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(-) Description

Title :  CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN SAGA4 IN COMPLEX WITH HBGA TYPE A (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 :  1.46
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
1A2G2Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2ACT2Ligand/IonACETATE ION
3FUC2Ligand/IonALPHA-L-FUCOSE
4GLA2Ligand/IonALPHA D-GALACTOSE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:505 , LEU A:507 , VAL A:508 , HOH A:744binding site for residue ACT A 601
2AC2SOFTWAREHIS B:505 , LEU B:507 , VAL B:508 , HOH B:747binding site for residue ACT B 601
3AC3SOFTWARESER A:343 , THR A:344 , ARG A:345 , HIS A:347 , ASP A:374 , HOH A:898 , HOH A:1010 , SER B:442 , GLY B:443 , TYR B:444 , HOH B:929binding site for Poly-Saccharide residues FUC A 602 through A2G A 604
4AC4SOFTWARESER A:343 , THR A:344 , ARG A:345 , HIS A:347 , ASP A:374 , SER A:442 , GLY A:443 , TYR A:444 , HOH A:898 , HOH A:921 , HOH A:1010 , SER B:343 , THR B:344 , ARG B:345 , HIS B:347 , ASP B:374 , SER B:442 , GLY B:443 , TYR B:444 , HOH B:903 , HOH B:929 , HOH B:1014binding site for Poly-Saccharide residues FUC B 602 through A2G B 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X07)

(-) 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 4X07)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X07)

(-) Exons   (0, 0)

(no "Exon" information available for 4X07)

(-) 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:307
                                                                                                                                                                                                                                                                                                                                                   
               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
                 4x07 A 224 SKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDGSTTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM 530
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       


Chain B from PDB  Type:PROTEIN  Length:307
                                                                                                                                                                                                                                                                                                                                                   
               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
                 4x07 B 224 SKPFTVPILTVEEMTNSRFPIPLEKLFTGPSGAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTKGDGSTRGHKATVYTGSAPFTPKLGSVQFSTDTENDFETHQNTKFTPVGVIQDGSTTHRNEPQQWVLPSYSGRNVHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM 530
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523
   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 4X07)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X07)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X07)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4X07)

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

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