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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 :  1.50
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 64-225
    Organism Scientific: HUMAN ROTAVIRUS A
    Organism Taxid: 10941

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:64 , LEU A:65 , ASN A:98 , ASN A:123 , ASN A:155 , TYR A:156 , ILE A:158 , GLY A:179 , SER A:180 , TYR A:183 , ASP A:185 , ARG A:187 , TYR A:207 , TYR A:220 , LEU A:225 , HOH A:1115 , HOH A:1122 , HOH A:1130 , HOH A:1141 , HOH A:1142 , HOH A:1173 , HOH A:1177 , HOH A:1180 , HOH A:1181 , HOH A:1187 , HOH A:1191 , HOH A:1199 , HOH A:1209 , HOH A:1220 , HOH A:1227 , HOH A:1279 , HOH A:1299binding site for Poly-Saccharide residues GAL A 1001 through BGC A 1004

(-) SS Bonds  (0, 0)

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

(-) 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 4YFZ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YFZ)

(-) 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:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eee.....eeeeee....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee....eeeeeeee.......eeeeeeee....eeeee.....eeeeeee......eeeee........eee..eeeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yfz A  64 ALDGPYTPDSSNLPSNYWYLINPLNDGVVFSVTNNSTFWMFTYLILPNTAQTNVTVNVMNETVNISIDNSGSTYRFVDYFKTSSTQSYRQRNYLITEHRLQAYRRDESGNISNYWGSSTYGDLRVGTYFNPVLNAVINLNADFYIIPDSQQEKCTEYIKGGL 225
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4YFZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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  4yfz
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 Related Entries

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

UniProtKB/TrEMBL
        B6RGK2_9REOV | B6RGK2: 4yfw 4yg0

(-) Related Entries Specified in the PDB File

4ye2
4yfw 4YFW CONTAINS THE SAME PROTEIN IN THE ABSENCE OF LIGAND
4yg0
4yg3
4yg6