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(-) Description

Title :  STRUCTURE OF THE P DOMAIN FROM A GI.7 NOROVIRUS VARIANT IN COMPLEX WITH LEY HBGA.
 
Authors :  S. Shanker, R. Czako, B. Sankaran, R. Atmar, M. Estes, B. V. V. Prasad
Date :  01 Mar 14  (Deposition) - 02 Apr 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
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, Ley, Lewis Hbga, 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 - MAJOR CAPSID PROTEIN
    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, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
1FUC8Ligand/IonALPHA-L-FUCOSE
2GAL4Ligand/IonBETA-D-GALACTOSE
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 8)
No.NameCountTypeFull Name
1FUC4Ligand/IonALPHA-L-FUCOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 8)
No.NameCountTypeFull Name
1FUC4Ligand/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 , VAL A:436 , SER A:437 , HOH A:702 , HOH A:707 , HOH A:721 , HOH A:732 , HOH A:835 , HOH A:844 , HOH A:982 , GLY B:346 , SER C:371 , ASP C:372 , HOH C:713binding site for Poly-Saccharide residues FUC A 601 through FUC A 604
2AC2SOFTWAREASP A:332 , HIS A:334 , SER A:345 , GLY A:346 , ARG A:351 , ASP A:353 , TRP A:385 , SER A:387 , PRO A:388 , THR A:390 , SER A:391 , VAL A:436 , SER A:437 , HOH A:702 , HOH A:707 , HOH A:721 , HOH A:732 , HOH A:835 , HOH A:844 , HOH A:977 , HOH A:982 , ASP B:332 , HIS B:334 , GLY B:346 , ARG B:351 , ASP B:353 , TRP B:385 , SER B:387 , PRO B:388 , THR B:390 , SER B:391 , VAL B:436 , SER B:437 , HOH B:827 , HOH B:890 , HOH B:930 , SER C:371 , ASP C:372 , HOH C:713binding site for Poly-Saccharide residues FUC B 601 through FUC B 604
3AC3SOFTWARESER A:345 , GLY A:346 , LYS A:355 , ASN A:357 , HOH A:738 , HOH A:977 , 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 , VAL B:436 , SER B:437 , HOH B:827 , HOH B:890 , HOH B:930 , 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 , VAL C:436 , HOH C:704 , HOH C:710 , HOH C:711 , HOH C:724 , HOH C:726 , HOH C:731 , HOH C:748 , HOH C:917 , HOH C:939 , HOH C:954 , HOH C:966 , HOH C:977 , HOH C:998 , SER D:345 , GLY D:346binding site for Poly-Saccharide residues FUC C 601 through FUC C 604
4AC4SOFTWARELYS A:355 , ASN A:357 , PRO A:416 , HOH A:738 , ASP C:332 , HIS C:334 , SER C:345 , GLY C:346 , ARG C:351 , ASP C:353 , TRP C:385 , SER C:387 , PRO C:388 , THR C:390 , SER C:391 , VAL C:436 , HOH C:704 , HOH C:710 , HOH C:711 , HOH C:724 , HOH C:726 , HOH C:731 , HOH C:748 , HOH C:917 , HOH C:939 , HOH C:954 , HOH C:966 , HOH C:977 , HOH C:998 , ASP D:332 , HIS D:334 , SER D:345 , GLY D:346 , ARG D:351 , ASP D:353 , TRP D:385 , SER D:387 , PRO D:388 , THR D:390 , SER D:391 , VAL D:436 , HOH D:701 , HOH D:703 , HOH D:707 , HOH D:795 , HOH D:825 , HOH D:873 , HOH D:890binding site for Poly-Saccharide residues FUC D 601 through FUC D 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P25)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4P25)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P25)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P25)

(-) Exons   (0, 0)

(no "Exon" information available for 4P25)

(-) 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:288
                                                                                                                                                                                                                                                                                                                                
               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.eeeee.......eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee......hhhhh....eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p25 A 232 LTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAFESPAPLGFPDIGACDWHVSTFKVLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGSTVTTHLAPPIFPPGFGEAIVYFMSDFPIVSGAQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPVG 526
                                   241       251       261       271       281       291       301       311       321       331       344       354       364       374       384       394       404   ||  416       426       436 ||    448       458       468       478       488       498       508       518        
                                                                                                                                      340|                                                             408|                        438|                                                                                     
                                                                                                                                       344                                                              411                         441                                                                                     


Chain B from PDB  Type:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhh..........eee............................hhhhh.eeeeeeee....eeeeee........................eeeeeeee.....eeeeee...........eeee........eeeeeeeeee................................ee.eeeee.........eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee......hhhhh....eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p25 B 230 RQLTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAFESPAPLGFPDIGACDWHVSTFKVDGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGSTHLAPPIFPPGFGEAIVYFMSDFPIVSGNTAQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPVG 526
                                   239       249       259       269       279       289       299       309       319       329       339 ||    353       363       373       383       393       403||     418       428       438       448       458       468       478       488       498       508       518        
                                                                                                                                         341|                                                       404|                                                                                                                    
                                                                                                                                          346                                                        410                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhh..........eee............................hhhhh.eeeeeeeee..eeeeeee........................eeeeeeee.......eeeeee......hhhh.eeee........eeeeeeeeee.....................................ee.eeee......eee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee......hhhhh....eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p25 C 232 LTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAFESPAPLGFPDIGACDWHVSTFKVDLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGSTVTESTHLAPPIFPPGFGEAIVYFMSDFPIVQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPVG 526
                                   241       251       261       271       281       291       301       311       321       331       341|      353       363       373       383       393       403       413       423       433  ||   448       458       468       478       488       498       508       518        
                                                                                                                                       341|                                                                                         436|                                                                                    
                                                                                                                                        344                                                                                          442                                                                                    


Chain D from PDB  Type:PROTEIN  Length:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.......hhhhh..........eee............................hhhhh.eeeeeeee....eeeeee.......................eeeeeeee.....eeeeee......hhhh.eee.........eeeeeeeeee..............................ee.eeeee........eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee......hhhhh....eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p25 D 225 AEQKTRQLTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAESPAPLGFPDIGACDWHVSTFKVSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGTHLAPPIFPPFGEAIVYFMSDFPIVSNTAQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPVG 526
                                   234       244       254       264       274       284       294       304       314 ||    325       335    || 349       359       369       379       389       399    || 415    || 426       436||     447       457       467       477       487       497       507       517         
                                                                                                                     316|                   340|                                                        404|      420|            437|                                                                                       
                                                                                                                      318                    345                                                         411       422             439
   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 4P25)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P25)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P25)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4P25)

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 Related Entries

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        G8FL04_9CALI | G8FL04: 4p12 4p1v 4p26 4p2n 4p3i

(-) Related Entries Specified in the PDB File

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