157       167       177       187   
                          -29        -28       -18  ||                                                                                                  104      113                                                                             
                                                  -17|                                                                                                                                                                                           
                                                     3
   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 4D8P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4D8P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4D8P)

(-) Gene Ontology  (9, 23)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (L8E864_HUMAN | L8E864)
biological process
    GO:0019882    antigen processing and presentation    The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
    GO:0002504    antigen processing and presentation of peptide or polysaccharide antigen via MHC class II    The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
cellular component
    GO:0042613    MHC class II protein complex    A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain B,D   (Q5Y7D3_HUMAN | Q5Y7D3)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0019882    antigen processing and presentation    The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
    GO:0002504    antigen processing and presentation of peptide or polysaccharide antigen via MHC class II    The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
cellular component
    GO:0042613    MHC class II protein complex    A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  4d8p
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  L8E864_HUMAN | L8E864
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  Q5Y7D3_HUMAN | Q5Y7D3
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  Q94G94_WHEAT | Q94G94
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 Related Entries

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

UniProtKB/TrEMBL
        L8E864_HUMAN | L8E864: 5ks9
        Q5Y7D3_HUMAN | Q5Y7D3: 4ozf 4ozg 4ozh 4ozi 5ksu 5ksv

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4D8P)