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(-) Description

Title :  CRYSTAL STRUCTURE OF MACHUPO VIRUS ENVELOPE GLYCOPROTEIN GP1
 
Authors :  T. A. Bowden, M. Crispin, S. C. Graham, D. J. Harvey, J. M. Grimes, E. Y. Jones, D. I. Stuart
Date :  09 Apr 09  (Deposition) - 16 Jun 09  (Release) - 04 Aug 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycoprotein, Arenavirus, New World Arenavirus, Hemorrhagic Fever Virus, Envelope Protein, Machupo, Junin, Guanarito, Sabia, Chapare, Virion, Macv, Gp1, Viral Attachment, Transferrin Receptor, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. A. Bowden, M. Crispin, S. C. Graham, D. J. Harvey, J. M. Grimes, E. Y. Jones, D. I. Stuart
Unusual Molecular Architecture Of The Machupo Virus Attachment Glycoprotein.
J. Virol. V. 83 8259 2009
PubMed-ID: 19494008  |  Reference-DOI: 10.1128/JVI.00761-09

(-) Compounds

Molecule 1 - GLYCOPROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HUMAN EMBRYONIC KIDNEY 293T
    Expression System Common: HUMAN
    Expression System Plasmid: PHLSEC
    Expression System Strain: CRL-1573
    Expression System Taxid: 9606
    Fragment: TFR1 RECEPTOR BINDING DOMAIN, RESIDUES 87-257
    Organism Scientific: MACHUPO VIRUS
    Organism Taxid: 11628
    Other Details: N-ACETYLGLUCOSAMINE LINKAGES OBSERVED IN STRUCTURE ASN95, ASN137, ASN166, AND ASN178
    Other Details - Source: SYNTHETICALLY OPTIMIZED CDNA (CODON DEVICES)
    Synonym: MACV-GP1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric/Biological Unit (1, 5)
No.NameCountTypeFull Name
1NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:166 , THR A:168 , HOH A:2189BINDING SITE FOR RESIDUE NAG A1240
2AC2SOFTWAREASN A:95 , SER A:97 , PHE A:98 , HOH A:2190 , HOH A:2191BINDING SITE FOR RESIDUE NAG A1241
3AC3SOFTWARELEU A:118 , GLN A:176 , ASN A:178 , SER A:180 , GLU A:184 , TYR A:214 , NAG A:1244 , HOH A:2130 , HOH A:2135 , HOH A:2192 , HOH A:2193 , HOH A:2194 , HOH A:2195BINDING SITE FOR RESIDUE NAG A1242
4AC4SOFTWAREASN A:137 , LYS A:167 , LYS A:169 , LYS A:170 , GLY A:172 , HOH A:2196BINDING SITE FOR RESIDUE NAG A1243
5AC5SOFTWAREGLY A:210 , NAG A:1242 , HOH A:2197 , HOH A:2198BINDING SITE FOR RESIDUE NAG A1244

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:92 -A:237
2A:135 -A:164
3A:207 -A:213
4A:220 -A:229

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WFO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2WFO)

(-) 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:153
 aligned with Q6PXS3_MACHU | Q6PXS3 from UniProtKB/TrEMBL  Length:257

    Alignment length:153
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236   
         Q6PXS3_MACHU    87 ELPSLCMLNNSFYYMKGGANIFLIRVSDVSVLMKEYDVSVYEPEDLGNCLNKSDSSWAIHWFSIALGHDWLMDPPMLCRNKTKKEGSNIQFNISKADESRVYGKKIRNGMRHLFRGFYDPCEEGKVCYVTINQCGDPSSFEYCGTNYLSKCQF 239
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Arena_glycoprot-2wfoA01 A:87-239                                                                                                                          Pfam domains
         Sec.struct. author ...eeee....eeeeee..eeeeeeee..........eee.hhhhhhhh..hhhhhhhhhhhhhhhh........eee..........eeee......hhhhhhhhhhhhhhhh.............eeeeee..hhhhh...hhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wfo A  87 ELPSLCMLNNSFYYMKGGANIFLIRVSDVSVLMKEYDVSVYEPEDLGNCLNKSDSSWAIHWFSIALGHDWLMDPPMLCRNKTKKEGSNIQFNISKADESRVYGKKIRNGMRHLFRGFYDPCEEGKVCYVTINQCGDPSSFEYCGTNYLSKCQF 239
                                    96       106       116       126       136       146       156       166       176       186       196       206       216       226       236
   Legend:   → Mismatch (orange background)
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    → 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 2WFO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Arena_glycoprot] (10)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q6PXS3_MACHU | Q6PXS3)
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.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.

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