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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RHESUS ROTAVIRUS VP5 ANTIGEN DOMAIN DIMER
 
Authors :  J. D. Yoder, P. R. Dormitzer
Date :  24 Sep 05  (Deposition) - 18 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Beta Sandwich; Greek Key; Membrane Penetration Protein; Non-Enveloped Virus; Spike Protein; Rearrangement, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Yoder, P. R. Dormitzer
Alternative Intermolecular Contacts Underlie The Rotavirus Vp5(*) Two- To Three-Fold Rearrangement
Embo J. V. 25 1559 2006
PubMed-ID: 16511559  |  Reference-DOI: 10.1038/SJ.EMBOJ.7601034

(-) Compounds

Molecule 1 - OUTER CAPSID PROTEIN VP4
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC-1
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: VP5* ANTIGEN DOMAIN
    Gene: GENOME SEGMENT 4
    Organism Scientific: RHESUS ROTAVIRUS
    Organism Taxid: 10969
    Other Details: SEE REMARK 400

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:412 , ARG A:425 , SER B:412 , ARG B:425BINDING SITE FOR RESIDUE TRS A 5001
2AC2SOFTWAREILE B:271 , ARG B:307 , ASP B:357 , SER B:359 , ALA B:361 , PHE B:362BINDING SITE FOR RESIDUE MPD B 1001
3AC3SOFTWAREHIS A:315 , TRP A:356 , HOH A:5110 , HOH A:5159 , VAL B:432 , GLU B:433 , HOH B:4058BINDING SITE FOR RESIDUE MPD A 2001
4AC4SOFTWARETHR A:335 , ASP A:336 , PHE A:337 , ARG A:441BINDING SITE FOR RESIDUE MPD A 3001
5AC5SOFTWAREHIS B:315 , THR B:317 , TRP B:356 , SER B:423 , HOH B:4064 , HOH B:4156BINDING SITE FOR RESIDUE MPD B 4001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B4H)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:434 -Pro A:435
2Glu B:434 -Pro B:435

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B4H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B4H)

(-) Exons   (0, 0)

(no "Exon" information available for 2B4H)

(-) 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:227
 aligned with VP4_ROTRH | P12473 from UniProtKB/Swiss-Prot  Length:776

    Alignment length:227
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       
            VP4_ROTRH   250 ANEDIVVSKTSLWKEMQYNRDITIRFKFASSIVKSGGLGYKWSEISFKPANYQYTYTRDGEDVTAHTTCSVNGMNDFNFNGGSLPTDFIISRYEVIKENSYVYVDYWDDSQAFRNMVYVRSLAANLNSVICTGGDYSFALPVGQWPVMTGGAVSLHSAGVTLSTQFTDFVSFNSLRFRFRLTVEEPSFSITRTRVGGLYGLPAAYPNNGKEYYEVAGRLSLISLVPS 476
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee....eeeeeeeeeeeeeeee..eeeeee......eeeeeeee.eeeeeeeee..eeeeeeeeeeee..eeeeee........eeeeeeee....eeeeeeee.hhhhhh...eeeeeeee..eeee...ee.........eeee.eeeeeeeeeeeeeee....eeeeeeeeeeeee....eee..........ee..........eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b4h A 250 ANEDIVVSKTSLWKEMQYNRDITIRFKFASSIVKSGGLGYKWSEISFKPANYQYTYTRDGEEVTAHTTCSVNGMNDFNFNGGSLPTDFVISRYEVIKENSYVYVDYWDDSQAFRNMVYVRSLAANLNSVICTGGDYSFALPVGQWPVMTGGAVSLHSAGVTLSTQFTDFVSLNSLRFRFRLTVEEPSFSITRTRVSRLYGLPAANPNNGKEYYEVAGRFSLISLVPS 476
                                   259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       


Chain B from PDB  Type:PROTEIN  Length:218
 aligned with VP4_ROTRH | P12473 from UniProtKB/Swiss-Prot  Length:776

    Alignment length:218
                                   268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468        
            VP4_ROTRH   259 TSLWKEMQYNRDITIRFKFASSIVKSGGLGYKWSEISFKPANYQYTYTRDGEDVTAHTTCSVNGMNDFNFNGGSLPTDFIISRYEVIKENSYVYVDYWDDSQAFRNMVYVRSLAANLNSVICTGGDYSFALPVGQWPVMTGGAVSLHSAGVTLSTQFTDFVSFNSLRFRFRLTVEEPSFSITRTRVGGLYGLPAAYPNNGKEYYEVAGRLSLISLVPS 476
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeee..eeeeee......eeeeeeee.eeeeeeeee..eeeeeeeeeeee..eeeeee........eeeeeeee....eeeeeeee.hhhhhh...eeeeeeee..eeee...ee.........eeee.eeeeeeeeeeeeeee....eeeeeeeeeeeee....eee..........ee..........eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b4h B 259 TSLWKEMQYNRDITIRFKFASSIVKSGGLGYKWSEISFKPANYQYTYTRDGEEVTAHTTCSVNGMNDFNFNGGSLPTDFVISRYEVIKENSYVYVDYWDDSQAFRNMVYVRSLAANLNSVICTGGDYSFALPVGQWPVMTGGAVSLHSAGVTLSTQFTDFVSLNSLRFRFRLTVEEPSFSITRTRVSRLYGLPAANPNNGKEYYEVAGRFSLISLVPS 476
                                   268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468
   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  (0, 0)

(no "SCOP Domain" information available for 2B4H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2B4H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B4H)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (VP4_ROTRH | P12473)
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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  VP4_ROTRH | P12473
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 Related Entries

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

UniProtKB/Swiss-Prot
        VP4_ROTRH | P12473: 1kqr 1kri 1slq 2b4i 2p3i 2p3j 2p3k 3tb0

(-) Related Entries Specified in the PDB File

1slq TRIMERIC CONFORMATION OF THE MEMBRANE INTERACTION DOMAIN, VP5CT
2b4h CRYSTAL STRUCTURE OF THE RHESUS ROTAVIRUS VP5* ANTIGEN DOMAIN TRIMER