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(-) Description

Title :  TAP-A-ASSOCIATED RAT MHC CLASS I MOLECULE
 
Authors :  M. G. Rudolph, J. Stevens, J. A. Speir, J. Trowsdale, G. W. Butcher, E. Jo I. A. Wilson
Date :  04 Dec 01  (Deposition) - 18 Dec 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B,P
Keywords :  Peptide-Mhc Complex, Heterodimer, Extracellular Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. G. Rudolph, J. Stevens, J. A. Speir, J. Trowsdale, G. W. Butcher, E. Joly, I. A. Wilson
Crystal Structures Of Two Rat Mhc Class Ia (Rt1-A) Molecule That Are Associated Differentially With Peptide Transporter Alleles Tap-A And Tap-B.
J. Mol. Biol. V. 324 975 2002
PubMed-ID: 12470953  |  Reference-DOI: 10.1016/S0022-2836(02)01095-1
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RT1 CLASS I HISTOCOMPATIBILITY ANTIGEN, AA ALPHA CHAIN, HEAVY CHAIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentEXTRACELLULAR DOMAIN, RESIDUES 25-300, NUMBERED 1-276, PLUS C-TERMINAL HIS TAG
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymMHC CLASS I RT1-AA HEAVY CHAIN
 
Molecule 2 - BETA-2-MICROGLOBULIN
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentRESIDUES 21-119, NUMBERED 1-99
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
 
Molecule 3 - B6 PEPTIDE
    ChainsP
    EngineeredYES
    Other DetailsTHE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE WAS DERIVED FROM BIOCHEMICAL BINDING DATA.
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABP

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:86 , LYS A:131 , ARG A:157 , HOH A:329 , HOH A:362BINDING SITE FOR RESIDUE SO4 A 286

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:101 -A:164
2A:203 -A:259
3B:25 -B:80

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:209 -Pro A:210
2His B:31 -Pro B:32

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KJM)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.B2MG_RAT98-104  1B:78-84
HA12_RAT281-287  1A:257-263

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000230171ENSRNOE00000164042chr3:108927919-10892799274B2MG_RAT1-23231B:1-33
1.2ENSRNOT000000230172ENSRNOE00000164162chr3:108930763-108931041279B2MG_RAT23-116941B:3-9694
1.3ENSRNOT000000230173ENSRNOE00000164268chr3:108931555-10893158329B2MG_RAT116-11941B:96-994
1.4ENSRNOT000000230174ENSRNOE00000164313chr3:108932497-108932718222B2MG_RAT-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:277
 aligned with HA12_RAT | P16391 from UniProtKB/Swiss-Prot  Length:371

    Alignment length:277
                                    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       
             HA12_RAT    25 GSHSLRYFYTAVSRPGLGEPRFIAVGYVDDTEFVRFDSDAENPRMEPRARWMEREGPEYWEQQTRIAKEWEQIYRVDLRTLRGYYNQSEGGSHTIQEMYGCDVGSDGSLLRGYRQDAYDGRDYIALNEDLKTWTAADFAAQITRNKWERARYAERLRAYLEGTCVEWLSRYLELGKETLLRSDPPEAHVTLHPRPEGDVTLRCWALGFYPADITLTWQLNGEDLTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVEHEGLPKPLSQRWEPS 301
               SCOP domains d1kjma2 A:1-181 Class I MHC, alpha-1 and alpha-2 domains                                                                                                                             d1kjma1 A:182-277 Class I MHC, alpha-3 domain                                                    SCOP domains
               CATH domains 1kjmA01 A:1-181 Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1                                                                                          1kjmA02 A:182-272 Immunoglobulins                                                          ----- CATH domains
               Pfam domains MHC_I-1kjmA02 A:1-179                                                                                                                                                              ------C1-set-1kjmA01 A:186-271                                                              ------ Pfam domains
         Sec.struct. author .eeeeeeeeeee........eeeeeeee..eeeeeee........ee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeeee....eeeeeeeeee..eeeeee......eee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.....eeeeeeeeee.....eeeeee..ee.....ee...ee.....eeeeeeeee...hhh.eeeeee.......eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kjm A   1 GSHSLRYFYTAVSRPGLGEPRFIAVGYVDDTEFVRFDSDAENPRMEPRARWMEREGPEYWEQQTRIAKEWEQIYRVDLRTLRGYYNQSEGGSHTIQEMYGCDVGSDGSLLRGYRQDAYDGRDYIALNEDLKTWTAADFAAQITRNKWERARYAERLRAYLEGTCVEWLSRYLELGKETLLRSDPPEAHVTLHPRPEGDVTLRCWALGFYPADITLTWQLNGEDLTQDMELVETRPAGDGTFQKWASVVVPLGKEQNYTCRVEHEGLPKPLSQRWEPL 277
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       

Chain B from PDB  Type:PROTEIN  Length:99
 aligned with B2MG_RAT | P07151 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:99
                                    30        40        50        60        70        80        90       100       110         
             B2MG_RAT    21 IQKTPQIQVYSRHPPENGKPNFLNCYVSQFHPPQIEIELLKNGKKIPNIEMSDLSFSKDWSFYILAHTEFTPTETDVYACRVKHVTLKEPKTVTWDRDM 119
               SCOP domains d1kjmb_ B: beta2-microglobulin                                                                      SCOP domains
               CATH domains 1kjmB00 B:1-99 Immunoglobulins                                                                      CATH domains
               Pfam domains ----------C1-set-1kjmB01 B:11-92                                                            ------- Pfam domains
         Sec.struct. author ........eee.........eeeeeeeeee....eeeeeee..ee....ee...ee.....eeeeeeeee.......eeeeeee.......eee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------IG_MHC --------------- PROSITE
           Transcript 1 (1) 1.1--------------------------------------------------------------------------------------------1.3  Transcript 1 (1)
           Transcript 1 (2) --Exon 1.2  PDB: B:3-96 UniProt: 23-116                                                         --- Transcript 1 (2)
                 1kjm B   1 IQKTPQIQVYSRHPPENGKPNFLNCYVSQFHPPQIEIELLKNGKKIPNIEMSDLSFSKDWSFYILAHTEFTPTETDVYACRVKHVTLKEPKTVTWDRDM  99
                                    10        20        30        40        50        60        70        80        90         

Chain P from PDB  Type:PROTEIN  Length:9
                                         
               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
                 1kjm P   1 AQFSASASR   9

   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  (3, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (2, 3)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)
(-)
Clan: MHC (252)

(-) Gene Ontology  (44, 49)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HA12_RAT | P16391)
molecular function
    GO:0042605    peptide antigen binding    Interacting selectively and non-covalently with an antigen peptide.
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: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: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: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: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   (B2MG_RAT | P07151)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
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: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: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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        B2MG_RAT | P071511ed3 1frt 1i1a 1kjv 2frt 3fru
        HA12_RAT | P163911ed3

(-) Related Entries Specified in the PDB File

1ed3 1kjv