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(-) Description

Title :  STRUCTURE OF THE MHC CLASS II MOLECULE HLA-DQ8 BOUND WITH A DEAMIDATED GLUTEN PEPTIDE
 
Authors :  K. N. Henderson, J. A. Tye-Din, J. Rossjohn, R. P. Anderson
Date :  24 Oct 06  (Deposition) - 04 Sep 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Major Histocompatibility Complex Hla-Dq8, Deamidated Gluten Peptide, Post Translational Modification, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. N. Henderson, J. A. Tye-Din, H. H. Reid, Z. Chen, N. A. Borg, T. Beissbarth, A. Tatham, S. I. Mannering, A. W. Purcell, N. L. Dudek, D. A. Van Heel, J. Mccluskey, J. Rossjohn, R. P. Anderson
A Structural And Immunological Basis For The Role Of Human Leukocyte Antigen Dq8 In Celiac Disease
Immunity V. 27 23 2007
PubMed-ID: 17629515  |  Reference-DOI: 10.1016/J.IMMUNI.2007.05.015

(-) Compounds

Molecule 1 - MHC CLASS II ANTIGEN
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFASTBACDUAL
    Expression System StrainHI5 CELLS
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentRESIDUES IN DATABASE 24-207
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - MHC CLASS II ANTIGEN
    ChainsB
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPFASTBACDUAL
    Expression System StrainHI5 CELLS
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS
    FragmentRESIDUES IN DATABASE 33-224
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - GLUTEN PEPTIDE
    ChainsC
    EngineeredYES
    Other DetailsTHE C TERMINUS OF CHAIN C WAS LINKED TO THE N TERMINUS OF CHAIN B WITH A FLEXIBLE SERINE GLYCINE LINKER. THIS FLEXIBLE LINKER WAS CLEAVED WITH TRYPSIN AT AN UNKNOWN POINT IN THE SEQUENCE DURING THE PURIFICATION PROCESS.
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2NNA)

(-) Sites  (0, 0)

(no "Site" information available for 2NNA)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:107 -A:163
2B:15 -B:79
3B:117 -B:173

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:17 -Pro A:18
2Phe A:113 -Pro A:114
3Tyr B:123 -Pro B:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (123, 123)

Asymmetric/Biological Unit (123, 123)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
001UniProtVAR_050382D25GDQA1_HUMANPolymorphism12722042AD0G
002UniProtVAR_062688S35PDQB1_HUMANPolymorphism12722106BS3P
003UniProtVAR_060494Y34CDQA1_HUMANPolymorphism1129740AY9C
004UniProtVAR_062689Y41FDQB1_HUMANPolymorphism9274407BY9F
005UniProtVAR_062690Y41LDQB1_HUMANPolymorphism  ---BY9L
006UniProtVAR_062691F43LDQB1_HUMANPolymorphism56173496BF11L
007UniProtVAR_061472A45GDQB1_HUMANPolymorphism1130375BG13G
008UniProtVAR_061473M46LDQB1_HUMANPolymorphism1130368BM14L
009UniProtVAR_033401S41FDQA1_HUMANPolymorphism1071630AS15F
010UniProtVAR_060495P44LDQA1_HUMANPolymorphism41549715AP18L
011UniProtVAR_033402Y48FDQA1_HUMANPolymorphism12722051AY22F
012UniProtVAR_062692R55LDQB1_HUMANPolymorphism41540813BR23L
013UniProtVAR_033403T49SDQA1_HUMANPolymorphism3188011AS23S
014UniProtVAR_062693Y58GDQB1_HUMANPolymorphism  ---BL26G
015UniProtVAR_062694Y58LDQB1_HUMANPolymorphism766817072BL26L
016UniProtVAR_062695V59LDQB1_HUMANPolymorphism41563539BV27L
017UniProtVAR_062696T60SDQB1_HUMANPolymorphism9274405BT28S
018UniProtVAR_062697Y62HDQB1_HUMANPolymorphism281862065BY30H
019UniProtVAR_062698Y62SDQB1_HUMANPolymorphism  ---BY30S
020UniProtVAR_014604Q57EDQA1_HUMANPolymorphism10093AE31E
021UniProtVAR_062699Y69DDQB1_HUMANPolymorphism1130370BY37D
022UniProtVAR_060496G63EDQA1_HUMANPolymorphism1142323AE37E
023UniProtVAR_062700Y69IDQB1_HUMANPolymorphism  ---BY37I
024UniProtVAR_050383R64KDQA1_HUMANPolymorphism36219699AR38K
025UniProtVAR_062701A70TDQB1_HUMANPolymorphism45519640BA38T
026UniProtVAR_062702A70VDQB1_HUMANPolymorphism1063318BA38V
027UniProtVAR_060497T67ADQA1_HUMANPolymorphism41543221AT41A
028UniProtVAR_060498V68ADQA1_HUMANPolymorphism1142324AV42A
029UniProtVAR_060499C70KDQA1_HUMANPolymorphism  ---AQ44K
030UniProtVAR_060500C70QDQA1_HUMANPolymorphism  ---AQ44Q
031UniProtVAR_060501C70RDQA1_HUMANPolymorphism1142326AQ44R
032UniProtVAR_033404C70YDQA1_HUMANPolymorphism3207983AQ44Y
033UniProtVAR_062703E77GDQB1_HUMANPolymorphism1049083BG45G
034UniProtVAR_060502L71WDQA1_HUMANPolymorphism1142328AL45W
035UniProtVAR_062704V78EDQB1_HUMANPolymorphism9274398BV46E
036UniProtVAR_033406V73DDQA1_HUMANPolymorphism760671632AL47D
037UniProtVAR_060503V73EDQA1_HUMANPolymorphism3208105AL47E
038UniProtVAR_062705Y79FDQB1_HUMANPolymorphism9274397BY47F
039UniProtVAR_033405V73LDQA1_HUMANPolymorphism12722061AL47L
040UniProtVAR_060504L74FDQA1_HUMANPolymorphism9272698AF48F
041UniProtVAR_060505R75HDQA1_HUMANPolymorphism  ---AR49H
042UniProtVAR_060506R75SDQA1_HUMANPolymorphism9272699AR49S
043UniProtVAR_062706A81VDQB1_HUMANPolymorphism41558214BA49V
044UniProtVAR_060507Q76KDQA1_HUMANPolymorphism1048052AR50K
045UniProtVAR_060508Q76RDQA1_HUMANPolymorphism12722069AR50R
046UniProtVAR_060509F77LDQA1_HUMANPolymorphism3188043AF51L
047UniProtVAR_062707P84LDQB1_HUMANPolymorphism9274395BP52L
048UniProtVAR_033407R78SDQA1_HUMANPolymorphism36219345AR52S
049UniProtVAR_062708L85QDQB1_HUMANPolymorphism1140313BL53Q
050UniProtVAR_062709P87LDQB1_HUMANPolymorphism1130380BP55L
051UniProtVAR_062710P87QDQB1_HUMANPolymorphism1130380BP55Q
052UniProtVAR_062711P87RDQB1_HUMANPolymorphism1130380BP55R
053UniProtVAR_062712P88LDQB1_HUMANPolymorphism1130381BP56L
054UniProtVAR_060512P81RDQA1_HUMANPolymorphism41541412AP56R
055UniProtVAR_062713D89ADQB1_HUMANPolymorphism1071637BA57A
056UniProtVAR_062714D89SDQB1_HUMANPolymorphism  ---BA57S
057UniProtVAR_062715D89VDQB1_HUMANPolymorphism1071637BA57V
058UniProtVAR_060513F83GDQA1_HUMANPolymorphism  ---AF58G
059UniProtVAR_062716Y92NDQB1_HUMANPolymorphism41562414BY60N
060UniProtVAR_033408T86RDQA1_HUMANPolymorphism1048073AT61R
061UniProtVAR_062717N94KDQB1_HUMANPolymorphism1130382BN62K
062UniProtVAR_033409I88MDQA1_HUMANPolymorphism1048080AI63M
063UniProtVAR_062718S95RDQB1_HUMANPolymorphism41556215BS63R
064UniProtVAR_060514L91ADQA1_HUMANPolymorphism  ---AL66A
065UniProtVAR_062719E98DDQB1_HUMANPolymorphism9274390BE66D
066UniProtVAR_060515L91TDQA1_HUMANPolymorphism  ---AL66T
067UniProtVAR_033410L91VDQA1_HUMANPolymorphism1048085AL66V
068UniProtVAR_062720V99DDQB1_HUMANPolymorphism41563814BV67D
069UniProtVAR_062721V99IDQB1_HUMANPolymorphism9274390BV67I
070UniProtVAR_062722R102EDQB1_HUMANPolymorphism  ---BR70E
071UniProtVAR_062723R102GDQB1_HUMANPolymorphism1130386BR70G
072UniProtVAR_062724T103ADQB1_HUMANPolymorphism1130390BT71A
073UniProtVAR_062725T103DDQB1_HUMANPolymorphism  ---BT71D
074UniProtVAR_062726T103KDQB1_HUMANPolymorphism  ---BT71K
075UniProtVAR_060516S97IDQA1_HUMANPolymorphism9279910AI72I
076UniProtVAR_060517L98MDQA1_HUMANPolymorphism1064944AV73M
077UniProtVAR_060518L98VDQA1_HUMANPolymorphism1064944AV73V
078UniProtVAR_062727E106ADQB1_HUMANPolymorphism1130387BE74A
079UniProtVAR_062728E106SDQB1_HUMANPolymorphism  ---BE74S
080UniProtVAR_062729L107VDQB1_HUMANPolymorphism9274384BL75V
081UniProtVAR_060519R101CDQA1_HUMANPolymorphism41542116AR76C
082UniProtVAR_062730T109RDQB1_HUMANPolymorphism1130392BT77R
083UniProtVAR_050384S102YDQA1_HUMANPolymorphism1129808AS77Y
084UniProtVAR_062731Q116EDQB1_HUMANPolymorphism1140316BQ84E
085UniProtVAR_062732L117VDQB1_HUMANPolymorphism1140317BL85V
086UniProtVAR_062733E118ADQB1_HUMANPolymorphism9274380BE86A
087UniProtVAR_062734E118GDQB1_HUMANPolymorphism9274380BE86G
088UniProtVAR_062735L119FDQB1_HUMANPolymorphism9274379BL87F
089UniProtVAR_062736L119YDQB1_HUMANPolymorphism  ---BL87Y
090UniProtVAR_062737T121GDQB1_HUMANPolymorphism  ---BT89G
091UniProtVAR_062738T122IDQB1_HUMANPolymorphism1140320BT90I
092UniProtVAR_060520L124VDQA1_HUMANPolymorphism41555012AL99V
093UniProtVAR_050385I129TDQA1_HUMANPolymorphism707952AT104T
094UniProtVAR_056571V148IDQB1_HUMANPolymorphism1049100BV116I
095UniProtVAR_062739A157GDQB1_HUMANPolymorphism1063322BA125G
096UniProtVAR_062740A157SDQB1_HUMANPolymorphism  ---BA125S
097UniProtVAR_062741Q158HDQB1_HUMANPolymorphism41542812BQ126H
098UniProtVAR_050386H151QDQA1_HUMANPolymorphism707950AH126Q
099UniProtVAR_060521S152ADQA1_HUMANPolymorphism41547417AS127A
100UniProtVAR_062742R162QDQB1_HUMANPolymorphism41544112BR130Q
101UniProtVAR_062744R165QDQB1_HUMANPolymorphism9273989BR133Q
102UniProtVAR_062743R165WDQB1_HUMANPolymorphism63626961BR133W
103UniProtVAR_062745D167GDQB1_HUMANPolymorphism2647032BD135G
104UniProtVAR_060522T160IDQA1_HUMANPolymorphism41545514AT135I
105UniProtVAR_062746Q168EDQB1_HUMANPolymorphism9273981BQ136E
106UniProtVAR_060524S161IDQA1_HUMANPolymorphism41544114AS136I
107UniProtVAR_060523S161RDQA1_HUMANPolymorphism41552014AS136R
108UniProtVAR_062747T172ADQB1_HUMANPolymorphism1063323BT140A
109UniProtVAR_060525Y175HDQA1_HUMANPolymorphism41550317AY150H
110UniProtVAR_060526L178FDQA1_HUMANPolymorphism707949AF153F
111UniProtVAR_060527A182DDQA1_HUMANPolymorphism7990AA157D
112UniProtVAR_060528A182SDQA1_HUMANPolymorphism41561312AA157S
113UniProtVAR_060529E183DDQA1_HUMANPolymorphism707963AD158D
114UniProtVAR_060530S185IDQA1_HUMANPolymorphism707962AI160I
115UniProtVAR_056572E194DDQB1_HUMANPolymorphism9273952BE162D
116UniProtVAR_059522P197LDQB1_HUMANPolymorphism9273948BP165L
117UniProtVAR_062748H199RDQB1_HUMANPolymorphism701564BR167R
118UniProtVAR_062750V202IDQB1_HUMANPolymorphism80255621BV170I
119UniProtVAR_060531K197EDQA1_HUMANPolymorphism2308891AE172E
120UniProtVAR_060532K197QDQA1_HUMANPolymorphism2308891AE172Q
121UniProtVAR_062751N214SDQB1_HUMANPolymorphism1130398BN182S
122UniProtVAR_062752T217IDQB1_HUMANPolymorphism1130399BI185I
123UniProtVAR_062753V218ADQB1_HUMANPolymorphism281864132BV186A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.DQA1_HUMAN186-192  1A:161-167
DQB1_HUMAN203-209  1B:171-177

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000003996781cENSE00001539590HSCHR6_MHC_QBL:32538667-32538767101DQA1_HUMAN1-28281A:0-34
1.2ENST000003996782ENSE00001673504HSCHR6_MHC_QBL:32542587-32542832246DQA1_HUMAN28-110831A:3-8584
1.3ENST000003996783ENSE00001753792HSCHR6_MHC_QBL:32543245-32543526282DQA1_HUMAN110-204951A:85-17995
1.6ENST000003996786ENSE00001747600HSCHR6_MHC_QBL:32543890-32544064175DQA1_HUMAN204-254511A:179-1802
1.7bENST000003996787bENSE00001539587HSCHR6_MHC_QBL:32544431-32544863433DQA1_HUMAN-00--

(-) 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
 aligned with DQA1_HUMAN | P01909 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:182
                                                                                  79                                                                                                                              
                                                                                78 |                                                                                                                              
                                    34        44        54        64        74   | |  83        93       103       113       123       133       143       153       163       173       183       193       203  
           DQA1_HUMAN    25 DIVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFR-FDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHWEP 205
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---2nnaA01 A:3-81                                                                  2nnaA02 A:82-180 Immunoglobulins                                                                    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) (1) G--------C------F--L---FS-------E-----EK--AA-KW-DFHKLS---R-G--R-M--A-----IM--CY---------------------V----T---------------------QA-------II-------------H--F---DD-I-----------E-------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------Q--E-SR---------------T------V--------------------------------------------------------------R--------------------S--------------Q-------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------------------R--L------------------V------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (3)
             SAPs(SNPs) (4) ---------------------------------------------Y---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (4)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
           Transcript 1 (1) 1.1c----------------------------------------------------------------------------------Exon 1.3  PDB: A:85-179 UniProt: 110-204                                                       - Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.2  PDB: A:3-85 UniProt: 28-110                                               ---------------------------------------------------------------------------------------------1. Transcript 1 (2)
                 2nna A   0 DIVADHVASYGVNLYQSYGPSGQYSHEFDGDEEFYVDLERKETVWQLPLFRRFRRFDPQFALTNIAVLKHNLNIVIKRSNSTAATNEVPEVTVFSKSPVTLGQPNTLICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTFLPSADEIYDCKVEHWGLDEPLLKHWEP 180
                                     9|       18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178  
                                     9A                                                                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with DQB1_HUMAN | P01920 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:192
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  
           DQB1_HUMAN    31 EGRDSPEDFVYQFKAMCYFTNGTERVRYVTRYIYNREEYARFDSDVEVYRAVTPLGPPDAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQHGDVYTCHVEHPSLQNPITVEWRA 222
               SCOP domains --------d2nnab2 B:7-92 Class II MHC beta chain, N-terminal domain                             d2nnab1 B:9          3-190 Class II MHC beta chain, C-terminal domain                              SCOP domains
               CATH domains 2nnaB01 B:-1-92 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1          2nnaB02 B:9          3-190 Immunoglobulins                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh....eeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.----------.eeeeeeee.....eeeeee..ee....eee...ee.....eeeeeee.........eeeeee.......eeeee.. Sec.struct. author
             SAPs(SNPs) (1) ----P-----F-L-GL--------L--GLS-H------DT------GEF-V--LQ-LLA--N-KR--DD--EA--AV-R------EVAF-GI-------------------------I--------GH---Q--Q-GE---A---------------------D--L-R--I-----------S--IA---- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------L----------------L---S------IV----------------Q-S---------I--GD--S-----------GY-------------------------------------S-------W--------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) --------------------------------------------------------R-V-------------K----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nna B  -1 GSRDSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISP----------LLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEWRA 190
                                     8        18        28        38        48        58        68        78        88        98    |    -     | 118       128       138       148       158       168       178       188  
                                                                                                                                  103        114                                                                            

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with U3PYM0_HUMAN | U3PYM0 from UniProtKB/TrEMBL  Length:261

    Alignment length:192
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  
         U3PYM0_HUMAN    31 EGRDSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEWRA 222
               SCOP domains --------d2nnab2 B:7-92 Class II MHC beta chain, N-terminal domain                             d2nnab1 B:9          3-190 Class II MHC beta chain, C-terminal domain                              SCOP domains
               CATH domains 2nnaB01 B:-1-92 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1          2nnaB02 B:9          3-190 Immunoglobulins                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh....eeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.----------.eeeeeeee.....eeeeee..ee....eee...ee.....eeeeeee.........eeeeee.......eeeee.. Sec.struct. author
             SAPs(SNPs) (1) ----P-----F-L-GL--------L--GLS-H------DT------GEF-V--LQ-LLA--N-KR--DD--EA--AV-R------EVAF-GI-------------------------I--------GH---Q--Q-GE---A---------------------D--L-R--I-----------S--IA---- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------L----------------L---S------IV----------------Q-S---------I--GD--S-----------GY-------------------------------------S-------W--------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) --------------------------------------------------------R-V-------------K----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (3)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2nna B  -1 GSRDSPEDFVYQFKGMCYFTNGTERVRLVTRYIYNREEYARFDSDVGVYRAVTPLGPPAAEYWNSQKEVLERTRAELDTVCRHNYQLELRTTLQRRVEPTVTISP----------LLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQNPIIVEWRA 190
                                     8        18        28        38        48        58        68        78        88        98    |    -     | 118       128       138       148       158       168       178       188  
                                                                                                                                  103        114                                                                            

Chain C from PDB  Type:PROTEIN  Length:13
 aligned with GDA9_WHEAT | P18573 from UniProtKB/Swiss-Prot  Length:307

    Alignment length:13
                                   256   
           GDA9_WHEAT   247 SGQGSFQPSQQNP 259
               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
                 2nna C   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2NNA)

(-) Gene Ontology  (32, 67)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DQA1_HUMAN | P01909)
molecular function
    GO:0032395    MHC class II receptor activity    Combining with an MHC class II protein complex and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0042605    peptide antigen binding    Interacting selectively and non-covalently with an antigen peptide.
biological process
    GO:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    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:0019886    antigen processing and presentation of exogenous peptide antigen via MHC class II    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
    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.
    GO:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
cellular component
    GO:0012507    ER to Golgi transport vesicle membrane    The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    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:0030669    clathrin-coated endocytic vesicle membrane    The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
    GO:0030666    endocytic vesicle membrane    The lipid bilayer surrounding an endocytic vesicle.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0071556    integral component of lumenal side of endoplasmic reticulum membrane    The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the lumenal side of the membrane.
    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:0005887    integral component of plasma membrane    The component of the plasma 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:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0032588    trans-Golgi network membrane    The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network.
    GO:0030658    transport vesicle membrane    The lipid bilayer surrounding a transport vesicle.

Chain B   (U3PYM0_HUMAN | U3PYM0)
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   (DQB1_HUMAN | P01920)
molecular function
    GO:0032395    MHC class II receptor activity    Combining with an MHC class II protein complex and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0042605    peptide antigen binding    Interacting selectively and non-covalently with an antigen peptide.
biological process
    GO:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    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:0019886    antigen processing and presentation of exogenous peptide antigen via MHC class II    The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class II protein complex. The peptide antigen is typically, but not always, processed from a whole protein.
    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:0002455    humoral immune response mediated by circulating immunoglobulin    An immune response dependent upon secreted immunoglobulin. An example of this process is found in Mus musculus.
    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.
    GO:0002381    immunoglobulin production involved in immunoglobulin mediated immune response    The appearance of immunoglobulin due to biosynthesis or secretion following a cellular stimulus during an immune response, resulting in an increase in its intracellular or extracellular levels.
    GO:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
cellular component
    GO:0012507    ER to Golgi transport vesicle membrane    The lipid bilayer surrounding a vesicle transporting substances from the endoplasmic reticulum to the Golgi.
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    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:0030669    clathrin-coated endocytic vesicle membrane    The lipid bilayer surrounding a clathrin-coated endocytic vesicle.
    GO:0030666    endocytic vesicle membrane    The lipid bilayer surrounding an endocytic vesicle.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0010008    endosome membrane    The lipid bilayer surrounding an endosome.
    GO:0071556    integral component of lumenal side of endoplasmic reticulum membrane    The component of the endoplasmic reticulum membrane consisting of the gene products that penetrate only the lumenal side of the membrane.
    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:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0032588    trans-Golgi network membrane    The lipid bilayer surrounding any of the compartments that make up the trans-Golgi network.
    GO:0030658    transport vesicle membrane    The lipid bilayer surrounding a transport vesicle.

Chain C   (GDA9_WHEAT | P18573)
molecular function
    GO:0045735    nutrient reservoir activity    Functions in the storage of nutritious substrates.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DQA1_HUMAN | P019091jk8 1nbn 1s9v 1uvq 4gg6 4ozf 4ozg 4ozh 4ozi 5ksa 5ksb 5ksu 5ksv
        DQB1_HUMAN | P019201jk8 1nbn 1s9v 1uvq 4gg6 4ozf 4ozg 4ozh 4ozi
        GDA9_WHEAT | P185734gg6 4ozf 4ozg 4ozh 4ozi 4z7u 4z7v 4z7w 5ks9
        U3PYM0_HUMAN | U3PYM05ks9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2NNA)