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(-) Description

Title :  PROTRUDING DOMAIN OF GII.4 HUMAN NOROVIRUS CHDC2094 IN COMPLEX WITH 2-FUCOSYLLACTOSE (2'FL)
 
Authors :  B. K. Singh, G. S. Hansman
Date :  24 Mar 16  (Deposition) - 05 Apr 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
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 - GII.4 NOROVIRUS CHDC2094 CAPSID
    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
    Fragment: PROTRUDING DOMAIN (UNP RESIDUES 225-530)
    Organism Scientific: NOROVIRUS HU/GII.4/CHDC2094/1974/US
    Organism Taxid: 660656

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2FUC2Ligand/IonALPHA-L-FUCOSE
3GAL2Ligand/IonBETA-D-GALACTOSE
4GLC2Ligand/IonALPHA-D-GLUCOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:355 , VAL B:356 , HIS B:357 , HIS B:394 , ASN B:397 , HOH B:745 , HOH B:796binding site for residue FLC B 604
2AC2SOFTWARESER A:343 , THR A:344 , ARG A:345 , ASP A:374 , HOH A:701 , HOH A:703 , HOH A:705 , HOH A:731 , HOH A:966 , HOH A:974 , SER B:441 , GLY B:442binding site for Poly-Saccharide residues FUC A 601 through GLC A 603
3AC3SOFTWARESER A:343 , THR A:344 , ARG A:345 , ASP A:374 , SER A:441 , GLY A:442 , HOH A:701 , HOH A:703 , HOH A:705 , HOH A:731 , HOH A:966 , HOH A:974 , SER B:343 , THR B:344 , ARG B:345 , ASP B:374 , SER B:441 , GLY B:442 , HOH B:703 , HOH B:750binding site for Poly-Saccharide residues FUC B 601 through GLC B 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:398 -Pro A:399
2Glu B:398 -Pro B:399

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IYR)

(-) 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:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhh..........eeee...........................hhhhh..eeeeeee.....eeeeee.........................eeeeeeeee......eeeeeeeee......hhhh.eeeee............eeeeeeeee................hhhhh...............eeeeeeeee.eeee.....eeee..hhhhhhhhhhhh......eeeeeeee....eeeeeeeee...eeeee.............eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iyr A 225 KPFTVPILTVEEMSNSRFPIPLEKLYTGPSSAFVVQPQNGRCTTDGVLLGTTQLSAVNICNFRGDVTRVGISHDYTMNLVSQNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTRADGSTRAHKATVSTGSVHFTPKLGSVQFTTDTNNDFQTGQNTKFTPVGVIQDGHQNEPQQWVLPNYSGTSGHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDCLLPQEWVSHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYITVAHTGPYDLVIPPNGYFRFDSWVNQFYTLAPM 529
                                   234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       396       406       416       426       436       446       456       466       476       486       496       506       516       526   
                                                                                                                                                                                                 392|                                                                                                                                      
                                                                                                                                                                                                  395                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhh..........eeee...........................hhhhh..eeeeeee.....eeeeee.........................eeeeeeeee......eeeeeeeee......hhhh.eeeee............eeeeeeeee..................hhhhh...............eeeeeeeee.eeee.....eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee.............eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5iyr B 224 SKPFTVPILTVEEMSNSRFPIPLEKLYTGPSSAFVVQPQNGRCTTDGVLLGTTQLSAVNICNFRGDVTRVGISHDYTMNLVSQNWNNYDPTEEIPAPLGTPDFVGKIQGLLTQTTRADGSTRAHKATVSTGSVHFTPKLGSVQFTTDTNNDFQTGQNTKFTPVGVIQDGDHHQNEPQQWVLPNYSGTSGHNVHLAPAVAPTFPGEQLLFFRSTMPGCSGYPNMNLDCLLPQEWVSHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYITVAHTGPYDLVIPPNGYFRFDSWVNQFYTLAPM 529
                                   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
   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 5IYR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
    Glu A:398 - Pro A:399   [ RasMol ]  
    Glu B:398 - Pro B:399   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        D0QJ68_9CALI | D0QJ68: 5iyn 5iyp 5iyq 5iyw

(-) Related Entries Specified in the PDB File

5hzb CRYSTAL STRUCTURE OF GII.10 P DOMAIN IN COMPLEX WITH 2- FUCOSYLLACTOSE (2'FL)
5iyn PROTRUDING DOMAIN OF GII.4 HUMAN NOROVIRUS CHDC2094
5iyp PROTRUDING DOMAIN OF GII.4 HUMAN NOROVIRUS CHDC2094 IN COMPLEX WITH HBGA TYPEA (TRIGLYCAN)
5iyq PROTRUDING DOMAIN OF GII.4 HUMAN NOROVIRUS CHDC2094 IN COMPLEX WITH HBGA TYPE B (TRIGLYCAN)