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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 :  2.29
Chains :  Asym./Biol. Unit :  A
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
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 65-225
    Organism Common: RV-A
    Organism Scientific: ROTAVIRUS A
    Organism Taxid: 10930
    Synonym: HEMAGGLUTININ

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:85 , HIS A:161 , ARG A:162 , PRO A:196 , HOH A:410 , HOH A:479binding site for residue SO4 A 301
2AC2SOFTWAREPRO A:86 , SER A:87 , ASN A:88 , ARG A:154 , ASN A:203 , ALA A:204 , HOH A:409 , HOH A:430 , HOH A:432binding site for residue SO4 A 302
3AC3SOFTWARETYR A:156 , ARG A:162 , ASN A:197 , HOH A:404 , HOH A:417binding site for residue SO4 A 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YG3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:67 -Pro A:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YG3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YG3)

(-) Exons   (0, 0)

(no "Exon" information available for 4YG3)

(-) 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:163
                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee.....eeeee.....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee....eeeeeeee.......eeeeeeee....eeeee.....eeeee........eeee........eeee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yg3 A  63 GSLDGPYAPDSSNLPSNCWYLVNPSNDGVVFSVTDNSTFWMFTYLVLPNTAQTNVTVNVMNETVNISIDNSGSTYRFVDYIKTSSTQAYGSRNYLNTAHRLQAYRRDGDGNISNYWGADTQGDLRVGTYSNPVPNAVINLNADFYVIPDSQQETCTEYIRGGL 225
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
   Legend:   → Mismatch (orange background)
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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 4YG3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YG3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YG3)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  4yg3
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  VP4_ROTBB | P35746
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 Related Entries

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

UniProtKB/Swiss-Prot
        VP4_ROTBB | P35746: 4yg6

(-) Related Entries Specified in the PDB File

4ye2
4yez
4yfw 4YFW CONTAINS THE VP8* PROTEIN OF ANOTHER ROTAVIRUS STRAIN
4yg0
4yg6