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(-) Description

Title :  CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4 IN COMPLEX WITH HBGA TYPE LEY (TETRAGLYCAN)
 
Authors :  B. K. Singh, G. S. Hansman
Date :  19 Nov 14  (Deposition) - 17 Dec 14  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.46
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Viral Protein, Protruding Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. K. Singh, M. M. Leuthold, G. S. Hansman
Human Noroviruses' Fondness For Histo-Blood Group Antigens.
J. Virol. V. 89 2024 2015
PubMed-ID: 25428879  |  Reference-DOI: 10.1128/JVI.02968-14

(-) Compounds

Molecule 1 - VP1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MBP-HTSHP
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: P DOMAIN (UNP RESIDUES 225-530)
    Organism Scientific: NOROVIRUS HU/GII-4/SAGA4/2006/JP
    Organism Taxid: 546981

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FUC4Ligand/IonALPHA-L-FUCOSE
3GAL2Ligand/IonBETA-D-GALACTOSE
4NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:505 , LEU A:507 , VAL A:508 , HOH A:740binding site for residue ACT A 601
2AC2SOFTWARELEU B:486 , HIS B:505 , LEU B:507 , VAL B:508 , HOH B:740binding site for residue ACT B 601
3AC3SOFTWARESER A:343 , THR A:344 , ARG A:345 , ASP A:374 , HOH A:900 , HOH A:970 , SER B:442 , GLY B:443 , TYR B:444 , ASP B:518 , SER B:519 , HOH B:889binding site for Poly-Saccharide residues FUC A 602 through FUC A 605
4AC4SOFTWARESER A:343 , THR A:344 , ARG A:345 , ASP A:374 , GLY A:392 , SER A:442 , GLY A:443 , TYR A:444 , ASP A:518 , SER A:519 , HOH A:888 , HOH A:900 , HOH A:970 , SER B:343 , THR B:344 , ARG B:345 , ASP B:374 , SER B:442 , GLY B:443 , TYR B:444 , ASP B:518 , SER B:519 , HOH B:889 , HOH B:901 , HOH B:971binding site for Poly-Saccharide residues FUC B 602 through FUC B 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WZE)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:399 -Pro A:400
2Glu B:399 -Pro B:400

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WZE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WZE)

(-) Exons   (0, 0)

(no "Exon" information available for 4WZE)

(-) 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:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..........eeeee.................................eeeeeee.....eeeeee.........................eeeeeeeee......eeeeeeeee......hhhh.eeeeee...........eeeeeeeee.......................................eeeeeeeee..eeee....eeee..hhhhhhhhhhhh......eeeeeeee....eeeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wze A 223 GSKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDGSTTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM 530
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522        


Chain B from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..........eeeee.................................eeeeeee.....eeeeee.........................eeeeeeeee......eeeeeeeee......hhhh.eeeeee...........eeeeeeeee.......................................eeeeeeeee..eeee....eeee..hhhhhhhhhhhh......eeeeeeee....eeeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wze B 223 GSKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDGSTTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM 530
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522
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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 4WZE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WZE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WZE)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4WZE)

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 Related Entries

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        B5BTR7_9CALI | B5BTR7: 4wzk 4wzl 4x06 4x07

(-) Related Entries Specified in the PDB File

400x CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4