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(-) Description

Title :  RHESUS MACAQUE MHC CLASS I MOLECULE MAMU-B*17-QW9
 
Authors :  Y. Wu, F. Gao, J. Liu, J. X. Qi, D. A. Price, G. F. Gao
Date :  09 May 11  (Deposition) - 21 Mar 12  (Release) - 21 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Antigenic Peptides, T Lymphocytes, Immune Response, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Wu, F. Gao, J. Liu, J. X. Qi, E. Gostick, D. A. Price, G. F. Gao
Structural Basis Of Diverse Peptide Accommodation By The Rhesus Macaque Mhc Class I Molecule Mamu-B*17: Insights Int Immune Protection From Simian Immunodeficiency Virus
J. Immunol. V. 187 6382 2011
PubMed-ID: 22084443  |  Reference-DOI: 10.4049/JIMMUNOL.1101726

(-) Compounds

Molecule 1 - MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 24-297
    Gene: MHCI-B
    Organism Common: RHESUS MACAQUE
    Organism Scientific: MACACA MULATTA
    Organism Taxid: 9544
 
Molecule 2 - BETA-2-MICROGLOBULIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: B2M
    Organism Common: RHESUS MACAQUE
    Organism Scientific: MACACA MULATTA
    Organism Taxid: 9544
 
Molecule 3 - NEF QW9 PEPTIDE FROM PROTEIN NEF
    Chains: C
    Engineered: YES
    Organism Common: SIV-CPZ
    Organism Scientific: SIMIAN IMMUNODEFICIENCY VIRUS
    Organism Taxid: 11723
    Other Details: SYNTHTIC PEPTIDE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3RWF)

(-) Sites  (0, 0)

(no "Site" information available for 3RWF)

(-) 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 3RWF)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.B2MG_MACMU98-104  1B:78-84

(-) Exons   (0, 0)

(no "Exon" information available for 3RWF)

(-) 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:276
 aligned with Q9GJ77_MACMU | Q9GJ77 from UniProtKB/TrEMBL  Length:361

    Alignment length:276
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293      
         Q9GJ77_MACMU    24 GSHSMKYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAESPREEPRAPWVEQEGPEYWEEATRRAKEAAQTHRENLRTALRYYNQSEAGSHTIQKMYGCDLGPDGRLLRGYHQSAYDGKDYIALNGDLRSWTAADMAAQNTQRKWEGNRYAERFRAYLEGECLEWLRRYLENGKETLQRADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEEQTQDTEFVETRPGGDGTFQKWGAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEP 299
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeee........eeeeeeee..eeeeeee........ee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeee.....eeeeeeeeee..eeeeee......eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee....eeeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeee..hhh.eeeeee.......eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3rwf A   1 GSHSMKYFYTSVSRPGRGEPRFISVGYVDDTQFVRFDSDAESPREEPRAPWVEQEGPEYWEEATRRAKEAAQTHRENLRTALRYYNQSEAGSHTIQKMYGCDLGPDGRLLRGYHQSAYDGKDYIALNGDLRSWTAADMAAQNTQRKWEGNRYAERFRAYLEGECLEWLRRYLENGKETLQRADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEEQTQDTEFVETRPGGDGTFQKWGAVVVPSGEEQRYTCHVQHEGLPEPLTLRWEP 276
                                    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:100
 aligned with B2MG_MACMU | Q6V7J5 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:100
                                    29        39        49        59        69        79        89        99       109       119
           B2MG_MACMU    20 AIQRTPKIQVYSRHPPENGKPNFLNCYVSGFHPSDIEVDLLKNGEKMGKVEHSDLSFSKDWSFYLLYYTEFTPNEKDEYACRVNHVTLSGPRTVKWDRDM 119
               SCOP domains ---------------------------------------------------------------------------------------------------- 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) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------IG_MHC --------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3rwf B   0 MIQRTPKIQVYSRHPPENGKPNFLNCYVSGFHPSDIEVDLLKNGEKMGKVEHSDLSFSKDWSFYLLYYTEFTPNEKDEYACRVNHVTLSGPRTVKWDRDM  99
                                     9        19        29        39        49        59        69        79        89        99


Chain C from PDB  Type:PROTEIN  Length:9
 aligned with Q5QGG3_SIV | Q5QGG3 from UniProtKB/TrEMBL  Length:263

    Alignment length:9
           Q5QGG3_SIV   199 QTSQWDDPW 207
               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
                 3rwf C   1 QTSQWDDPW   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  (0, 0)

(no "SCOP Domain" information available for 3RWF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 20)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9GJ77_MACMU | Q9GJ77)
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_MACMU | Q6V7J5)
biological process
    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: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.

Chain C   (Q5QGG3_SIV | Q5QGG3)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
biological process
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    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:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.
    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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  3rwf
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 Related Entries

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

UniProtKB/Swiss-Prot
        B2MG_MACMU | Q6V7J5: 3jtt 3rwc 3rwd 3rwe 3rwg 3rwh 3rwi 4zfz
        Q5QGG3_SIV | Q5QGG3: 3ik5
UniProtKB/TrEMBL
        Q5QGG3_SIV | Q5QGG3: 3ioz 3rwc 3rwd 3rwg
        Q9GJ77_MACMU | Q9GJ77: 3rwc 3rwd 3rwe 3rwg 3rwh 3rwi 3rwj

(-) Related Entries Specified in the PDB File

3rwc 3rwd 3rwe 3rwg 3rwh 3rwi 3rwj