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(-) Description

Title :  MHC CLASS II BETA CHAIN FROM SEA BASS
 
Authors :  S. Costantini, A. Facchiano
Date :  22 May 06  (Deposition) - 01 May 07  (Release) - 01 May 07  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Mhc Class Ii (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. Buonocore, E. Randelli, D. Casani, S. Costantini, A. Facchiano, G. Scapigliati, R. J. Stet
Molecular Cloning, Differential Expression And 3D Structural Analysis Of The Mhc Class-Ii Beta Chain From Sea Bass (Dicentrarchus Labrax L. )
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MHC CLASS II ANTIGEN BETA CHAIN
    Chains: A
    Fragment: RESIDUES 1-190(17-206 IN SEQ DB)
    Organism Common: EUROPEAN SEA BASS
    Organism Scientific: DICENTRARCHUS LABRAX
    Synonym: MHC CLASS II BETA CHAIN

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2H38)

(-) Sites  (0, 0)

(no "Site" information available for 2H38)

(-) SS Bonds  (2, 2)

Theoretical Model
No.Residues
1A:14 -A:79
2A:117 -A:173

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Tyr A:123 -Pro A:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H38)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2H38)

(-) Exons   (0, 0)

(no "Exon" information available for 2H38)

(-) Sequences/Alignments

Theoretical Model
   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:190
 aligned with Q05HG5_DICLA | Q05HG5 from UniProtKB/TrEMBL  Length:250

    Alignment length:190
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206
         Q05HG5_DICLA    17 YTADGFLNFITTRCDFNSTDLKDIEYINSYYFNKMKYLRFSSSVGEYVGYTELGVKNAERLNKDPSELARRRGEKERYCLTNVNADYQGALDKSVKPYVVLHSVAPPAGKHPSMLVCSVYGFYPKHIRVSWLRDGQEVTSDVTSTDELADADWFYQIHSHLEYTPRSGEKISCVVEHASLREPLVTDWDP 206
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeee.....eeeeeeeee....eeeeee....eeee.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.........eeeeeeeeeee....eeeeee..ee....eee...ee.....eeeeeeeee.......eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h38 A   1 YTADGFLNFITTRCDFNSTDLKDIEYINSYYFNKMKYLRFSSSVGEYVGYTELGVKNAERLNKDPSELARRRGEKERYCLTNVNADYQGALDKSVKPYVVLHSVAPPAGKHPSMLVCSVYGFYPKHIRVSWLRDGQEVTSDVTSTDELADADWFYQIHSHLEYTPRSGEKISCVVEHASLREPLVTDWDP 190
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 2H38)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2H38)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H38)

(-) Gene Ontology  (6, 6)

Theoretical Model(hide GO term definitions)
Chain A   (Q05HG5_DICLA | Q05HG5)
biological process
    GO:0019882    antigen processing and presentation    The process in which an antigen-presenting cell expresses antigen (peptide or lipid) on its cell surface in association with an MHC protein complex.
    GO:0002504    antigen processing and presentation of peptide or polysaccharide antigen via MHC class II    The process in which an antigen-presenting cell expresses antigen (peptide or polysaccharide) on its cell surface in association with an MHC class II protein complex.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
cellular component
    GO:0042613    MHC class II protein complex    A transmembrane protein complex composed of an MHC class II alpha and MHC class II beta chain, and with or without a bound peptide or polysaccharide antigen.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  Cis Peptide Bonds
    Tyr A:123 - Pro A:124   [ RasMol ]  
 

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  2h38
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q05HG5_DICLA | Q05HG5: 2h37

(-) Related Entries Specified in the PDB File

1jl4 MOUSE MHC-II BETA CHAIN STRUCTURE
2h41 THE SAME PROTEIN