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(-) Description

Title :  STRUCTURE OF THE P DOMAIN FROM A GI.7 NOROVIRUS VARIANT IN COMPLEX WITH LEX HBGA
 
Authors :  S. Shanker, R. Czako, B. Sankaran, R. Atmar, M. Estes, B. V. V. Prasad
Date :  04 Mar 14  (Deposition) - 02 Apr 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
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, 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 - MAJOR CAPSID PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 226-526
    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 , SER A:391 , VAL A:436 , HOH A:711 , HOH A:840 , HOH A:873 , HOH A:894 , HOH A:979 , SER B:345 , GLY B:346 , PHE C:418binding 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 , SER A:391 , VAL A:436 , HOH A:711 , HOH A:840 , HOH A:873 , HOH A:894 , HOH A:979 , ASP B:332 , HIS B:334 , SER B:345 , GLY B:346 , SER B:387 , PRO B:388 , SER B:391 , VAL B:436 , HOH B:708 , HOH B:717 , HOH B:821 , HOH B:936 , LYS C:355 , ASN C:357 , PHE C:418binding 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:708 , HOH B:717 , HOH B:726 , HOH B:747 , HOH B:821 , HOH B:936 , ASP C:332 , HIS C:334 , LYS C:355 , ASN C:357 , SER C:387 , PRO C:388 , SER C:391 , VAL C:436 , HOH C:843 , SER D:345 , GLY D:346binding site for Poly-Saccharide residues GAL C 601 through FUC C 603
4AC4SOFTWAREHOH B:726 , HOH B:747 , ASP C:332 , HIS C:334 , GLY C:346 , SER C:387 , PRO C:388 , SER C:391 , VAL C:436 , HOH C:843 , ASP D:332 , HIS D:334 , SER D:345 , GLY D:346 , SER D:387 , PRO D:388 , SER D:391 , VAL D:436 , HOH D:823 , HOH D:836 , HOH D:952binding site for Poly-Saccharide residues GAL D 601 through FUC D 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P2N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4P2N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P2N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P2N)

(-) Exons   (0, 0)

(no "Exon" information available for 4P2N)

(-) 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:285
                                                                                                                                                                                                                                                                                                                             
               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.eeee...........eee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee......hhhhh....eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p2n A 231 QLTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHASPAPLGFPDIGACDWHVSTFKVDQNLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYHLAPPIFPPGFGEAIVYFMSDFPIVSGNTAQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPV 525
                                   240       250       260       270       280       290       300       310     ||322       332       342       352       362       372       382       392       402||     420       430       440       450       460       470       480       490       500       510       520     
                                                                                                               316|                                                                                 403|                                                                                                                 
                                                                                                                319                                                                                  412                                                                                                                 


Chain B 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.eeee........eeeeeeeeee....................................ee.eeeee......eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee......hhhhh....eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p2n B 232 LTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAFESPAPLGFPDIGACDWHVSTFKVDQLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGSTTESTHLAPPIFPPGFGEAIVYFMSDFPIVSAQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPV 525
                                   241       251       261       271       281       291       301       311       321       331       341||     352       362       372       382       392       402   ||  413       423       433   ||  446       456       466       476       486       496       506       516         
                                                                                                                                        342|                                                           406|                          437|                                                                                    
                                                                                                                                         344                                                            408                           441                                                                                    


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.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
                 4p2n C 232 LTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAFESPAPLGFPDIGACDWHVSTFKVLSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYGSTVTESTHLAPPIFPPGFGEAIVYFMSDFPIVSAQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPV 525
                                   241       251       261       271       281       291       301       311       321       331       344       354       364       374       384       394       404       414       424       434  ||   447       457       467       477       487       497       507       517        
                                                                                                                                      340|                                                                                          437|                                                                                    
                                                                                                                                       344                                                                                           441                                                                                    


Chain D from PDB  Type:PROTEIN  Length:286
                                                                                                                                                                                                                                                                                                                              
               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
                 4p2n D 230 RQLTVPNIPLNNLANSRVPAMINKMTVSTDQNQVVQFQNGRCTLEGQLLGTTPVSASQVARIRGKVFSTASGKGLNLTELDGTPYHAFESPAPLGFPDIGACDWHVSTFKVSGDPMSRLDVKQNAPFAPHLGSIEFTSDQDPTGDQLGTLAWVSPSTSGARVDPWKIPSYTHLAPPIFPPGFGEAIVYFMSDFPIVSGNTAQVPCTLPQEFVSHFVEQQAPVRGEAALLHYVDPDTHRNLGEFKLYPDGFITCVPNTGGGPQNLPTNGVFVFSSWVSRYYQLKPVG 526
                                   239       249       259       269       279       289       299       309       319       329       339||     353       363       373       383       393       403|      420       430       440       450       460       470       480       490       500       510       520      
                                                                                                                                        340|                                                       403|                                                                                                                   
                                                                                                                                         345                                                        411
   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 4P2N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P2N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P2N)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4P2N)

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UniProtKB/TrEMBL
        G8FL04_9CALI | G8FL04: 4p12 4p1v 4p25 4p26 4p3i

(-) Related Entries Specified in the PDB File

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