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(-) Description

Title :  PROTRUDING DOMAIN OF GII.17 NOROVIRUS KAWASAKI308
 
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 :  1.59
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Norovirus, Capsid Protein, 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 - CAPSID PROTEIN 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
    Fragment: P DOMAIN (UNP RESIDUES 225-530)
    Gene: VP1
    Organism Scientific: NOROVIRUS HU/GII/JP/2015/GII.P17_GII.17/KAWASAKI308
    Organism Taxid: 1634342

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1EDO9Ligand/Ion1,2-ETHANEDIOL
2MG2Ligand/IonMAGNESIUM ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:456 , HIS A:460 , HOH A:729 , HOH A:834 , HOH A:871binding site for residue EDO A 601
02AC2SOFTWAREGLN A:402 , TRP A:403 , HOH A:702 , HOH A:790 , HOH A:952binding site for residue EDO A 602
03AC3SOFTWAREGLN A:277 , ASN A:306 , LEU A:307 , ASN A:308 , HOH A:755 , HOH A:769 , HOH A:789binding site for residue EDO A 603
04AC4SOFTWARELEU A:272 , GLN A:273 , GLY A:274 , THR A:276 , LEU A:322 , HOH A:734binding site for residue EDO A 604
05AC5SOFTWAREPHE A:379 , GLN A:380 , HOH A:709 , HOH A:892binding site for residue EDO A 605
06AC6SOFTWARELEU A:229 , ARG A:516 , PHE A:517binding site for residue MG A 606
07AC7SOFTWAREHOH A:729 , PRO B:230 , GLU B:456 , HIS B:460 , HOH B:850 , HOH B:852binding site for residue EDO B 601
08AC8SOFTWAREPHE B:379 , GLN B:380 , HOH B:719 , HOH B:807binding site for residue EDO B 602
09AC9SOFTWARELEU B:272 , GLN B:273 , GLY B:274 , THR B:276 , LEU B:322binding site for residue EDO B 603
10AD1SOFTWAREGLN B:277 , ASN B:306 , LEU B:307 , ASN B:308 , HOH B:720 , HOH B:730 , HOH B:803binding site for residue EDO B 604
11AD2SOFTWARELEU B:229 , ARG B:516 , PHE B:517 , HOH B:757binding site for residue MG B 605

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5F4O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5F4O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5F4O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5F4O)

(-) Exons   (0, 0)

(no "Exon" information available for 5F4O)

(-) 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:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh..........eeee.........................hhhhh..eeeeeeee......eeeeee........................eeeeeeeee.........eeeeeeeee...........eeeeee.........eeeeeeeeee....................................eeeeeeeee..........eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f4o A 224 SKPFSLPILTLSELTNSRFPVPIDSLFTAQNNQVQCQNGRCTLDGELQGTTQLLPTGICAFRGRVTAQINQRDRWHMQLQNLNGTTYDPTDDVPAPLGTPDFKGVVFGMVSQRNVGNDAPGSTRAQQAWVSTYSPQFVPKLGSVNLRISDNDDFQFQPTKFTPVGVNDDDDGHPFRQWELPNYSGELTLNMNLAPPVAPNFPGEQLLFFRSFVPCSGGYNQGIIDCLIPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRSGYITVAHSGDYPLVVPANGHFRFDSWVNQFYSLAPM 530
                                   233       243       253 ||    265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525     
                                                         255|                                                                                                                                                                                                                                                                                
                                                          258                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh..........eeee.........................hhhhh..eeeeeeee......eeeeee........................eeeeeeeee.........eeeeeeeee...........eeeeee.........eeeeeeeeee....................................eeeeeeeee..........eeee..hhhhhhhhhhhh......eeeeeeee....eeeeeeeee...eeeee....ee.......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5f4o B 224 SKPFSLPILTLSELTNSRFPVPIDSLFTAQNNQVQCQNGRCTLDGELQGTTQLLPTGICAFRGRVTAQINQRDRWHMQLQNLNGTTYDPTDDVPAPLGTPDFKGVVFGMVSQRNVGNDAPGSTRAQQAWVSTYSPQFVPKLGSVNLRISDNDDFQFQPTKFTPVGVNDDDDGHPFRQWELPNYSGELTLNMNLAPPVAPNFPGEQLLFFRSFVPCSGGYNQGIIDCLIPQEWIQHFYQESAPSQSDVALIRYVNPDTGRTLFEAKLHRSGYITVAHSGDYPLVVPANGHFRFDSWVNQFYSLAPM 530
                                   233       243       253 ||    265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525     
                                                         255|                                                                                                                                                                                                                                                                                
                                                          258
   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 5F4O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5F4O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5F4O)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5F4O)

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 Related Entries

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(-) Related Entries Specified in the PDB File

5f4j PROTRUDING DOMAIN OF GII.17 NOROVIRUS SAITAMA/T87
5f4m PROTRUDING DOMAIN OF GII.17 NOROVIRUS KAWASAKI323