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(-) Description

Title :  STRUCTURE OF THE MOUSE CD1D-GLC-DAG-S2-INKT TCR COMPLEX
 
Authors :  E. Girardi, E. D. Yu, D. M. Zajonc
Date :  03 Aug 11  (Deposition) - 23 Nov 11  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Antigen Presentation, Glycolipid, Nkt Cells, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Girardi, E. D. Yu, Y. Li, N. Tarumoto, B. Pei, J. Wang, P. Illarionov, Y. Kinjo, M. Kronenberg, D. M. Zajonc
Unique Interplay Between Sugar And Lipid In Determining The Antigenic Potency Of Bacterial Antigens For Nkt Cells.
Plos Biol. V. 9 01189 2011
PubMed-ID: 22069376  |  Reference-DOI: 10.1371/JOURNAL.PBIO.1001189

(-) Compounds

Molecule 1 - ANTIGEN-PRESENTING GLYCOPROTEIN CD1D1
    ChainsA
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPBACP10PH
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS TRANSFER VECTOR
    FragmentRESIDUES 19-297
    GeneCD1.1, CD1D, CD1D1
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - BETA-2-MICROGLOBULIN
    ChainsB
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPBACP10PH
    Expression System Taxid7108
    Expression System Vector TypeBACULOVIRUS TRANSFER VECTOR
    FragmentRESIDUES 21-119
    GeneB2M, BETA-2-MICROGLOBULIN
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 3 - VALPHA14 CHIMERA (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainBL21DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneVALPHA14 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)
    Organism ScientificMUS MUSCULUS, HOMO SAPIENS
    Organism Taxid10090, 9606
 
Molecule 4 - VBETA8.2 CHIMERA (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)
    ChainsD
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30A
    Expression System StrainBL21DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneVBETA8.2 (MOUSE VARIABLE DOMAIN, HUMAN CONSTANT DOMAIN)
    Organism ScientificMUS MUSCULUS, HOMO SAPIENS
    Organism Taxid10090, 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
13TF1Ligand/Ion(2S)-1-(ALPHA-D-GLUCOPYRANOSYLOXY)-3-(HEXADECANOYLOXY)PROPAN-2-YL (11Z)-OCTADEC-11-ENOATE
2FUC1Ligand/IonALPHA-L-FUCOSE
3NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:19 , ASN A:20BINDING SITE FOR RESIDUE NAG A 500
2AC2SOFTWARETRP A:23 , SER A:24 , ASN A:42 , HOH A:294 , NAG A:502BINDING SITE FOR RESIDUE NAG A 501
3AC3SOFTWARENAG A:501BINDING SITE FOR RESIDUE NAG A 502
4AC4SOFTWAREGLN A:161 , ASN A:165 , NAG A:512 , FUC A:513BINDING SITE FOR RESIDUE NAG A 511
5AC5SOFTWAREGLY A:130 , NAG A:511BINDING SITE FOR RESIDUE NAG A 512
6AC6SOFTWARESER A:114 , TRP A:129 , GLY A:130 , ASN A:165 , NAG A:511BINDING SITE FOR RESIDUE FUC A 513
7AC7SOFTWAREGLN A:14 , TYR A:73 , SER A:76 , PHE A:77 , ASP A:80 , PHE A:120 , TRP A:133 , LEU A:150 , ASP A:153 , GLY A:155 , THR A:156 , PRO C:28 , ASN C:30 , ARG C:95 , GLY C:96 , HOH C:221BINDING SITE FOR RESIDUE 3TF A 286

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:104 -A:168
2A:208 -A:263
3B:25 -B:80
4C:22 -C:90
5C:139 -C:189
6D:23 -D:91
7D:142 -D:207

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ser A:89 -Pro A:90
2Tyr A:94 -Pro A:95
3Tyr A:214 -Pro A:215
4His B:31 -Pro B:32
5Ser C:6 -Pro C:7
6Thr C:27 -Pro C:28
7Ser D:7 -Pro D:8
8Tyr D:148 -Pro D:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

Asymmetric/Biological Unit (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_B2MG_MOUSE_002 *H54QB2MG_MOUSE  ---  ---BH34Q
2UniProtVAR_B2MG_MOUSE_003 *K64EB2MG_MOUSE  ---  ---BK44E
3UniProtVAR_B2MG_MOUSE_004 *R101TB2MG_MOUSE  ---  ---BR81T
4UniProtVAR_B2MG_MOUSE_005 *A105DB2MG_MOUSE  ---  ---BA85D
5UniProtVAR_B2MG_MOUSE_006 *A105VB2MG_MOUSE  ---  ---BA85V
   * ID not provided by source

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.B2MG_MOUSE98-104  1B:78-84

(-) Exons   (0, 0)

(no "Exon" information available for 3TA3)

(-) 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:267
 aligned with CD1D1_MOUSE | P11609 from UniProtKB/Swiss-Prot  Length:336

    Alignment length:273
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294   
          CD1D1_MOUSE    25 NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSADGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYW 297
               SCOP domains d3ta3a1 A:7-185 automated matches                                                                                                                                                  d3ta3a2 A:18      6-279 automated matches                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee.....eeeeeeeee..eeeeee.......ee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.....eeeeeeeee..eeeeeee..eeee....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee.------.eeeeeeeee.....eeeeee..ee...eee...ee.....eeeeeeee.........eeeee........eeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ta3 A   7 NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVKMMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLNDTCPLFVRGLLEAGKSDLEKQEKPVAWLSSVP------RQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWYLQATLDVEAGEEAGLACRVKHSSLGGQDIILYW 279
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196|      206       216       226       236       246       256       266       276   
                                                                                                                                                                                                                        197    204                                                                           

Chain B from PDB  Type:PROTEIN  Length:96
 aligned with B2MG_MOUSE | P01887 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:96
                                    31        41        51        61        71        81        91       101       111      
           B2MG_MOUSE    22 QKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDR 117
               SCOP domains d3ta3b_ B: beta2-microglobulin                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeee.........eeeeeeeeee.....eeeeee..ee....ee...ee.....eeeeeeeee.......eeeeee.......eeee... Sec.struct. author
             SAPs(SNPs) (1) --------------------------------Q---------E------------------------------------T---D------------ SAPs(SNPs) (1)
             SAPs(SNPs) (2) -----------------------------------------------------------------------------------V------------ SAPs(SNPs) (2)
                    PROSITE ----------------------------------------------------------------------------IG_MHC ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 3ta3 B   2 QKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDR  97
                                    11        21        31        41        51        61        71        81        91      

Chain C from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains d3ta3c1 C:1-117 automated matches                                                                                 d3ta3c2 C:118-206 automated matches                                                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee......eeeeeee......eeeeee...eeeeee..eeeeee....eeeeee...hhhhheeeeeeee........eee...eeeeee........eeeeeee......eeeeee...............eee...eeeeehhhheeeeeeeeee....hhhhh.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ta3 C   1 TQVEQSPQSLVVRQGENCVLQCNYSVTPDNHLRWFKQDTGKGLVSLTVLVDQKDKTSNGRYSATLDKDAKHSTLHITATLLDDTATYICVVGDRGSALGRLHFGAGTQLIVIPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKDFACANAFNNSIIPEDTFFPS 206
                                    10        20        30        40        50        60||      71        81        91       103       113       123       133       143       153       163       173       183||     194       204  
                                                                                       61|                                  100|                                                                              184|                    
                                                                                        63                                   103                                                                               186                    

Chain D from PDB  Type:PROTEIN  Length:239
 aligned with TRBC2_HUMAN | A0A5B9 from UniProtKB/Swiss-Prot  Length:178

    Alignment length:239
                                                                                                                                           1                                                                                                                               
                                     -         -         -         -         -         -         -         -         -         -         - |       9        19        29        39        49        59        69        79        89        99       109       119         
          TRBC2_HUMAN     - ---------------------------------------------------------------------------------------------------------------DLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVSTDPQPLKEQPALNDSRYCLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 128
               SCOP domains d3ta3d1 D:2-112 automated matches                                                                              d3ta3d2 D:113-240 automated matches                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.....eeeeeee......eeeeee......ee.......eee.....eeeeee...hhhhheeeeeeee......ee...eeeeee.........eeeeee.hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ta3 D   2 AAVTQSPRNKVAVTGGKVTLSCNQTNNHNNMYWYRQDTGHGLRLIHYSYGAGSTEKGDIPDGYKASRPSQENFSLILELATPSQTSVYFCASGDEGYTQYFGPGTRLLVLEDLRNVTPPKVSLFEPSKAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYSLSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 240
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231         

   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  (5, 7)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TA3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TA3)

(-) Gene Ontology  (74, 85)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CD1D1_MOUSE | P11609)
molecular function
    GO:0042608    T cell receptor binding    Interacting selectively and non-covalently with a T cell receptor, the antigen-recognizing receptor on the surface of T cells.
    GO:0030881    beta-2-microglobulin binding    Interacting selectively and non-covalently with beta-2-microglobulin.
    GO:0050839    cell adhesion molecule binding    Interacting selectively and non-covalently with a cell adhesion molecule.
    GO:0030883    endogenous lipid antigen binding    Interacting selectively and non-covalently with an endogenous cellular lipid antigen.
    GO:0030884    exogenous lipid antigen binding    Interacting selectively and non-covalently with an exogenous lipid antigen (examples include microbial lipids and glycolipids).
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    GO:0030882    lipid antigen binding    Interacting selectively and non-covalently with a lipid antigen.
    GO:0071723    lipopeptide binding    Interacting selectively and non-covalently with a lipopeptide, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds and containing a nonprotein group consisting of a lipid or lipids.
    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).
biological process
    GO:0001865    NK T cell differentiation    The process in which a precursor cell type acquires the specialized features of a NK 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:0048006    antigen processing and presentation, endogenous lipid antigen via MHC class Ib    The process in which an antigen-presenting cell expresses lipid antigen of endogenous origin in association with an MHC class Ib protein complex on its cell surface. Class Ib here refers to non-classical class I molecules, such as those of the CD1 family.
    GO:0048007    antigen processing and presentation, exogenous lipid antigen via MHC class Ib    The process in which an antigen-presenting cell expresses lipid antigen of exogenous origin in association with an MHC class Ib protein complex on its cell surface. Class Ib here refers to non-classical class I molecules, such as those of the CD1 family.
    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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0051135    positive regulation of NK T cell activation    Any process that activates or increases the frequency, rate or extent of natural killer T cell activation.
    GO:0051138    positive regulation of NK T cell differentiation    Any process that activates or increases the frequency, rate or extent of natural killer T cell differentiation.
    GO:0001916    positive regulation of T cell mediated cytotoxicity    Any process that activates or increases the frequency, rate or extent of T cell mediated cytotoxicity.
    GO:0042102    positive regulation of T cell proliferation    Any process that activates or increases the rate or extent of T cell proliferation.
    GO:0045078    positive regulation of interferon-gamma biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interferon-gamma.
    GO:0045086    positive regulation of interleukin-2 biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-2.
    GO:0045404    positive regulation of interleukin-4 biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of interleukin-4.
    GO:0043032    positive regulation of macrophage activation    Any process that stimulates, induces or increases the rate of macrophage activation.
    GO:0045059    positive thymic T cell selection    The process of sparing immature T cells in the thymus which react with self-MHC protein complexes with low affinity levels from apoptotic death.
    GO:0033084    regulation of immature T cell proliferation in thymus    Any process that modulates the frequency, rate or extent of immature T cell proliferation in the thymus.
    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:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    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: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:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    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.

Chain B   (B2MG_MOUSE | P01887)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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).
biological process
    GO:0033077    T cell differentiation in thymus    The process in which a precursor cell type acquires the specialized features of a T cell via a differentiation pathway dependent upon transit through the thymus.
    GO:0019731    antibacterial humoral response    An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
    GO:0019885    antigen processing and presentation of endogenous peptide antigen via MHC class I    The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class I protein complex. The peptide antigen is typically, but not always, processed from a whole protein. Class I here refers to classical class I molecules.
    GO:0002479    antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent    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 I protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class I molecule. Class I here refers to classical class I molecules.
    GO:0002481    antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent    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 Ib protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class Ib molecule. Class Ib here refers to non-classical class I molecules, such as those of the HLA-E gene family.
    GO:0002474    antigen processing and presentation of peptide antigen via MHC class I    The process in which an antigen-presenting cell expresses a peptide antigen on its cell surface in association with an MHC class I protein complex. Class I here refers to classical class I molecules.
    GO:0006968    cellular defense response    A defense response that is mediated by cells.
    GO:0071281    cellular response to iron ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron ion stimulus.
    GO:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0050829    defense response to Gram-negative bacterium    Reactions triggered in response to the presence of a Gram-negative bacterium that act to protect the cell or organism.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    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:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
    GO:0010977    negative regulation of neuron projection development    Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:1900121    negative regulation of receptor binding    Any process that stops, prevents or reduces the frequency, rate or extent of a protein or other molecule binding to a receptor.
    GO:0002726    positive regulation of T cell cytokine production    Any process that activates or increases the frequency, rate, or extent of T cell cytokine production.
    GO:0001916    positive regulation of T cell mediated cytotoxicity    Any process that activates or increases the frequency, rate or extent of T cell mediated cytotoxicity.
    GO:1904434    positive regulation of ferrous iron binding    Any process that activates or increases the frequency, rate or extent of ferrous iron binding.
    GO:0032092    positive regulation of protein binding    Any process that activates or increases the frequency, rate or extent of protein binding.
    GO:1900122    positive regulation of receptor binding    Any process that activates or increases the frequency, rate or extent of a protein or other molecule binding to a receptor.
    GO:0048260    positive regulation of receptor-mediated endocytosis    Any process that activates or increases the frequency, rate or extent of receptor mediated endocytosis, the uptake of external materials by cells, utilizing receptors to ensure specificity of transport.
    GO:1904437    positive regulation of transferrin receptor binding    Any process that activates or increases the frequency, rate or extent of transferrin receptor binding.
    GO:0042026    protein refolding    The process carried out by a cell that restores the biological activity of an unfolded or misfolded protein, using helper proteins such as chaperones.
    GO:0003254    regulation of membrane depolarization    Any process that modulates the rate, frequency or extent of membrane depolarization. Membrane depolarization is the process in which membrane potential changes in the depolarizing direction from the resting potential, usually from negative to positive.
    GO:0046686    response to cadmium ion    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0002237    response to molecule of bacterial origin    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin.
    GO:0001895    retina homeostasis    A tissue homeostatic process involved in the maintenance of an internal equilibrium within the retina of the eye, including control of cellular proliferation and death and control of metabolic function.
cellular component
    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:1990712    HFE-transferrin receptor complex    A protein complex containing at least HFE and a transferrin receptor (either TFR1/TFRC or TFR2), proposed to play a role in the sensing of transferrin-bound Fe (Fe2-Tf) on the plasma membrane to regulate hepcidin transcription.
    GO:0042612    MHC class I protein complex    A transmembrane protein complex composed of a MHC class I alpha chain and an invariant beta2-microglobin chain, and with or without a bound peptide antigen. Class I here refers to classical class I molecules.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    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:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030670    phagocytic vesicle membrane    The lipid bilayer surrounding a phagocytic vesicle.
    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   (TRBC2_HUMAN | A0A5B9)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        B2MG_MOUSE | P018871bii 1bqh 1bz9 1cd1 1ddh 1ffn 1ffo 1ffp 1fg2 1fo0 1fzj 1fzk 1fzm 1fzo 1g6r 1g7p 1g7q 1hoc 1inq 1jpf 1jpg 1juf 1k8d 1kbg 1kj2 1kj3 1kpu 1kpv 1l6q 1ld9 1ldp 1leg 1lek 1lk2 1mhc 1mwa 1n3n 1n59 1n5a 1nam 1nan 1nez 1osz 1p1z 1p4l 1pqz 1qo3 1rjy 1rjz 1rk0 1rk1 1s7q 1s7r 1s7s 1s7t 1s7u 1s7v 1s7w 1s7x 1t0m 1t0n 1u58 1vac 1vad 1wbx 1wby 1wbz 1yn6 1yn7 1z5l 1zhb 1zhn 1zt1 1zt7 2akr 2ckb 2clv 2clz 2fik 2fo4 2fwo 2gaz 2mha 2ol3 2q7y 2qri 2qrs 2qrt 2vaa 2vab 2ve6 2zok 2zol 2zsv 2zsw 3arb 3ard 3are 3arf 3arg 3au1 3buy 3c8k 3cc5 3cch 3ch1 3cpl 3cvh 3dmm 3e6f 3e6h 3ecb 3fol 3fom 3fon 3ftg 3g08 3gml 3gmm 3gmn 3gmo 3gmp 3gmq 3gmr 3he6 3he7 3ilp 3ilq 3l3h 3ma7 3nwm 3o8x 3o9w 3p4m 3p4n 3p4o 3p9l 3p9m 3pab 3pqy 3pwu 3qi9 3quk 3qul 3qux 3quy 3quz 3rgv 3rol 3roo 3rtq 3rug 3rzc 3scm 3sda 3sdc 3sdd 3t1f 3tbs 3tbt 3tbv 3tbw 3tby 3tn0 3to4 3tvm 3ubx 3vj6 3ws3 3ws6 4apq 4ei5 4elm 4hs3 4huu 4huv 4huw 4hux 4hv8 4iho 4irj 4irs 4l8b 4l8c 4l8d 4mng 4mq7 4mx7 4nsk 4pg2 4pg9 4pgb 4pgc 4pgd 4pge 4pv8 4pv9 4y16 4y2d 4y4f 4y4h 4y4k 4zak 4zus 4zut 4zuu 4zuv 4zuw 5e8n 5e8o 5e8p 5efi 5fkp 5ivx 5j6g 5j6h 5jwd 5jwe 5sws 5swz
        CD1D1_MOUSE | P116091cd1 1z5l 1zhn 2akr 2fik 2gaz 2q7y 3arb 3ard 3are 3arf 3arg 3au1 3g08 3gml 3gmm 3gmn 3gmo 3gmp 3gmq 3gmr 3he6 3he7 3ilp 3ilq 3ma7 3o8x 3o9w 3qi9 3qux 3quy 3quz 3rtq 3rug 3rzc 3scm 3sda 3sdc 3sdd 3t1f 3tn0 3to4 3tvm 3ubx 4apq 4ei5 4elm 4irj 4irs 4mng 4mq7 4mx7 4y16 4y2d 4y4f 4y4h 4y4k 4zak 5efi 5fkp
        TRBC2_HUMAN | A0A5B91ao7 1bd2 2eyr 2eys 2eyt 3kxf 3o6f 3o8x 3o9w 3qux 3t0e 3tvm 4c56 4mvb 4mxq 4n0c 4n5e 4nhu 4onh 4p4k 4udt 4udu 4ww1 4ww2 4wwk 4y16 4y2d 4y4f 4y4h 4y4k 4zak 4zez 5brz 5bs0 5c07 5c08 5c09 5c0a 5c0b 5c0c 5eu6 5fk9 5fka 5hhm 5hho 5hyj 5ks9 5ksa 5ksb

(-) Related Entries Specified in the PDB File

3t1f