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(-) Description

Title :  PROTRUDING DOMAIN OF GII.17 NOROVIRUS SAITAMA/T87
 
Authors :  B. K. Singh, G. S. Hansman
Date :  03 Dec 15  (Deposition) - 13 Jan 16  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Norovirus, Virus Capsid, Protruding Domain, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. K. Singh, A. Koromyslova, L. Hefele, C. Gurth, G. S. Hansman
Structural Evolution Of The Emerging 2014-2015 Gii. 17 Noroviruses.
J. Virol. V. 90 2710 2015
PubMed-ID: 26699640  |  Reference-DOI: 10.1128/JVI.03119-15

(-) Compounds

Molecule 1 - PROTRUDING DOMAIN OF GII.17 NOROVIRUS CAPSID
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: MBP-HTSHP
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: P DOMAIN (UNP RESIDUES 225-530)
    Gene: VP1
    Organism Scientific: NOROVIRUS GII/HU/JP/2002/GII.P16_GII.17/SAITAMA/T87
    Organism Taxid: 1529916

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:456 , HIS A:460 , HOH A:711 , HOH A:766 , HOH A:780binding site for residue EDO A 601
2AC2SOFTWAREASN A:308 , LEU A:309 , ASN A:310 , HOH A:718 , HOH A:822binding site for residue EDO A 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F4J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F4J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F4J)

(-) Exons   (0, 0)

(no "Exon" information available for 5F4J)

(-) 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:306
                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhh..........eeee...........................hhhhh..eeeeeeee........eeeeee........................eeeeeeeee........eeeeeeeee......hhhh.eeee...........eeeeeeeeee...................................eeeeeeeee..........eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5f4j A 225 KPFSLPILTISELTNSRFPAPIDSLFTAQNNNLNVQCQNGRCTLDGELQGTTQLLPSGICAFRGRLTADVDGSHDDRWHMQLTNLNGTPFDPTEDVPAPLGTPDFTGLLFGVASQRNVGSNPNTTRAHEAVISTTSSQFVPKLGSVNFGSTSTDFQLQQPTKFTPVGIKIESGHEFDQWALPRYSGHLTLNMNLAPPIAPNFPGEQLLFFRSNVPCAGGVSDGVIDCLLPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRTGYITVAHSGDYPLVVPSNGYFRFDSWVNQFYSLAPM 530
                                   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
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  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 5F4J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F4J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F4J)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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