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(-) Description

Title :  STRUCTURAL BASIS OF GLYCAN RECOGNITION IN NEONATE-SPECIFIC ROTAVIRUSES
 
Authors :  L. Hu, B. V. V. Prasad
Date :  25 Feb 15  (Deposition) - 30 Sep 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Rotavirus, Structural Biology, Glycan, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Hu, S. Ramani, R. Czako, B. Sankaran, Y. Yu, D. F. Smith, R. D. Cummings, M. K. Estes, B. V. Venkataram Prasad
Structural Basis Of Glycan Specificity In Neonate-Specific Bovine-Human Reassortant Rotavirus.
Nat Commun V. 6 8346 2015
PubMed-ID: 26420502  |  Reference-DOI: 10.1038/NCOMMS9346

(-) Compounds

Molecule 1 - OUTER CAPSID PROTEIN VP4
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 64-225
    Organism Scientific: ROTAVIRUS A
    Organism Taxid: 28875
    Strain: N155

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4YFW)

(-) Sites  (0, 0)

(no "Site" information available for 4YFW)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YFW)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:67 -Pro A:68
2Gly B:67 -Pro B:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YFW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YFW)

(-) Exons   (0, 0)

(no "Exon" information available for 4YFW)

(-) 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:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee.....eeeeee....eeeeeee.....eeeeeee......eeeeeee..eeeeeee......eeeeeeee.......eeeeeeee....eeeee.....eeeeeee......eeeee........eee..eeeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yfw A  65 LDGPYTPDSSNLPSNYWYLINPLNDGVVFSVTNNSTFWMFTYLILPNTAQTNVTVNVMNETVNISIDNSGSTYRFVDYFKTSSTQSYRQRNYLITEHRLQAYRRDESGNISNYWGSSTYGDLRVGTYFNPVLNAVINLNADFYIIPDSQQEKCTEYIKGGL 225
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224 


Chain B from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eee.....eeeee.....eeeeeee.....eeeeeee......eeeeeee..eeeeeee......eeeeeeee.......eeeeeeee....eeeee.....eeeeeee......eeeee........eee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yfw B  65 LDGPYTPDSSNLPSNYWYLINPLNDGVVFSVTNNSTFWMFTYLILPNTAQTNVTVNVMNETVNISIDNSGSTYRFVDYFKTSSTQSYRQRNYLITEHRLQAYRRDESGNISNYWGSSTYGDLRVGTYFNPVLNAVINLNADFYIIPDSQQEKCTEYIKGGL 225
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224
   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 4YFW)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YFW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YFW)

(-) Gene Ontology  (10, 10)

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  Ligands, Modified Residues, Ions
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  Sites
(no "Sites" information available for 4yfw)
 
  Cis Peptide Bonds
    Gly A:67 - Pro A:68   [ RasMol ]  
    Gly B:67 - Pro B:68   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/TrEMBL
        B6RGK2_9REOV | B6RGK2: 4yfz 4yg0

(-) Related Entries Specified in the PDB File

4drv 4DRV CONTAINS VP8* PROTEIN OF ANOTHER ROTAVIRUS STRAIN
4ye2
4yfz
4yg0
4yg3
4yg6