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(-) Description

Title :  STRUCTURAL BASIS FOR RECOGNITION OF MUTANT SELF BY A TUMOR-SPECIFIC, MHC CLASS II-RESTRICTED TCR
 
Authors :  L. Deng, R. J. Langley, R. A. Mariuzza
Date :  08 Sep 06  (Deposition) - 03 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D,P
Keywords :  X-Ray Crystallography, Major Histocompatibility Complex, T Cell Receptor, T Cell Stimulation, Melanoma, Tumor Antigen, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Deng, R. J. Langley, P. H. Brown, G. Xu, L. Teng, Q. Wang, M. I. Gonzales, G. G. Callender, M. I. Nishimura, S. L. Topalian, R. A. Mariuzza
Structural Basis For The Recognition Of Mutant Self By A Tumor-Specific, Mhc Class Ii-Restricted T Cell Receptor
Nat. Immunol. V. 8 398 2007
PubMed-ID: 17334368  |  Reference-DOI: 10.1038/NI1447
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPT7-7
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-182 (26-207)
    GeneHLA-DRA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMHC CLASS II ANTIGEN DRA, MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II HLA-DR1 ALPHA CHAIN
 
Molecule 2 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1 BETA CHAIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPT7-7
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 1-190 (30-219)
    GeneHLA-DRB1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMHC CLASS I ANTIGEN DRB1*1, DR-1, DR1, MAJOR HISTOCOMPATIBILITY COMPLEX CLASS II HLA-DR1 BETA CHAIN
 
Molecule 3 - 15-MER PEPTIDE FROM TRIOSEPHOSPHATE ISOMERASE
    ChainsP
    EC Number5.3.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPT7-7
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentRESIDUES 23-37 (22-36)
    GeneTPI1, TPI
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 4 - CD4+ T CELL RECEPTOR E8 ALPHA CHAIN
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPT7-7
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 5 - CD4+ T CELL RECEPTOR E8 BETA CHAIN
    ChainsD
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPT7-7
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit ABCDP

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2IAM)

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:107 -A:163
2B:15 -B:79
3B:117 -B:173
4C:22 -C:86
5C:131 -C:181
6C:156 -D:167
7D:23 -D:91
8D:141 -D:206

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IAM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (25, 25)

Asymmetric/Biological Unit (25, 25)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_033379R33K2B11_HUMANPolymorphism34716432BR4K
02UniProtVAR_033380R33Q2B11_HUMANPolymorphism34716432BR4Q
03UniProtVAR_016740Q39E2B11_HUMANPolymorphism  ---BQ10E
04UniProtVAR_033381S66Y2B11_HUMANPolymorphism16822820BS37Y
05UniProtVAR_016741G74R2B11_HUMANPolymorphism  ---BG45R
06UniProtVAR_033382Y76F2B11_HUMANPolymorphism1060346BY47F
07UniProtVAR_033383Y89S2B11_HUMANPolymorphism36074728BY60S
08UniProtVAR_016710L96I2B11_HUMANPolymorphism  ---BL67I
09UniProtVAR_016711Q99D2B11_HUMANPolymorphism  ---BQ70D
10UniProtVAR_033384Q99E2B11_HUMANPolymorphism17881965BQ70E
11UniProtVAR_033385Q99H2B11_HUMANPolymorphism17879599BQ70H
12UniProtVAR_016742R100A2B11_HUMANPolymorphism  ---BR71A
13UniProtVAR_016712R100E2B11_HUMANPolymorphism  ---BR71E
14UniProtVAR_033386A102G2B11_HUMANPolymorphism17878857BA73G
15UniProtVAR_033387A103E2B11_HUMANPolymorphism16822805BA74E
16UniProtVAR_016713T106N2B11_HUMANPolymorphism16822752BT77N
17UniProtVAR_033388Y107H2B11_HUMANPolymorphism16822512BY78H
18UniProtVAR_016714V114A2B11_HUMANPolymorphism17424145BV85A
19UniProtVAR_016715G115V2B11_HUMANPolymorphism2230810BG86V
20UniProtVAR_033389G164D2B11_HUMANPolymorphism1059633BG135D
21UniProtVAR_033390A169T2B11_HUMANPolymorphism2308768BA140T
22UniProtVAR_033391V171M2B11_HUMANPolymorphism701829BV142M
23UniProtVAR_033392Q178H2B11_HUMANPolymorphism701830BQ149H
24UniProtVAR_033393R195Q2B11_HUMANPolymorphism3205588BR166Q
25UniProtVAR_033394T210I2B11_HUMANPolymorphism17423930BT181I

  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.DRA_HUMAN186-192  1A:161-167
2B11_HUMAN200-206  1B:171-177

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002292701aENSE00001164420chr12:6976283-6976845563TPIS_HUMAN1-76761P:23-3715
1.2eENST000002292702eENSE00000716159chr12:6978028-6978151124TPIS_HUMAN76-117420--
1.3ENST000002292703ENSE00000716160chr12:6978263-697834785TPIS_HUMAN117-145290--
1.4bENST000002292704bENSE00000716161chr12:6978422-6978554133TPIS_HUMAN146-190450--
1.5cENST000002292705cENSE00000716162chr12:6978852-697893786TPIS_HUMAN190-218290--
1.6dENST000002292706dENSE00000716163chr12:6979213-697930088TPIS_HUMAN219-248300--
1.7dENST000002292707dENSE00001385368chr12:6979429-6980112684TPIS_HUMAN248-286390--

2.3ENST000003600043ENSE00001930619chr6:32557625-325574202062B11_HUMAN1-34341B:1-55
2.4ENST000003600044ENSE00001731226chr6:32552155-325518862702B11_HUMAN34-124911B:5-9591
2.5bENST000003600045bENSE00001801024chr6:32549615-325493342822B11_HUMAN124-218951B:95-189 (gaps)95
2.6ENST000003600046ENSE00001717727chr6:32548633-325485231112B11_HUMAN218-255381B:189-1902
2.7ENST000003600047ENSE00001773376chr6:32548047-32548024242B11_HUMAN255-26390--
2.8ENST000003600048ENSE00001954617chr6:32546881-325465463362B11_HUMAN263-26640--

3.6aENST000003832596aENSE00001839042HSCHR6_MHC_QBL:32365090-32365280191DRA_HUMAN1-28281A:3-31
3.7bENST000003832597bENSE00001719010HSCHR6_MHC_QBL:32367694-32367939246DRA_HUMAN28-110831A:3-8583
3.8cENST000003832598cENSE00001737588HSCHR6_MHC_QBL:32368431-32368712282DRA_HUMAN110-204951A:85-17995
3.9aENST000003832599aENSE00001770912HSCHR6_MHC_QBL:32369002-32369167166DRA_HUMAN204-254511A:179-1813
3.10bENST0000038325910bENSE00001925700HSCHR6_MHC_QBL:32369906-32370300395DRA_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:179
 aligned with DRA_HUMAN | P01903 from UniProtKB/Swiss-Prot  Length:254

    Alignment length:179
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197         
            DRA_HUMAN    28 EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD 206
               SCOP domains d2iama2 A:3-81 Class II MHC alpha chain, N-terminal domain                     d2iama1 A:82-181 Class II MHC alpha chain, C-terminal domain                                         SCOP domains
               CATH domains 2iamA01 A:3-81                                                                 2iamA02 A:82-181 Immunoglobulins                                                                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee....eeeeeeee...eeeeee....eeee.hhhhhhhee..hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..ee.....ee...ee.....eeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
           Transcript 3 (1) 3---------------------------------------------------------------------------------Exon 3.8c  PDB: A:85-179 UniProt: 110-204                                                      -- Transcript 3 (1)
           Transcript 3 (2) Exon 3.7b  PDB: A:3-85 UniProt: 28-110                                             ---------------------------------------------------------------------------------------------3.9 Transcript 3 (2)
                 2iam A   3 EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD 181
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172         

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with 2B11_HUMAN | P04229 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:190
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219
           2B11_HUMAN    30 GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA 219
               SCOP domains d2iamb2 B:1-92 Class II MHC beta chain, N-terminal domain                                   d2iamb1 B:93        -190 Class II MHC beta chain, C-terminal domain                                SCOP domains
               CATH domains 2iamB01 B:1-92 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1         2iamB02 B:93        -190 Immunoglobulins                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.--------.eeeeeeeee.....eeeeee..ee....eeeeeeee.....eeeeeeee.......eeeeeee.......eeeeee. Sec.struct. author
             SAPs(SNPs) (1) ---K-----E--------------------------Y-------R-F------------S------I--DA-GE--NH------AV------------------------------------------------D----T-M------H----------------Q--------------I--------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---Q-----------------------------------------------------------------EE----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
             SAPs(SNPs) (3) ---------------------------------------------------------------------H------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs) (3)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
           Transcript 2 (1) 2.3  -----------------------------------------------------------------------------------------Exon 2.5b  PDB: B:95-189 (gaps) UniProt: 124-218                                               - Transcript 2 (1)
           Transcript 2 (2) ----Exon 2.4  PDB: B:5-95 UniProt: 34-124                                                      ---------------------------------------------------------------------------------------------2. Transcript 2 (2)
                 2iam B   1 GDTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPS--------NLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA 190
                                    10        20        30        40        50        60        70        80        90       100   |     -  |    120       130       140       150       160       170       180       190
                                                                                                                                 104      113                                                                             

Chain C from PDB  Type:PROTEIN  Length:198
 aligned with TCA_HUMAN | P01848 from UniProtKB/Swiss-Prot  Length:142

    Alignment length:198
                                                                                                                                       1                                                                                          
                                     -         -         -         -         -         -         -         -         -         -       | 3        13        23        33        43        53        63        73        83        
            TCA_HUMAN     - -----------------------------------------------------------------------------------------------------------PNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKTVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS  91
               SCOP domains d2iamc1 C:1-109 automated matches                                                                            d2iamc2 C:110-198 automated matches                                                       SCOP domains
               CATH domains 2iamC01 C:1-108 Immunoglobulins                                                                             ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eee...eeeee....eeeeeee...eeeeeeeee.....eeeeee...eeeee..eeeee.hhh.eeeeee...hhhhheeeeeeeee.....eee...eeeeee........eeeeeee......eeeeee................ee...eeeeehhhheeeeeeeee......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2iam C   1 IQVEQSPPDLILQEGANSTLRCNFSDSVNNLQWFHQNPWGQLINLFYIPSGTKQNGRLSATTVATERYSLLYISSSQTTDSGVYFCAALIQGAQKLVFGQGTRLTINPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS 198
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190        

Chain D from PDB  Type:PROTEIN  Length:239
 aligned with TRBC1_HUMAN | P01850 from UniProtKB/Swiss-Prot  Length:177

    Alignment length:239
                                                                                                                                         1                                                                                                                                 
                                     -         -         -         -         -         -         -         -         -         -         1        11        21        31        41        51        61        71        81        91       101       111       121         
          TRBC1_HUMAN     - -------------------------------------------------------------------------------------------------------------EDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 130
               SCOP domains d2iamd1 D:2-112 automated matches                                                                              d2iamd2 D:113-240 automated matches                                                                                              SCOP domains
               CATH domains 2iamD01 D:2-111 Immunoglobulins                                                                               2iamD02 D:112-237 Immunoglobulins                                                                                             --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.....eeeeeee.....eeeeeeeee..eeee......eee.........eee...hhhhheeeeeeee.....ee...eeeeee.hhhhh...eeeeee.hhhhhhhhheeeeeeeeeee....eeeeeee..ee....eee....ee.........eeeeeeeeeehhhhhh...eeeeeeee..................eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iam D   2 AGVTQTPKFRILKIGQSMTLQCTQDMNHNYMYWYRQDPGMGLKLIYYSVGAGITDKGEVPNGYNVSRSTTEDFPLRLELAAPSQTSVYFCASTYHGTGYFGEGSWLTVVEDLNKVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRAD 240
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231         

Chain P from PDB  Type:PROTEIN  Length:15
 aligned with TPIS_HUMAN | P60174 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:15
                                    69     
           TPIS_HUMAN    60 GELIGTLNAAKVPAD  74
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .ee............ Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
               Transcript 1 Exon 1.1a       Transcript 1
                 2iam P  23 GELIGILNAAKVPAD  37
                                    32     

   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  (6, 8)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 7)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (70, 114)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DRA_HUMAN | P01903)
molecular function
    GO:0023026    MHC class II protein complex binding    Interacting selectively and non-covalently with the class II major histocompatibility complex.
    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:0050890    cognition    The operation of the mind by which an organism becomes aware of objects of thought or perception; it includes the mental activities associated with thinking, learning, and memory.
    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.
    GO:0002503    peptide antigen assembly with MHC class II protein complex    The binding of a peptide to the antigen binding groove of an MHC class II protein complex.
    GO:0002506    polysaccharide assembly with MHC class II protein complex    The binding of a polysaccharide to the antigen binding groove of an MHC class II protein complex.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0031902    late endosome membrane    The lipid bilayer surrounding a late endosome.
    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   (2B11_HUMAN | P04229)
molecular function
    GO:0023026    MHC class II protein complex binding    Interacting selectively and non-covalently with the class II major histocompatibility complex.
    GO:0042605    peptide antigen binding    Interacting selectively and non-covalently with an antigen peptide.
    GO:0001618    virus receptor activity    Combining with a virus component and mediating entry of the virus into the cell.
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:0042088    T-helper 1 type immune response    An immune response which is associated with resistance to intracellular bacteria, fungi, and protozoa, and pathological conditions such as arthritis, and which is typically orchestrated by the production of particular cytokines by T-helper 1 cells, most notably interferon-gamma, IL-2, and lymphotoxin.
    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:0016045    detection of bacterium    The series of events in which a stimulus from a bacterium is received and converted into a molecular signal.
    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:0002437    inflammatory response to antigenic stimulus    An inflammatory response to an antigenic stimulus, which can be include any number of T cell or B cell epitopes.
    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.
    GO:0042130    negative regulation of T cell proliferation    Any process that stops, prevents or reduces the rate or extent of T cell proliferation.
    GO:0032689    negative regulation of interferon-gamma production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interferon-gamma production. Interferon-gamma is also known as type II interferon.
    GO:0035774    positive regulation of insulin secretion involved in cellular response to glucose stimulus    Any process that increases the frequency, rate or extent of the regulated release of insulin that contributes to the response of a cell to glucose.
    GO:0051262    protein tetramerization    The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
    GO:2001179    regulation of interleukin-10 secretion    Any process that modulates the frequency, rate or extent of interleukin-10 secretion.
    GO:0032673    regulation of interleukin-4 production    Any process that modulates the frequency, rate, or extent of interleukin-4 production.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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:0009897    external side of plasma membrane    The leaflet of the plasma membrane that faces away from the cytoplasm and any proteins embedded or anchored in it or attached to its surface.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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:0031902    late endosome membrane    The lipid bilayer surrounding a late endosome.
    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   (TCA_HUMAN | P01848)
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:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
cellular component
    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.
    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.

Chain D   (TRBC1_HUMAN | P01850)
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:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0050776    regulation of immune response    Any process that modulates the frequency, rate or extent of the immune response, the immunological reaction of an organism to an immunogenic stimulus.
cellular component
    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.
    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.

Chain P   (TPIS_HUMAN | P60174)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004807    triose-phosphate isomerase activity    Catalysis of the reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0061621    canonical glycolysis    The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP.
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    GO:0046166    glyceraldehyde-3-phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of glyceraldehyde-3-phosphate, an important intermediate in glycolysis.
    GO:0019682    glyceraldehyde-3-phosphate metabolic process    The chemical reactions and pathways involving glyceraldehyde-3-phosphate, an important intermediate in glycolysis.
    GO:0019563    glycerol catabolic process    The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
    GO:0006096    glycolytic process    The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0006098    pentose-phosphate shunt    The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        2B11_HUMAN | P042291aqd 1bx2 1dlh 1fyt 1hxy 1jwm 1jws 1jwu 1kg0 1klg 1klu 1lo5 1pyw 1r5i 1seb 1sje 1sjh 1t5w 1t5x 2fse 2g9h 2ian 2icw 2ipk 2oje 2xn9 3l6f 3pdo 3pgc 3pgd 3qxa 3qxd 3s4s 3s5l 4aen 4ah2 4c56 4e41 4fqx 4gbx 4i5b 4ov5 4x5w 4x5x 5v4n
        DRA_HUMAN | P019031a6a 1aqd 1bx2 1d5m 1d5x 1d5z 1d6e 1dlh 1fv1 1fyt 1h15 1hqr 1hxy 1j8h 1jwm 1jws 1jwu 1kg0 1klg 1klu 1lo5 1pyw 1r5i 1seb 1sje 1sjh 1t5w 1t5x 1ymm 1zgl 2fse 2g9h 2ian 2icw 2ipk 2oje 2q6w 2seb 2wbj 2xn9 3c5j 3l6f 3o6f 3pdo 3pgc 3pgd 3qxa 3qxd 3s4s 3s5l 3t0e 4aen 4ah2 4c56 4e41 4fqx 4gbx 4h1l 4h25 4h26 4i5b 4is6 4mcy 4mcz 4md0 4md4 4md5 4mdi 4mdj 4ov5 4x5w 4x5x 4y19 4y1a 5jlz 5lax 5v4m 5v4n
        TCA_HUMAN | P018481ao7 1bd2 1fyt 1j8h 1kgc 1mi5 1oga 1qrn 1qsf 1ymm 1zgl 2ak4 2bnq 2bnr 2bnu 2cdf 2cdg 2esv 2eyr 2eys 2eyt 2f53 2f54 2gj6 2ial 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 5ksa 5ksb
        TPIS_HUMAN | P601741hti 1klg 1klu 1wyi 2ian 2jk2 2vom 4br1 4e41 4poc 4pod 4unk 4unl 4zvj
        TRBC1_HUMAN | P018501ao7 1fyt 1j8h 1kgc 1ktk 1mi5 1oga 1ymm 1zgl 2ak4 2axh 2bnq 2bnr 2bnu 2cde 2cdf 2cdg 2esv 2f53 2f54 2gj6 2ial 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 4ozf 4ozg 4ozh 4ozi 4p46 4prh 4pri 4prp 4x6b 4x6c 4x6d 4zdh

(-) Related Entries Specified in the PDB File

1klg UNBOUND FORM OF E8 LIGAND
1klu UNBOUND FORM OF E8 LIGAND
2ial CD4+ T CELL RECEPTOR E8
2ian THE SAME COMPLEX IN DIFFERENT SPACE GROUP