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(-) Description

Title :  STRUCTURAL BASIS FOR NOROVIRUS INHIBITION AND FUCOSE MIMICRY BY CITRATE
 
Authors :  G. S. Hansman, J. S. Mclellan, P. D Kwong
Date :  11 May 11  (Deposition) - 09 Nov 11  (Release) - 25 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. S. Hansman, S. Shahzad-Ul-Hussan, J. S. Mclellan, G. Y. Chuang, I. Georgiev, T. Shimoike, K. Katayama, C. A. Bewley, P. D. Kwong
Structural Basis For Norovirus Inhibition And Fucose Mimicr By Citrate.
J. Virol. V. 86 284 2012
PubMed-ID: 22031945  |  Reference-DOI: 10.1128/JVI.05909-11

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MBP-HTSHP
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: P DOMAIN (UNP RESIDUES 225-538)
    Organism Scientific: NORWALK VIRUS
    Organism Taxid: 11983
    Strain: VIETNAM 026

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric/Biological Unit (2, 12)
No.NameCountTypeFull Name
1EDO11Ligand/Ion1,2-ETHANEDIOL
2FLC1Ligand/IonCITRATE ANION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:14 , HOH A:33 , HOH A:164 , ASN A:309 , LEU A:310 , ASN A:311 , LEU A:325BINDING SITE FOR RESIDUE EDO A 4
02AC2SOFTWARELEU A:272 , GLN A:273 , GLY A:274 , THR A:276 , LEU A:325 , HOH A:570 , HOH A:647BINDING SITE FOR RESIDUE EDO A 5
03AC3SOFTWAREHOH A:72 , LEU A:279 , THR A:281 , HOH A:621 , HOH B:25 , PRO B:245BINDING SITE FOR RESIDUE EDO A 6
04AC4SOFTWAREHOH A:51 , HOH A:84 , PRO A:245 , ILE A:246 , HOH B:57 , ASN B:311BINDING SITE FOR RESIDUE EDO A 8
05AC5SOFTWAREGLY A:300 , SER A:379 , THR A:380 , TRP A:381 , HOH A:753 , THR B:534BINDING SITE FOR RESIDUE EDO A 9
06AC6SOFTWAREHOH A:58 , ARG A:341 , HOH A:612 , HOH A:721 , HOH B:197 , ILE B:446 , PRO B:447BINDING SITE FOR RESIDUE EDO A 10
07AC7SOFTWARELEU A:234 , VAL A:248 , LEU A:249 , TYR A:485 , VAL A:515 , ALA A:517 , PRO A:518BINDING SITE FOR RESIDUE EDO A 11
08AC8SOFTWAREHOH A:135 , HOH A:147 , ALA A:354 , ASN A:355 , ARG A:356 , ASP A:385 , HOH A:675 , HOH A:740 , HOH A:749 , HOH A:769 , HOH A:809 , GLY B:451BINDING SITE FOR RESIDUE FLC A 1
09AC9SOFTWAREHOH B:32 , HOH B:57 , THR B:281BINDING SITE FOR RESIDUE EDO B 1
10BC1SOFTWARELEU B:272 , GLN B:273 , GLY B:274 , THR B:276 , LEU B:325 , HOH B:612 , HOH B:716BINDING SITE FOR RESIDUE EDO B 2
11BC2SOFTWAREHOH B:19 , HOH B:20 , HOH B:156 , ASN B:309 , LEU B:310 , ASN B:311 , LEU B:325BINDING SITE FOR RESIDUE EDO B 3
12BC3SOFTWAREASN A:311 , HOH B:25 , HOH B:61 , HOH B:76 , PRO B:245 , ILE B:246 , HOH B:741BINDING SITE FOR RESIDUE EDO B 7

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RY8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RY8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RY8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RY8)

(-) Exons   (0, 0)

(no "Exon" information available for 3RY8)

(-) 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:310
 aligned with Q5F4T5_9CALI | Q5F4T5 from UniProtKB/TrEMBL  Length:548

    Alignment length:314
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534    
         Q5F4T5_9CALI   225 KPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTVPGEGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh..........eeee...........................hhhhh..eeeeeeeee.----.eeeeeee.........................eeeeeeeee....hhhhh...eeeeeeeeee......hhhh.eeeeee..........eeeeeeeee...hhhhh.............................eeeeeeeee....eee...eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ry8 A 225 KPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQ----GTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTVPGEGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
                                   234       244       254       264       274       284       294|    | 304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534    
                                                                                                295  300                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:301
 aligned with Q5F4T5_9CALI | Q5F4T5 from UniProtKB/TrEMBL  Length:548

    Alignment length:314
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534    
         Q5F4T5_9CALI   225 KPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTVPGEGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh..........eeee...........................hhhhh..eeeeeeeee.-----.eeeeee.........................eeeeeeeee..--------..eeeeeeeeee......hhhh.eeeeee..........eeeeeeeee.....................................eeeeeeeee....eee...eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ry8 B 225 KPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQ-----THWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNT--------LPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
                                   234       244       254       264       274       284       294|     |304       314       324       334        |-       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534    
                                                                                                295   301                                       343      352
   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 3RY8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RY8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RY8)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3RY8)

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 Related Entries

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

UniProtKB/TrEMBL
        Q5F4T5_9CALI | Q5F4T5: 3onu 3ony 3pa1 3pa2 3q38 3q39 3q3a 3q6q 3q6r 3v7a 4x7e 4x7f 4z4r 4z4s 4z4t 4z4u 4z4v 4z4w 4z4y 4z4z 5bsx 5bsy 5hza 5hzb

(-) Related Entries Specified in the PDB File

3onu 3q39 3q3a