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(-) Description

Title :  CRYSTAL STRUCTURE OF P DOMAIN FROM NORWALK VIRUS STRAIN VIETNAM 026 IN COMPLEX WITH FUCOSE
 
Authors :  G. S. Hansman, C. Biertumpfel, L. Chen, I. Georgiev, J. S. Mclellan, K. K P. D. Kwong
Date :  30 Aug 10  (Deposition) - 11 May 11  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  B  (1x)
Biol. Unit 5:  C  (1x)
Keywords :  Capsid Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. S. Hansman, C. Biertumpfel, I. Georgiev, J. S. Mclellan, L. Chen, T. Zhou, K. Katayama, P. D. Kwong
Crystal Structures Of Gii. 10 And Gii. 12 Norovirus Protrudin Domains In Complex With Histo-Blood Group Antigens Reveal Details For A Potential Site Of Vulnerability.
J. Virol. V. 85 6687 2011
PubMed-ID: 21525337  |  Reference-DOI: 10.1128/JVI.00246-11

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MBP-HTSHP
    Expression System Taxid: 562
    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

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): AB 
Biological Unit 2 (2x):   C
Biological Unit 3 (1x): A  
Biological Unit 4 (1x):  B 
Biological Unit 5 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 13)

Asymmetric Unit (2, 13)
No.NameCountTypeFull Name
1EDO10Ligand/Ion1,2-ETHANEDIOL
2FUC3Ligand/IonALPHA-L-FUCOSE
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2FUC2Ligand/IonALPHA-L-FUCOSE
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2FUC2Ligand/IonALPHA-L-FUCOSE
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2FUC1Ligand/IonALPHA-L-FUCOSE
Biological Unit 4 (2, 5)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2FUC1Ligand/IonALPHA-L-FUCOSE
Biological Unit 5 (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2FUC1Ligand/IonALPHA-L-FUCOSE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:50 , HOH A:98 , ASN A:309 , LEU A:310 , ASN A:311 , LEU A:325 , HOH A:557BINDING SITE FOR RESIDUE EDO A 3
02AC2SOFTWAREHOH A:220 , GLU A:464 , HIS A:468 , HOH A:583 , HOH A:681 , GLN B:467BINDING SITE FOR RESIDUE EDO A 6
03AC3SOFTWAREHOH A:182 , HOH A:203 , THR A:281 , LYS A:393BINDING SITE FOR RESIDUE EDO A 10
04AC4SOFTWAREALA A:354 , ASN A:355 , ARG A:356 , ASP A:385 , GLY B:451 , TYR B:452BINDING SITE FOR RESIDUE FUC A 1
05AC5SOFTWAREHOH B:15 , PHE B:445 , PRO B:447 , HOH B:589 , HOH B:647BINDING SITE FOR RESIDUE EDO B 4
06AC6SOFTWAREHOH A:220 , GLN A:467 , GLN A:471 , PRO B:230 , GLU B:464 , HIS B:468 , HOH B:635 , HOH B:649BINDING SITE FOR RESIDUE EDO B 5
07AC7SOFTWAREPRO A:245 , HOH B:111 , HOH B:136 , THR B:281 , GLY B:282 , ARG B:287 , LYS B:393BINDING SITE FOR RESIDUE EDO B 7
08AC8SOFTWAREHOH B:34 , HOH B:69 , ASN B:309 , LEU B:310 , ASN B:311 , LEU B:325 , HOH B:595BINDING SITE FOR RESIDUE EDO B 9
09AC9SOFTWAREGLY A:451 , TYR A:452 , ALA B:354 , ASN B:355 , ARG B:356 , ASP B:385BINDING SITE FOR RESIDUE FUC B 2
10BC1SOFTWAREHOH C:80 , HOH C:107 , GLU C:464 , HIS C:468 , HOH C:695BINDING SITE FOR RESIDUE EDO C 1
11BC2SOFTWAREHOH C:45 , HOH C:86 , LEU C:279 , THR C:281 , GLY C:282BINDING SITE FOR RESIDUE EDO C 2
12BC3SOFTWAREHOH C:22 , HOH C:63 , HOH C:110 , ASN C:309 , LEU C:310 , ASN C:311BINDING SITE FOR RESIDUE EDO C 8
13BC4SOFTWAREALA C:354 , ASN C:355 , ARG C:356 , ASP C:385 , GLY C:451 , TYR C:452BINDING SITE FOR RESIDUE FUC C 3

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3ONY)

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

    Alignment length:315
                                   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     
         Q5F4T5_9CALI   224 SKPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTVPGEGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 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
                 3ony A 224 SKPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQV-----GTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTVPGEGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
                                   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     
                                                                                                294   300                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:309
 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-----.eeeeeeee........................eeeeeeeee............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
                 3ony B 225 KPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQV-----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    
                                                                                               294   300                                                                                                                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:309
 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 (1) Calici_coat-3onyC01 C:225-291                                      ---------------Calici_coat_C-3onyC04 C:307-538                                                                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) Calici_coat-3onyC02 C:225-291                                      ---------------Calici_coat_C-3onyC05 C:307-538                                                                                                                                                                                                          Pfam domains (2)
           Pfam domains (3) Calici_coat-3onyC03 C:225-291                                      ---------------Calici_coat_C-3onyC06 C:307-538                                                                                                                                                                                                          Pfam domains (3)
         Sec.struct. author ........hhhhh..........eeee...........................hhhhh..eeeeeeeee-----.eeeeeee.........................eeeeeeeee....hhhhh....eeeeeeeee......hhhh.eeeeee..........eeeeeeeee...hhhhh.............................eeeeeeeee..........eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ony C 225 KPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQV-----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    
                                                                                               294   300
   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 3ONY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 6)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)
(-)
Clan: no clan defined [family: Calici_coat_C] (19)

(-) Gene Ontology  (0, 0)

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

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 Related Entries

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

UniProtKB/TrEMBL
        Q5F4T5_9CALI | Q5F4T5: 3onu 3pa1 3pa2 3q38 3q39 3q3a 3q6q 3q6r 3ry8 3v7a 4x7e 4x7f 4z4r 4z4s 4z4t 4z4u 4z4v 4z4w 4z4y 4z4z 5bsx 5bsy 5hza 5hzb

(-) Related Entries Specified in the PDB File

3onu