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(-) Description

Title :  CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS FUNABASHI258 STAIN IN THE COMPLEX WITH A-ANTIGEN
 
Authors :  T. Kubota, A. Kumagai, H. Itoh, S. Furukawa, H. Narimatsu, T. Wakita, K. N. Takeda, Y. Someya, H. Shirato
Date :  17 Dec 10  (Deposition) - 25 Jan 12  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Sugar Complex, Histo-Blood Group Antigen, Capsid Protein, Lectin-Like Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Kubota, A. Kumagai, H. Ito, S. Furukawa, Y. Someya, N. Takeda, K. Ishii, T. Wakita, H. Narimatsu, H. Shirato
Structural Basis For The Recognition Of Lewis Antigens By Genogroup I Norovirus
J. Virol. V. 86 11138 2012
PubMed-ID: 22855491  |  Reference-DOI: 10.1128/JVI.00278-12

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-2
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 221-541
    Gene: CAPSID, ORF2
    Organism Scientific: NORWALK-LIKE VIRUS
    Organism Taxid: 95340
    Strain: GI/2 FUNABASHI 258

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1A2G2Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2FUC2Ligand/IonALPHA-L-FUCOSE
3GAL2Ligand/IonBETA-D-GALACTOSE
4NA2Ligand/IonSODIUM ION
5NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:360 , ASP A:405 , GLY A:407 , HOH A:2372BINDING SITE FOR RESIDUE NA A 701
2AC2SOFTWAREPHE B:360 , ASP B:405 , GLY B:407 , HOH B:2392BINDING SITE FOR RESIDUE NA B 701
3AC3SOFTWAREASP A:330 , HIS A:332 , GLN A:354 , TRP A:386 , SER A:388 , GLN A:389 , SER A:391 , HOH A:2054 , HOH A:2058 , HOH A:2157 , HOH A:2160 , HOH A:2221 , HOH A:2234 , HOH A:2289 , HOH A:2339 , HOH A:2342 , ALA B:314 , PHE B:315 , ASP B:330 , HIS B:332 , GLN B:354 , TRP B:386 , SER B:388 , GLN B:389 , SER B:391 , PHE B:421 , ARG B:524 , HOH B:2047 , HOH B:2117 , HOH B:2123 , HOH B:2159 , HOH B:2216 , HOH B:2269 , HOH B:2281 , HOH B:2309BINDING SITE FOR LINKED RESIDUES A 1002 TO 1006, B 1002 TO 1006

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ASP)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Thr A:338 -Pro A:339
2Thr A:392 -Pro A:393
3Thr B:338 -Pro B:339
4Thr B:392 -Pro B:393

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ASP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ASP)

(-) Exons   (0, 0)

(no "Exon" information available for 3ASP)

(-) Sequences/Alignments

Asymmetric/Biological 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:311
 aligned with Q8JW44_9CALI | Q8JW44 from UniProtKB/TrEMBL  Length:546

    Alignment length:311
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533 
         Q8JW44_9CALI   224 TIEQKTRAFTVPNIPLQTLSNSRFPSLIQGMILSPDASQVVQFQNGRCLIDGQLLGTTPATSGQLFRVRGKINQGARTLNLTEVDGKPFMAFDSPAPVGFPDFGKCDWHMRISKTPNNTSSGDPMRSVSVQTNVQGFVPHLGSIQFDEVFNHPTGDYIGTIEWISQPSTPPGTDINLWEIPDYGSSLSQAANLAPPVFPPGFGEALVYFVSAFPGPNNRSAPNDVPCLLPQEYITHFVSEQAPTMGDAALLHYVDPDTNRNLGEFKLYPGGYLTCVPNGVGAGPQQLPLNGVFLFVSWVSRFYQLKPVGTA 534
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.......hhhhh..........eee............................hhhhh..eeeee.....eeeee........................eeeeeeee...........eeeeee......hhhh.eee.........eeeeeeeeeee.......................................ee.eeeeee.........eeeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee.......hhhhh....eeeeeeee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3asp A 224 TIEQKTRAFTVPNIPLQTLSNSRFPSLIQGMILSPDASQVVQFQNGRCLIDGQLLGTTPATSGQLFRVRGKINQGARTLNLTEVDGKPFMAFDSPAPVGFPDFGKCDWHMRISKTPNNTSSGDPMRSVSVQTNVQGFVPHLGSIQFDEVFNHPTGDYIGTIEWISQPSTPPGTDINLWEIPDYGSSLSQAANLAPPVFPPGFGEALVYFVSAFPGPNNRSAPNDVPCLLPQEYITHFVSEQAPTMGDAALLHYVDPDTNRNLGEFKLYPGGYLTCVPNGVGAGPQQLPLNGVFLFVSWVSRFYQLKPVGTA 534
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533 


Chain B from PDB  Type:PROTEIN  Length:302
 aligned with Q8JW44_9CALI | Q8JW44 from UniProtKB/TrEMBL  Length:546

    Alignment length:302
                                   239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529  
         Q8JW44_9CALI   230 RAFTVPNIPLQTLSNSRFPSLIQGMILSPDASQVVQFQNGRCLIDGQLLGTTPATSGQLFRVRGKINQGARTLNLTEVDGKPFMAFDSPAPVGFPDFGKCDWHMRISKTPNNTSSGDPMRSVSVQTNVQGFVPHLGSIQFDEVFNHPTGDYIGTIEWISQPSTPPGTDINLWEIPDYGSSLSQAANLAPPVFPPGFGEALVYFVSAFPGPNNRSAPNDVPCLLPQEYITHFVSEQAPTMGDAALLHYVDPDTNRNLGEFKLYPGGYLTCVPNGVGAGPQQLPLNGVFLFVSWVSRFYQLKPV 531
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh..........eee...................................eeeee.....eeeee........................eeeeeeee...........eeeeee......hhhh.eee.........eeeeeeeeeee.......................................eeeeeeeee.........eeeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeee.......hhhhh....eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3asp B 230 RAFTVPNIPLQTLSNSRFPSLIQGMILSPDASQVVQFQNGRCLIDGQLLGTTPATSGQLFRVRGKINQGARTLNLTEVDGKPFMAFDSPAPVGFPDFGKCDWHMRISKTPNNTSSGDPMRSVSVQTNVQGFVPHLGSIQFDEVFNHPTGDYIGTIEWISQPSTPPGTDINLWEIPDYGSSLSQAANLAPPVFPPGFGEALVYFVSAFPGPNNRSAPNDVPCLLPQEYITHFVSEQAPTMGDAALLHYVDPDTNRNLGEFKLYPGGYLTCVPNGVGAGPQQLPLNGVFLFVSWVSRFYQLKPV 531
                                   239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529
   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 3ASP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ASP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ASP)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3ASP)

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    Thr A:338 - Pro A:339   [ RasMol ]  
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 Related Entries

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

UniProtKB/TrEMBL
        Q8JW44_9CALI | Q8JW44: 3asq 3asr 3ass 3ast

(-) Related Entries Specified in the PDB File

3asq 3asr 3ass 3ast