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(-) Description

Title :  STRUCTURE OF THE P DOMAIN FROM A GI.7 NOROVIRUS VARIANT IN COMPLEX WITH LEA HBGA.
 
Authors :  S. Shanker, R. Czako, B. Sankaran, R. Atmar, M. Estes, B. V. V. Prasad
Date :  07 Mar 14  (Deposition) - 02 Apr 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
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, Lea, Lewis Hbga, Nonsecretor, 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  (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 , SER A:387 , PRO A:388 , THR A:390 , SER A:391 , VAL A:436 , HOH A:832 , HOH A:957 , GLY B:346binding site for Poly-Saccharide residues GAL A 601 through FUC A 603
2AC2SOFTWAREASP A:332 , HIS A:334 , SER A:345 , GLY A:346 , SER A:387 , PRO A:388 , THR A:390 , SER A:391 , VAL A:436 , HOH A:832 , HOH A:957 , ASP B:332 , HIS B:334 , GLY B:346 , SER B:387 , PRO B:388 , SER B:391 , VAL B:436 , HOH B:865binding site for Poly-Saccharide residues GAL B 601 through FUC B 603
3AC3SOFTWARESER A:345 , GLY A:346 , ASP B:332 , HIS B:334 , SER B:387 , PRO B:388 , SER B:391 , VAL B:436 , HOH B:865 , ASP C:332 , HIS C:334 , SER C:387 , PRO C:388 , SER C:391 , VAL C:436 , HOH C:801 , HOH C:1000 , SER D:345 , GLY D:346binding site for Poly-Saccharide residues GAL C 601 through FUC C 603
4AC4SOFTWARETHR B:390 , ASP C:332 , HIS C:334 , GLY C:346 , SER C:387 , PRO C:388 , SER C:391 , VAL C:436 , HOH C:801 , HOH C:1000 , ASP D:332 , HIS D:334 , SER D:345 , GLY D:346 , ARG D:351 , SER D:387 , PRO D:388 , VAL D:436 , HOH D:701 , HOH D:703 , HOH D:708 , HOH D:927 , HOH D:1017binding site for Poly-Saccharide residues GAL D 601 through FUC D 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P3I)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4P3I)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P3I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P3I)

(-) Exons   (0, 0)

(no "Exon" information available for 4P3I)

(-) 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:290
                                                                                                                                                                                                                                                                                                                                  
               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
                 4p3i A 231 QLTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAFESPAPLGFPDIGACDWHVSTFKVDNLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGESTHLAPPIFPPGFGEAIVYFMSDFPIVSGNTAQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPV 525
                                   240       250       260       270       280       290       300       310       320       330       340||     351       361       371       381       391       401  ||   415       425       435       445       455       465       475       485       495       505       515       525
                                                                                                                                        341|                                                          404|                                                                                                                    
                                                                                                                                         343                                                           409                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:282
                                                                                                                                                                                                                                                                                                                          
               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.......eeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p3i B 232 LTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAFESPAPLGFPDIGACDWHVSTFKVLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGHLAPPIFPPGFGEAIVYFMSDFPIVSTAQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPV 525
                                   241       251       261       271       281       291       301       311       321       331       344       354       364       374       384       394       404|      421       431     ||443       453       463       473       483       493       503       513       523  
                                                                                                                                      340|                                                         404|                      437|                                                                                     
                                                                                                                                       344                                                          412                       440                                                                                     


Chain C from PDB  Type:PROTEIN  Length:282
                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......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
                 4p3i C 232 LTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHASPAPLGFPDIGACDWHVSTFKVDQNLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYTHLAPPIFPPGFGEAIVYFMSDFPIVAQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPVG 526
                                   241       251       261       271       281       291       301       311    || 323       333       343       353       363       373       383       393       403|      420       430     ||444       454       464       474       484       494       504       514       524  
                                                                                                              316|                                                                                 403|                      436|                                                                                     
                                                                                                               319                                                                                  411                       441                                                                                     


Chain D 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....eeeeee........................eeeeeeee.......eeeeee......hhhh.eeeee.......eeeeeeeeee.....................................ee.eeee.......eee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee......hhhhh....eeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p3i D 232 LTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAFESPAPLGFPDIGACDWHVSTFKVDLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGSTVTESTHLAPPIFPPGFGEAIVYFMSDFPIVSQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPVG 526
                                   241       251       261       271       281       291       301       311       321       331       341|      353       363       373       383       393       403       413       423       433   ||  447       457       467       477       487       497       507       517         
                                                                                                                                       341|                                                                                          437|                                                                                    
                                                                                                                                        344                                                                                           442
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 4P3I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P3I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P3I)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4P3I)

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        G8FL04_9CALI | G8FL04: 4p12 4p1v 4p25 4p26 4p2n

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