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(-) Description

Title :  CRYSTAL STRUCTURE OF PORCINE ROTAVIRUS CRW-8 VP8* IN COMPLEX WITH N-GLYCOLYLNEURAMINIC ACID
 
Authors :  X. Yu, H. Blanchard
Date :  04 Aug 11  (Deposition) - 17 Oct 12  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Sandwich, Lectin, Sugar Binding Protein, Viral Protein, Neu5Gc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Yu, V. T. Dang, F. E. Fleming, M. Von Itzstein, B. S. Coulson, H. Blanchard
Structural Basis Of Rotavirus Strain Preference Toward N-Acetyl- Or N-Glycolylneuraminic Acid-Containing Receptors
J. Virol. V. 86 13456 2012
PubMed-ID: 23035213  |  Reference-DOI: 10.1128/JVI.06975-11

(-) Compounds

Molecule 1 - OUTER CAPSID PROTEIN VP4
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P-GEX
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: RV-A
    Organism Scientific: PORCINE ROTAVIRUS
    Organism Taxid: 31578
    Strain: SEROTYPE 3 / STRAIN CRW-8
    Synonym: HEMAGGLUTININ, OUTER CAPSID PROTEIN VP8*, OUTER CAPSID PROTEIN VP5*

 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  (6, 12)

Asymmetric Unit (6, 12)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MN02Ligand/IonMETHYL 3,5-DIDEOXY-5-[(HYDROXYACETYL)AMINO]-D-GLYCERO-ALPHA-D-GALACTO-NON-2-ULOPYRANOSIDONIC ACID
4MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NA2Ligand/IonSODIUM ION
6SO42Ligand/IonSULFATE ION
Biological Unit 1 (5, 7)
No.NameCountTypeFull Name
1BEN1Ligand/IonBENZAMIDINE
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MN01Ligand/IonMETHYL 3,5-DIDEOXY-5-[(HYDROXYACETYL)AMINO]-D-GLYCERO-ALPHA-D-GALACTO-NON-2-ULOPYRANOSIDONIC ACID
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NA-1Ligand/IonSODIUM ION
6SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1BEN-1Ligand/IonBENZAMIDINE
2EPE-1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MN01Ligand/IonMETHYL 3,5-DIDEOXY-5-[(HYDROXYACETYL)AMINO]-D-GLYCERO-ALPHA-D-GALACTO-NON-2-ULOPYRANOSIDONIC ACID
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5NA-1Ligand/IonSODIUM ION
6SO4-1Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:52 , ARG A:101 , GLY A:187 , TYR A:188 , TYR A:189 , SER A:190 , HOH A:277 , HOH A:320 , HOH A:342 , HOH A:357 , HOH A:368 , HOH A:388 , EPE A:2691 , PRO B:68 , GLN B:70BINDING SITE FOR RESIDUE MN0 A 1000
02AC2SOFTWAREHOH A:34 , THR A:153 , GLN A:154 , HOH A:325BINDING SITE FOR RESIDUE SO4 A 2000
03AC3SOFTWARESER A:134 , GLN A:135 , THR A:136 , HOH A:232 , HOH A:253 , GLY B:62 , SER B:63 , LEU B:64 , LEU B:65BINDING SITE FOR RESIDUE SO4 A 225
04AC4SOFTWAREPRO A:86 , THR A:87 , VAL A:88 , GLY A:90 , VAL A:91 , VAL A:92 , PHE A:202 , CYS A:203 , HOH A:328BINDING SITE FOR RESIDUE MPD A 4210
05AC5SOFTWAREPRO A:68 , ASP A:204 , HOH A:305 , HOH A:379 , THR B:73 , GLN B:94 , THR B:96 , ASN B:198 , THR B:200BINDING SITE FOR RESIDUE MPD A 226
06AC6SOFTWAREASP A:100 , ARG A:101 , HOH A:368 , MN0 A:1000 , HOH B:35 , ASP B:66 , PRO B:68 , TYR B:69 , GLN B:70 , HOH B:239BINDING SITE FOR RESIDUE EPE A 2691
07AC7SOFTWARETYR A:175 , THR A:186 , ARG A:210 , GLU A:213BINDING SITE FOR RESIDUE BEN A 1561
08AC8SOFTWAREASP A:142 , GLY A:156 , TYR A:165 , THR A:176 , TYR A:177 , HOH A:342BINDING SITE FOR RESIDUE NA A 1
09AC9SOFTWAREHOH B:46 , ASN B:75 , ARG B:101 , ASN B:178 , GLY B:187 , TYR B:188 , TYR B:189 , SER B:190 , MPD B:225 , HOH B:325 , HOH B:336 , HOH B:360 , HOH B:361 , HOH B:362BINDING SITE FOR RESIDUE MN0 B 1000
10BC1SOFTWAREPRO B:86 , THR B:87 , VAL B:88 , VAL B:91 , VAL B:92 , CYS B:203BINDING SITE FOR RESIDUE MPD B 4210
11BC2SOFTWARETYR B:69 , HOH B:327 , MN0 B:1000BINDING SITE FOR RESIDUE MPD B 225
12BC3SOFTWAREASP B:142 , GLY B:156 , TYR B:165 , THR B:176 , TYR B:177 , ASN B:178 , HOH B:363BINDING SITE FOR RESIDUE NA B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TAY)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:67 -Pro A:68
2Thr A:181 -Pro A:182
3Gly B:67 -Pro B:68
4Thr B:181 -Pro B:182

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TAY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TAY)

(-) Exons   (0, 0)

(no "Exon" information available for 3TAY)

(-) 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:163
 aligned with VP4_ROTP3 | P0C6Y8 from UniProtKB/Swiss-Prot  Length:776

    Alignment length:174
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
            VP4_ROTP3    51 GAGETNDSTTVEPLLDGPYRPTTFNPPTSYWVLLAPTVEGVVIQGTNNIDRWLATILIEPNVQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSKTTPTGSYTQHGPLFSTPKLYAVMKFSGRIYTYNGTTPNATTGYYSTTNYDTVNMTLFCDFYIIPRNQEEKCTEYINHGL 224
               SCOP domains d3           taya_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-----------..eeee..eee.....eeeeee....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee.....eeeeeeee.......eeeeeeee....eeeeee..eeeeeeee....eeeeee..hhhhheeee..eeeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tay A  62 GS-----------LLDGPYQPTTFNPPTSYWILLAPTVEGVVIQGTNNIDRWLATILIEPNVQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSKTTPTGNYTQHGSLFSTPKLYAVMKFSGRIYTYNGTTPNATTGYYSTTNYDTVNMTSFCDFYIIPRNQEEKCTEYINHGL 224
                             |       -   |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
                             |          64                                                                                                                                                                
                            63                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:163
 aligned with VP4_ROTP3 | P0C6Y8 from UniProtKB/Swiss-Prot  Length:776

    Alignment length:174
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
            VP4_ROTP3    51 GAGETNDSTTVEPLLDGPYRPTTFNPPTSYWVLLAPTVEGVVIQGTNNIDRWLATILIEPNVQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSKTTPTGSYTQHGPLFSTPKLYAVMKFSGRIYTYNGTTPNATTGYYSTTNYDTVNMTLFCDFYIIPRNQEEKCTEYINHGL 224
               SCOP domains d3           tayb_ B: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-----------..eeee..eee.....eeeeee....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee.....eeeeeeee.......eeeeeeee....eeeeee..eeeeeeee....eeeeee..hhhhheeee..eeeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3tay B  62 GS-----------LLDGPYQPTTFNPPTSYWILLAPTVEGVVIQGTNNIDRWLATILIEPNVQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSKTTPTGNYTQHGSLFSTPKLYAVMKFSGRIYTYNGTTPNATTGYYSTTNYDTVNMTSFCDFYIIPRNQEEKCTEYINHGL 224
                             |       -   |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
                            63          64
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TAY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TAY)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (VP4_ROTP3 | P0C6Y8)
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

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        VP4_ROTP3 | P0C6Y8: 2i2s 3sis 3sit

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3tb0