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(-) Description

Title :  CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4 IN COMPLEX WITH HBGA TYPE H2 (TRIGLYCAN)
 
Authors :  B. K. Singh, G. S. Hansman
Date :  20 Nov 14  (Deposition) - 17 Dec 14  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Viral Capsid Protein, Protruding Domain, Viral Protein (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 BL21(DE3)
    Expression System Plasmid: MBP-HTSHP
    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, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FUC2Ligand/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 , MET A:530binding site for residue ACT A 601
2AC2SOFTWAREHIS B:505 , LEU B:507 , VAL B:508binding site for residue ACT B 601
3AC3SOFTWARESER A:343 , THR A:344 , ARG A:345 , ASP A:374 , HOH A:703 , HOH A:706 , GLY B:392 , SER B:393 , SER B:442 , GLY B:443 , SER B:519 , HOH B:702binding site for Poly-Saccharide residues FUC A 602 through NDG A 604
4AC4SOFTWARESER A:343 , THR A:344 , ARG A:345 , ASP A:374 , GLY A:392 , SER A:393 , SER A:442 , GLY A:443 , TYR A:444 , ASP A:518 , HOH A:703 , HOH A:706 , SER B:343 , THR B:344 , ARG B:345 , ASP B:374 , GLY B:392 , SER B:393 , SER B:442 , GLY B:443 , SER B:519 , HOH B:702binding site for Poly-Saccharide residues FUC B 602 through NDG B 604

(-) SS Bonds  (0, 0)

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

(-) 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 4WZK)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WZK)

(-) 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:309
                                                                                                                                                                                                                                                                                                                                                     
               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
                 4wzk A 222 TGSKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDGSTTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM 530
                                   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521         


Chain B from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh..........eeee..................................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
                 4wzk B 222 TGSKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDGSTTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM 530
                                   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521
   Legend:   → Mismatch (orange background)
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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 4WZK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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

UniProtKB/TrEMBL
        B5BTR7_9CALI | B5BTR7: 4wze 4wzl 4x06 4x07

(-) Related Entries Specified in the PDB File

4oox CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4
4wze CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4 IN COMPLEX WITH HBGA TYPE LEY (TETRAGLYCAN)