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(-) Description

Title :  STRUCTURE OF THE P DOMAIN FROM A GI.7 NOROVIRUS VARIANT IN COMPLEX WITH A-TYPE 2 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 :  1.90
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, A Type 2, Type 2 Hbga, 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 VP1
    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  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1A2G3Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2FUC3Ligand/IonALPHA-L-FUCOSE
3GAL3Ligand/IonBETA-D-GALACTOSE
4NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 8)
No.NameCountTypeFull Name
1A2G2Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2FUC2Ligand/IonALPHA-L-FUCOSE
3GAL2Ligand/IonBETA-D-GALACTOSE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3GAL1Ligand/IonBETA-D-GALACTOSE
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:332 , HIS A:334 , ARG A:351 , LYS A:355 , TRP A:385 , SER A:387 , PRO A:388 , THR A:390 , SER A:391 , HOH A:723 , HOH A:766 , HOH A:790 , HOH A:868 , ARG B:463binding site for Poly-Saccharide residues A2G A 601 through NAG A 604
2AC2SOFTWAREASP A:332 , HIS A:334 , ARG A:351 , LYS A:355 , TRP A:385 , SER A:387 , PRO A:388 , THR A:390 , SER A:391 , HOH A:723 , HOH A:766 , HOH A:790 , HOH A:868 , ASP B:332 , HIS B:334 , ARG B:351 , LYS B:355 , TRP B:385 , SER B:387 , PRO B:388 , THR B:390 , SER B:391 , ARG B:463 , HOH B:718 , HOH B:758 , HOH B:760 , HOH B:784 , HOH B:823 , HOH B:826 , HOH B:841 , HOH C:647binding site for Poly-Saccharide residues A2G B 601 through NAG B 604
3AC3SOFTWAREASP B:332 , HIS B:334 , ARG B:351 , LYS B:355 , TRP B:385 , SER B:387 , PRO B:388 , THR B:390 , SER B:391 , HOH B:718 , HOH B:758 , HOH B:760 , HOH B:784 , HOH B:823 , HOH B:826 , HOH B:841 , HOH C:647 , ASP D:332 , HIS D:334 , ARG D:351 , LYS D:355 , TRP D:385 , SER D:387 , PRO D:388 , SER D:391 , HOH D:763 , HOH D:781 , HOH D:789 , HOH D:812 , HOH D:845 , HOH D:876binding site for Poly-Saccharide residues A2G D 601 through NAG D 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P26)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4P26)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P26)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P26)

(-) Exons   (0, 0)

(no "Exon" information available for 4P26)

(-) 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:292
                                                                                                                                                                                                                                                                                                                                    
               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
                 4p26 A 230 RQLTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAFESPAPLGFPDIGACDWHVSTFKVNLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGSESTHLAPPIFPPGFGEAIVYFMSDFPIVSGNTAQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPVG 526
                                   239       249       259       269       279       289       299       309       319       329       339||     351       361       371       381       391       401   ||  414       424       434       444       454       464       474       484       494       504       514       524  
                                                                                                                                        340|                                                           405|                                                                                                                     
                                                                                                                                         343                                                            409                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               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.eeee........eee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee......hhhhh....eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p26 B 232 LTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAFESPAPLGFPDIGACDWHVSTFKVDNLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGSHLAPPIFPPGFGEAIVYFMSDFPIVSGQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPVG 526
                                   241       251       261       271       281       291       301       311       321       331       341|      352       362       372       382       392       402  ||   418       428       438|      451       461       471       481       491       501       511       521     
                                                                                                                                       341|                                                           405|                       438|                                                                                    
                                                                                                                                        343                                                            412                        442                                                                                    


Chain C from PDB  Type:PROTEIN  Length:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh..........eee............................hhhhh.eeeeeeee....eeeee.........................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
                 4p26 C 231 QLTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAFESPAPLGFPDIGACDWHVSTFKVSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGSTVTESTHLAPPIFPPGFGEAIVYFMSDFPIVSAQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPVG 526
                                   240       250       260       270       280       290       300       310       320       330       340|      354       364       374       384       394       404       414       424       434  ||   447       457       467       477       487       497       507       517         
                                                                                                                                       340|                                                                                         437|                                                                                     
                                                                                                                                        345                                                                                          441                                                                                     


Chain D from PDB  Type:PROTEIN  Length:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh..........eee............................hhhhh.eeeeeeee....eeeeee......................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
                 4p26 D 231 QLTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHASPAPLGFPDIGACDWHVSTFKVDQNLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGSHLAPPIFPPGFGEAIVYFMSDFPIVSQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPVG 526
                                   240       250       260       270       280       290       300       310     ||322       332       342       352       362       372       382       392       402  ||   418       428       442       452       462       472       482       492       502       512       522    
                                                                                                               316|                                                                                   405|                      437|                                                                                    
                                                                                                                319                                                                                    412                       442
   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 4P26)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P26)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P26)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4P26)

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 Related Entries

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

UniProtKB/TrEMBL
        G8FL04_9CALI | G8FL04: 4p12 4p1v 4p25 4p2n 4p3i

(-) Related Entries Specified in the PDB File

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