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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN WA ROTAVIRUS VP8* CARBOHYDRATE-RECOGNISING DOMAIN
 
Authors :  H. Blanchard
Date :  16 Aug 06  (Deposition) - 03 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta-Sandwich, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Blanchard, X. Yu, B. S. Coulson, M. Von Itzstein
Insight Into Host Cell Carbohydrate-Recognition By Human An Porcine Rotavirus From Crystal Structures Of The Virion Spike Associated Carbohydrate-Binding Domain (Vp8*)
J. Mol. Biol. V. 367 1215 2007
PubMed-ID: 17306299  |  Reference-DOI: 10.1016/J.JMB.2007.01.028
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OUTER CAPSID PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-VP8(64-223)
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: VP8* DOMAIN
    Organism Scientific: HUMAN ROTAVIRUS A
    Organism Taxid: 10941
    Strain: STRAIN WA
    Synonym: SPIKE PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2IPA2Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:167 , TRP A:174 , THR A:185 , ARG A:209 , GLU A:212BINDING SITE FOR RESIDUE GOL A 4000
2AC2SOFTWAREGLY A:90 , VAL A:91 , TYR A:119 , THR A:120 , ARG A:155 , THR A:156 , HIS A:177 , IPA A:5001 , HOH A:5054BINDING SITE FOR RESIDUE GOL A 4001
3AC3SOFTWAREARG A:117 , GLN A:118 , HIS A:177 , GLY A:178 , HOH A:5091BINDING SITE FOR RESIDUE IPA A 5000
4AC4SOFTWAREASN A:153 , ARG A:154 , THR A:156 , HIS A:201 , GOL A:4001BINDING SITE FOR RESIDUE IPA A 5001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DWR)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:67 -Pro A:68
2Thr A:180 -Pro A:181

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DWR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DWR)

(-) Exons   (0, 0)

(no "Exon" information available for 2DWR)

(-) 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:160
 aligned with VP4_ROTHW | P11193 from UniProtKB/Swiss-Prot  Length:775

    Alignment length:160
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
            VP4_ROTHW    64 ILDGPYQPTTFTPPNDYWILINSNTNGVVYESTNNSDFWTAVVAIEPHVNPVDRQYTIFGESKQFNVSNDSNKWKFLEMFRSSSQNEFYNRRTLTSDTRFVGILKYGGRVWTFHGETPRATTDSSSTANLNNISITIHSEFYIIPRSQESKCNEYINNGL 223
               SCOP domains d2dwra_ A: automated matches                                                                                                                                     SCOP domains
               CATH domains -2dwrA01 A:65-223  [code=2.60.120.200, no name defined]                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee.....eeeeee.....eeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee....eeeeeeee.......eeeeeeee...eeeeeee..eeeeeeee....eeeeee.......eeee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dwr A  64 MLDGPYQPTTFTPPNDYWILINSNTNGVVYESTNNSDFWTAVVAIEPHVNPVDRQYTIFGESKQFNVSNDSNKWKFLEMFRSSSQNEFYNRRTLTSDTRLVGILKYGGRVWTFHGETPRATTDSSSTANLNNISITIHSEFYIIPRSQESKCNEYINNGL 223
                                    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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  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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DWR)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (VP4_ROTHW | P11193)
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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2i2s