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(-) Description

Title :  STRUCTURE OF THE P DOMAIN FROM A GI.7 NOROVIRUS VARIANT IN COMPLEX WITH H-TYPE 2 HBGA
 
Authors :  S. Shanker, R. Czako, B. Sankaran, R. Atmar, M. Estes, B. V. V. Prasad
Date :  27 Feb 14  (Deposition) - 02 Apr 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  P Domain, Capsid Protein, Norovirus, Hbga, H-Type2, Secretor, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Shanker, R. Czako, B. Sankaran, R. L. Atmar, M. K. Estes, B. V. Prasad
Structural Analysis Of Determinants Of Histo-Blood Group Antigen Binding Specificity In Genogroup I Noroviruses.
J. Virol. V. 88 6168 2014
PubMed-ID: 24648450  |  Reference-DOI: 10.1128/JVI.00201-14

(-) Compounds

Molecule 1 - P DOMAIN OF VPI
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: NOROVIRUS HU/GI.7/TCH-060/USA/2003
    Organism Taxid: 1097017

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1FUC4Ligand/IonALPHA-L-FUCOSE
2GAL4Ligand/IonBETA-D-GALACTOSE
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 6)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:332 , HIS A:334 , ARG A:351 , ASP A:353 , TRP A:385 , SER A:387 , PRO A:388 , THR A:390 , SER A:391 , HOH A:715 , HOH A:737 , HOH A:745 , HOH A:752 , HOH A:811 , HOH A:821 , HOH A:916 , HOH A:923 , HOH A:957 , HOH A:1078 , LYS D:355 , ASN D:357 , HOH D:727binding site for Poly-Saccharide residues FUC A 601 through NAG A 603
2AC2SOFTWAREASP A:332 , HIS A:334 , ARG A:351 , ASP A:353 , TRP A:385 , SER A:387 , PRO A:388 , THR A:390 , SER A:391 , HOH A:715 , HOH A:737 , HOH A:745 , HOH A:752 , HOH A:810 , HOH A:811 , HOH A:821 , HOH A:916 , HOH A:923 , HOH A:957 , HOH A:1078 , ASP B:332 , HIS B:334 , ARG B:351 , ASP B:353 , TRP B:385 , SER B:387 , PRO B:388 , THR B:390 , SER B:391 , HOH B:704 , HOH B:711 , HOH B:712 , HOH B:721 , HOH B:785 , HOH B:815 , HOH B:832 , HOH B:932 , HOH B:1022 , HOH B:1044 , LYS D:355 , ASN D:357 , PRO D:415 , HOH D:727binding site for Poly-Saccharide residues FUC B 601 through NAG B 603
3AC3SOFTWAREHOH A:810 , ASP B:332 , HIS B:334 , ARG B:351 , ASP B:353 , TRP B:385 , SER B:387 , PRO B:388 , THR B:390 , SER B:391 , HOH B:704 , HOH B:711 , HOH B:712 , HOH B:721 , HOH B:785 , HOH B:815 , HOH B:832 , HOH B:932 , HOH B:1022 , HOH B:1044 , ASP C:332 , HIS C:334 , ARG C:351 , ASP C:353 , TRP C:385 , SER C:387 , PRO C:388 , THR C:390 , SER C:391 , HOH C:831 , HOH C:925 , HOH C:952 , HOH C:1021 , HOH C:1048 , PRO D:415 , HOH D:793binding site for Poly-Saccharide residues FUC C 601 through NAG C 603
4AC4SOFTWARESER A:371 , ASP A:372 , HOH A:738 , ASP C:332 , HIS C:334 , ARG C:351 , ASP C:353 , TRP C:385 , SER C:387 , PRO C:388 , THR C:390 , SER C:391 , HOH C:831 , HOH C:925 , HOH C:952 , HOH C:1021 , HOH C:1048 , ASP D:332 , HIS D:334 , ARG D:351 , ASP D:353 , TRP D:385 , SER D:387 , PRO D:388 , THR D:390 , SER D:391 , HOH D:704 , HOH D:707 , HOH D:709 , HOH D:717 , HOH D:739 , HOH D:782 , HOH D:793 , HOH D:830 , HOH D:855 , HOH D:859 , HOH D:900 , HOH D:974 , HOH D:1045binding site for Poly-Saccharide residues FUC D 601 through NAG D 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P1V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4P1V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P1V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P1V)

(-) Exons   (0, 0)

(no "Exon" information available for 4P1V)

(-) Sequences/Alignments

Asymmetric 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:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh..........eee............................hhhhh.eeeeeeeee..eeeeeee........................eeeeeeee..........eeeee......hhhh.eeee........eeeeeeeeee....................................ee.eeee.......eee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee......hhhhh....eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p1v A 232 LTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAFESPAPLGFPDIGACDWHVSTFKVDQNLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGSTTESTHLAPPIFPPGFGEAIVYFMSDFPIVSQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPV 525
                                   241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401    || 412       422       432    || 446       456       466       476       486       496       506       516         
                                                                                                                                                                                                        406|                          437|                                                                                   
                                                                                                                                                                                                         408                           442                                                                                   


Chain B from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh..........eee............................hhhhh.eeeeeee..eeeee......................eeeeeeee..........eeeee......hhhh.eee.........eeeeeeeeee...............................ee.eeee........eee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee......hhhhh....eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p1v B 231 QLTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSKGLNLTELDGTPYHASPAPLGFPDIGACDWHVSTFKVDQNLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGTHLAPPIFPPGFGEAIVYFMSDFPIVSAQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPV 525
                                   240       250       260       270       280       290      |304       314 ||    326       336       346       356       366       376       386       396       412       422       432    || 445       455       465       475       485       495       505       515       525
                                                                                            297|           316|                                                                                  404|                       437|                                                                                    
                                                                                             302            319                                                                                   411                        441                                                                                    


Chain C from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh..........eee............................hhhhh.eeeeeeee....eeeee.........................eeeeeeee.......eeeeee...........eeee........eeeeeeeeee..................................ee.eeeee.........eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee......hhhhh....eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p1v C 231 QLTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAFESPAPLGFPDIGACDWHVSTFKVNLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGSESTHLAPPIFPPGFGEAIVYFMSDFPIVSGNTAQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPVG 526
                                   240       250       260       270       280       290       300       310       320       330       340|      352       362       372       382       392       402  ||   415       425       435       445       455       465       475       485       495       505       515       525 
                                                                                                                                       340|                                                           405|                                                                                                                     
                                                                                                                                        343                                                            409                                                                                                                     


Chain D from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh..........eee............................hhhhh.eeeeeeee....eeeeee........................eeeeeeee.......eeeeee...........eee.........eeeeeeeeee.....................................ee.eeee........eee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee......hhhhh....eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p1v D 232 LTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAFESPAPLGFPDIGACDWHVSTFKVNLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGSTVTESTHLAPPIFPPGFGEAIVYFMSDFPIVSAQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPVG 526
                                   241       251       261       271       281       291       301       311       321       331       343       353       363       373       383       393       403       413       423       433   ||  446       456       466       476       486       496       506       516       526
                                                                                                                                      340|                                                                                           437|                                                                                     
                                                                                                                                       343                                                                                            441
   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 4P1V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P1V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P1V)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4P1V)

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 Related Entries

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UniProtKB/TrEMBL
        G8FL04_9CALI | G8FL04: 4p12 4p25 4p26 4p2n 4p3i

(-) Related Entries Specified in the PDB File

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