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(-) Description

Title :  CRYSTAL STRUCTURE OF PORCINE CRW-8 ROTAVIRUS VP8* IN COMPLEX WITH ACERAMIDO-GM3
 
Authors :  H. Blanchard, X. Yu
Date :  20 Jun 11  (Deposition) - 28 Sep 11  (Release) - 30 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Sandwich, Lectin, Gm3, Sugar Binding Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Yu, B. S. Coulson, F. E. Fleming, J. C. Dyason, M. Von Itzstein, H. Blanchard
Novel Structural Insights Into Rotavirus Recognition Of Ganglioside Glycan Receptors.
J. Mol. Biol. V. 413 929 2011
PubMed-ID: 21945555  |  Reference-DOI: 10.1016/J.JMB.2011.09.005

(-) 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: 469008
    Expression System Vector Type: PLASMID
    Fragment: OUTER CAPSID PROTEIN VP8* (UNP RESIDUES 64-224)
    Mutation: YES
    Organism Common: RV-A
    Organism Scientific: PORCINE ROTAVIRUS
    Organism Taxid: 31578
    Strain: CRW-8
    Synonym: VP8* CARBOHYDRATE RECOGNITION PROTEIN

 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  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
1GAL2Ligand/IonBETA-D-GALACTOSE
2GLC2Ligand/IonALPHA-D-GLUCOSE
3MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4NA2Ligand/IonSODIUM ION
5SIA2Ligand/IonO-SIALIC ACID
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2GLC1Ligand/IonALPHA-D-GLUCOSE
3MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4NA-1Ligand/IonSODIUM ION
5SIA1Ligand/IonO-SIALIC ACID
Biological Unit 2 (4, 4)
No.NameCountTypeFull Name
1GAL1Ligand/IonBETA-D-GALACTOSE
2GLC1Ligand/IonALPHA-D-GLUCOSE
3MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
4NA-1Ligand/IonSODIUM ION
5SIA1Ligand/IonO-SIALIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:19 , HOH A:20 , ARG A:101 , HIS A:155 , TYR A:188 , TYR A:189 , SER A:190 , HOH A:262 , HOH A:277 , HOH A:278 , HOH A:280 , HOH A:347 , GAL A:6536 , GLN B:70BINDING SITE FOR RESIDUE SIA A 6535
02AC2SOFTWAREHOH A:283 , HOH A:297 , SIA A:6535 , GLC A:6537 , GLN B:70BINDING SITE FOR RESIDUE GAL A 6536
03AC3SOFTWAREHOH A:21 , TYR A:69 , GLN A:70 , THR A:72 , HOH A:279 , HOH A:282 , HOH A:283 , HOH A:297 , GAL A:6536 , PRO B:71 , THR B:72 , THR B:73 , HOH B:310 , HOH B:345BINDING SITE FOR RESIDUE GLC A 6537
04AC4SOFTWAREASP A:142 , GLY A:156 , TYR A:165 , THR A:176 , TYR A:177 , HOH A:235BINDING SITE FOR RESIDUE NA A 3000
05AC5SOFTWAREPRO A:86 , THR A:87 , VAL A:88 , GLY A:90 , VAL A:91BINDING SITE FOR RESIDUE MRD A 4210
06AC6SOFTWAREHOH B:44 , ARG B:101 , HIS B:155 , TYR B:188 , TYR B:189 , SER B:190 , HOH B:294 , HOH B:295 , HOH B:296 , HOH B:305 , GAL B:6536BINDING SITE FOR RESIDUE SIA B 6535
07AC7SOFTWARETHR A:147 , HOH A:287 , HOH B:296 , SIA B:6535 , GLC B:6537BINDING SITE FOR RESIDUE GAL B 6536
08AC8SOFTWAREASP A:100 , THR A:146 , HOH A:233 , GAL B:6536BINDING SITE FOR RESIDUE GLC B 6537
09AC9SOFTWAREASP B:142 , GLY B:156 , TYR B:165 , THR B:176 , TYR B:177 , HOH B:241BINDING SITE FOR RESIDUE NA B 3001
10BC1SOFTWAREPRO B:86 , THR B:87 , VAL B:88 , GLY B:90 , VAL B:91 , PHE B:202 , CYS B:203 , HOH B:273BINDING SITE FOR RESIDUE MRD B 4210

(-) SS Bonds  (0, 0)

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

(-) 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 3SIT)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SIT)

(-) 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           sita_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-----------..eeee...ee.....eeeee.....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee.....eeeeeeee.......eeeeeeee....eeeeee..eeeeeeee....eeeeee..hhhhheeee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3sit A  62 GS-----------LLDGPYQPTTFNPPTSYWILLAPTVEGVVIQGTNNIDRWLATILIEPNVQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSKTTPTGNYTQHGPLFSTPKLYAVMKFSGRIYTYNGTTPNATTGYYSTTNYDTVNMTSFCDFYIIPRNQEEKCTEYINHGL 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:161
 aligned with VP4_ROTP3 | P0C6Y8 from UniProtKB/Swiss-Prot  Length:776

    Alignment length:161
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 
            VP4_ROTP3    64 LLDGPYRPTTFNPPTSYWVLLAPTVEGVVIQGTNNIDRWLATILIEPNVQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSKTTPTGSYTQHGPLFSTPKLYAVMKFSGRIYTYNGTTPNATTGYYSTTNYDTVNMTLFCDFYIIPRNQEEKCTEYINHGL 224
               SCOP domains d3sitb_ 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
                 3sit B  64 LLDGPYQPTTFNPPTSYWILLAPTVEGVVIQGTNNIDRWLATILIEPNVQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSKTTPTGNYTQHGPLFSTPKLYAVMKFSGRIYTYNGTTPNATTGYYSTTNYDTVNMTSFCDFYIIPRNQEEKCTEYINHGL 224
                                    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)
    → 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 3SIT)

(-) Pfam Domains  (0, 0)

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

(-) 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

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

UniProtKB/Swiss-Prot
        VP4_ROTP3 | P0C6Y8: 2i2s 3sis 3tay

(-) Related Entries Specified in the PDB File

2i2s ROTAVIRUS CRW-8 VP8* IN COMPLEX WITH MONOSACCHARIDE AMENEU5AC
3sis PORCINE CRW-8 ROTAVIRUS VP8* IN COMPLEX WITH ACERAMIDO-GM3_ GC