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(-) Description

Title :  CELL ATTACHMENT PROTEIN VP8* OF A HUMAN ROTAVIRUS SPECIFICALLY INTERACTS WITH A-TYPE HISTO-BLOOD GROUP ANTIGEN
 
Authors :  L. Hu, S. E. Crawford, R. Czako, N. W. Cortes-Penfield, D. F. Smith, J. Le M. K. Estes, B. V. V. Prasad
Date :  17 Feb 12  (Deposition) - 11 Apr 12  (Release) - 23 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym./Biol. Unit :  A
Keywords :  Otavirus, Viral Protein, Cell Attachment Factor, Histo Blood Group Antigen, Galectin-Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Hu, S. E. Crawford, R. Czako, N. W. Cortes-Penfield, D. F. Smith, J. Le Pendu, M. K. Estes, B. V. Prasad
Cell Attachment Protein Vp8* Of A Human Rotavirus Specifically Interacts With A-Type Histo-Blood Group Antigen.
Nature V. 485 256 2012
PubMed-ID: 22504179  |  Reference-DOI: 10.1038/NATURE10996

(-) Compounds

Molecule 1 - OUTER CAPSID PROTEIN VP4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 64-224
    Gene: VP4
    Organism Scientific: ROTAVIRUS SP.
    Organism Taxid: 10970
    Synonym: ROTAVIRUS CELL ATTACHMENT PROTEIN VP8*

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3GLA1Ligand/IonALPHA D-GALACTOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:101 , TYR A:188 , TYR A:189 , LEU A:190 , THR A:191 , GLA A:302 , FUC A:303 , HOH A:563 , HOH A:652 , HOH A:674BINDING SITE FOR RESIDUE A2G A 301
2AC2SOFTWAREPRO A:71 , SER A:187 , TYR A:188 , TYR A:189 , A2G A:301 , FUC A:303 , HOH A:528 , HOH A:545 , HOH A:674BINDING SITE FOR RESIDUE GLA A 302
3AC3SOFTWAREASP A:202 , A2G A:301 , GLA A:302 , HOH A:462 , HOH A:512BINDING SITE FOR RESIDUE FUC A 303

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:67 -Pro A:68
2Thr A:181 -Pro A:182

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DRV)

(-) 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
 aligned with Q86169_9REOV | Q86169 from UniProtKB/TrEMBL  Length:776

    Alignment length:163
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221   
         Q86169_9REOV    62 QPTLDGPYQPTTFNLPIDYWMLIAPTQIGRVAEGTNTTDRWFACVLVEPNVQNTQREYVLDGQTVQLQVSNNSSTLWKFILFIKLEKNGAYSQYSTLSTSNKLCAWMKREGRVYWYAGTTPNASESYYLTINNDNSNVSCDAEFYLIPRSQTELCTQYINNGL 224
               SCOP domains d4drva_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...ee.....eeeeee....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee.....eeeeeeee.......eeeeeeee....eeeeee..eeeeeeee....eeeeeee......eeee..eeeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4drv A  62 GSTLDGPYQPTTFNLPIDYWMLIAPTQIGRVAEGTNTTDRWFACVLVEPNVQNTQREYVLDGQTVQLQVSNNSSTLWKFILFIKLEKNGAYSQYSTLSTSNKLCAWMKREGRVYWYAGTTPNASESYYLTINNDNSNVSCDAEFYLIPRSQTELCTQYINNGL 224
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q86169_9REOV | Q86169)
biological process
    GO:0039665    permeabilization of host organelle membrane involved in viral entry into host cell    Induction of organellar membrane permeabilization triggered by an interaction between the host membrane and a membrane-penetration protein associated with a viral capsid. Results in release of the virus contents from an organelle into the host cell cytoplasm.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0019058    viral life cycle    A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0044165    host cell endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the host cell cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The host ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0044168    host cell rough endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the host cell cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The host rough ER has ribosomes adhering to the outer surface.
    GO:0019028    viral capsid    The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
    GO:0039624    viral outer capsid    The outer layer of a double or triple concentric icosahedral capsid. Outer capsids are part of reoviridae and cystoviridae virions.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.

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 Related Entries

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

UniProtKB/TrEMBL
        Q86169_9REOV | Q86169: 4drr 4ds0

(-) Related Entries Specified in the PDB File

4drr CELL ATTACHMENT PROTEIN VP8* OF ROTAVIRUS
4ds0 CELL ATTACHMENT PROTEIN VP8* OF A HUMAN ROTAVIRUS SPECIFICALLY INTERACTS WITH A-TYPE HISTO-BLOOD GROUP ANTIGEN