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(-) Description

Title :  PROTRUDING DOMAIN OF GII.4 HUMAN NOROVIRUS NSW0514 IN COMPLEX WITH 3-FUCOSYLLACTOSE (3FL)
 
Authors :  B. K. Singh, G. S. Hansman
Date :  31 Mar 16  (Deposition) - 12 Apr 17  (Release) - 12 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Viral Capsid Protein, Protruding Domain, Viral Protein, Norovirus, Human Milk Oligosaccharides (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. K. Singh, G. S. Hansman
Structural Basis For Gii. 4 Norovirus Inhibition By Human Milk Oligosaccharides.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - VP1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MBP-HTSHP
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: NOROVIRUS HU/GII.4/SYDNEY/NSW0514/2012/AU
    Organism Taxid: 1241973

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2FUC2Ligand/IonALPHA-L-FUCOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:272 , LEU A:273 , GLY A:274 , THR A:276 , LEU A:321 , HOH A:736 , HOH A:767binding site for residue EDO A 601
2AC2SOFTWAREASP A:289 , ASN A:378 , ASN A:479 , THR A:482 , LEU A:486binding site for residue EDO A 602
3AC3SOFTWAREHIS A:505 , LEU A:507 , VAL A:508 , MET A:530 , HOH A:741binding site for residue EDO A 603
4AC4SOFTWARESER A:343 , THR A:344 , ARG A:345 , ASP A:374 , SER B:442 , GLY B:443 , TYR B:444binding site for residue FUC A 604
5AC5SOFTWARELEU B:272 , LEU B:273 , GLY B:274 , THR B:276 , LEU B:321 , HOH B:734 , HOH B:767binding site for residue EDO B 601
6AC6SOFTWAREASP B:289 , ASN B:378 , ASN B:479 , THR B:482 , LEU B:486binding site for residue EDO B 602
7AC7SOFTWAREHIS B:505 , LEU B:507 , VAL B:508 , MET B:530 , HOH B:739binding site for residue EDO B 603
8AC8SOFTWARESER A:442 , GLY A:443 , TYR A:444 , SER B:343 , THR B:344 , ARG B:345 , ASP B:374binding site for residue FUC B 604

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J3O)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:399 -Pro A:400
2Glu B:399 -Pro B:400

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J3O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J3O)

(-) Exons   (0, 0)

(no "Exon" information available for 5J3O)

(-) 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:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh..........eeee...........................hhhhh..eeeeeee.....eeeeee.........................eeeeeeeee......eeeeeeeee......hhhh.eeeee............eeeeeeee........................................eeeeeeeee..........eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee.............eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j3o A 222 PGSKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHITGSRNYTMNLASQNWNDYDPTEEIPAPLGTPDFVGKIQGVLTQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDRDFEANQNTKFTPVGVIQDGGTTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM 530
                                   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521         


Chain B from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhh..........eeee...........................hhhhh..eeeeeee.....eeeeee.........................eeeeeeeee......eeeeeeeee......hhhh.eeeee............eeeeeeee........................................eeeeeeeee..........eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee.............eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j3o B 222 PGSKPFSVPVLTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTTQLSPVNICTFRGDVTHITGSRNYTMNLASQNWNDYDPTEEIPAPLGTPDFVGKIQGVLTQTTRTDGSTRGHKATVYTGSADFAPKLGRVQFETDTDRDFEANQNTKFTPVGVIQDGGTTHRNEPQQWVLPSYSGRNTHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMDLDCLLPQEWVQYFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLVIPPNGYFRFDSWVNQFYTLAPM 530
                                   231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521
   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 5J3O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J3O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J3O)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5J3O)

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 Related Entries

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

UniProtKB/Swiss-Prot
        K4LM89_9CALI | K4LM89: 5j35
UniProtKB/TrEMBL
        K4LM89_9CALI | K4LM89: 4oos 4op7 4wzt 4x0c 4x7d

(-) Related Entries Specified in the PDB File

4oos CRYSTAL STRUCTURE OF P DOMAIN FROM NOROVIRUS STRAIN NSW0514
5hza CRYSTAL STRUCTURE OF GII.10 P DOMAIN IN COMPLEX WITH 3- FUCOSYLLACTOSE (3 FL)
5hzb CRYSTAL STRUCTURE OF GII.10 P DOMAIN IN COMPLEX WITH 2- FUCOSYLLACTOSE (2'FL)
5iyr PROTRUDING DOMAIN OF GII.4 HUMAN NOROVIRUS CHDC2094 IN COMPLEX WITH 2-FUCOSYLLACTOSE (2'FL)
5iyw PROTRUDING DOMAIN OF GII.4 HUMAN NOROVIRUS CHDC2094 IN COMPLEX WITH 3-FUCOSYLLACTOSE (3FL)
5j35 PROTRUDING DOMAIN OF GII.4 HUMAN NOROVIRUS NSW0514 IN COMPLEX WITH 2-FUCOSYLLACTOSE (2'FL)