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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MURINE CLASS II ALLELE I-A(G7) COMPLEXED WITH THE GLUTAMIC ACID DECARBOXYLASE (GAD65) PEPTIDE 207-220
 
Authors :  A. L. Corper, L. Teyton, I. A. Wilson
Date :  07 Apr 00  (Deposition) - 28 Jun 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Histocompatibility Antigen, Class Ii Mhc I-A(G7), Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Corper, T. Stratmann, V. Apostolopoulos, C. A. Scott, K. C. Garcia, A. S. Kang, I. A. Wilson, L. Teyton
A Structural Framework For Deciphering The Link Between I-Ag7 And Autoimmune Diabetes.
Science V. 288 505 2000
PubMed-ID: 10775108  |  Reference-DOI: 10.1126/SCIENCE.288.5465.505

(-) Compounds

Molecule 1 - H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN
    Chains: A
    Engineered: YES
    Expression System Common: INSECT
    Fragment: ALPHA CHAIN
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - 65 KD GLUTAMIC ACID DECARBOXYLASE+H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN
    Chains: B
    Engineered: YES
    Expression System Common: INSECT
    Fragment: PEPTIDE (RESIDUES 222-235) + BETA CHAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1ES0)

(-) Sites  (0, 0)

(no "Site" information available for 1ES0)

(-) SS Bonds  (3, 3)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser A:15 -Pro A:16
2Phe A:113 -Pro A:114
3Tyr B:123 -Pro B:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ES0)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.HA2D_MOUSE188-194  1A:161-167

(-) Exons   (0, 0)

(no "Exon" information available for 1ES0)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:182
 aligned with HA2D_MOUSE | P04228 from UniProtKB/Swiss-Prot  Length:256

    Alignment length:182
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205  
          HA2D_MOUSE     26 DIEADHVGFYGTTVYQSPGDIGQYTHEFDGDELFYVDLDKKKTVWRLPEFGQLILFEPQGGLQNIAAEKHNLGILTKRSNFTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWEP  207
               SCOP domains d1es0a2 A:1B-82 Class II MHC alpha chain, N-terminal domain                         d1es0a1 A:83-180 Class II MHC alpha chain, C-terminal domain                                       SCOP domains
               CATH domains ---1es0A01 A:2-81                                                                  1es0A02 A:82-180 Immunoglobulins                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeee...eeeeeeee..eeeeeee....eeee...hhhhh...hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC ------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1es0 A   1B DIEADHVGFYGTTVYQSPGDIGQYTHEFDGDELFYVDLDKKKTVWRLPEFGQLILFEPQGGLQNIAAEKHNLGILTKRSNFTPATNEAPQATVFPKSPVLLGQPNTLICFVDNIFPPVINITWLRNSKSVTDGVYETSFLVNRDHSFHKLSYLTFIPSDDDIYDCKVEHWGLEEPVLKHWSS  180
                            ||       8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178  
                            ||                                                                                                                                                                                    
                           1B|                                                                                                                                                                                    
                            1A                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                               
               SCOP domains --------------d1es0b2 B:5-93 Class II MHC beta chain, N-terminal domain                              d1es0b1 B:94-189 Class II MHC beta chain, C-terminal domain                               SCOP domains
               CATH domains --------------1es0B01 B:5-93 Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1    1es0B02 B:94-189 Immunoglobulins                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh....eeeeee..eeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeee........eeeeee.......eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1es0 B 207P YEIAPVFVLLEYVTRHFVHQFKGECYFTNGTQRIRLVTRYIYNREEYLRFDSDVGEYRAVTELGRHSAEYYNKQYLERTRAELDTACRHNYEETEVPTSLRRLEQPNVAISLSNTLVCSVTDFYPAKIKVRWFRNGQEETVGVSSTQLIRNGDWTFQVLVMLEMTPHQGEVYTCHVEHPSLKSPITVEWS  189
                            ||||||216P|||||   10        20        30        40        50        60   |||  72        82        92  |    101  ||   119       129       139       149       159       169       179       189
                         207P|||||216P|||||                                                         64||                        94A       104|                                                                            
                          208P|||||217P||||                                                          66|                                   113                                                                            
                           209P|||||218P|||                                                           68                                                                                                                  
                            210P|||||219P||                                                                                                                                                                               
                             211P|||| 220P|                                                                                                                                                                               
                              212P|||     5                                                                                                                                                                               
                               213P||                                                                                                                                                                                     
                                214P|                                                                                                                                                                                     
                                 215P
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ES0)

(-) Gene Ontology  (42, 45)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HA2D_MOUSE | P04228)
molecular function
    GO:0042605    peptide antigen binding    Interacting selectively and non-covalently with an antigen peptide.
    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: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:0048002    antigen processing and presentation of peptide antigen    The process in which an antigen-presenting cell expresses peptide antigen in association with an MHC protein complex on its cell surface, including proteolysis and transport steps for the peptide antigen both prior to and following assembly with the MHC protein complex. The peptide antigen is typically, but not always, processed from an endogenous or exogenous protein.
    GO:0002504    antigen processing and presentation of peptide or polysaccharide antigen via MHC class II    The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045582    positive regulation of T cell differentiation    Any process that activates or increases the frequency, rate or extent of T cell differentiation.
cellular component
    GO:0042613    MHC class II protein complex    A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
    GO: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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DCE2_HUMAN | Q05329: 2okk
        HA2D_MOUSE | P04228: 1f3j 1iao 2iad 3cup 3mbe 5dmk

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