Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE RHESUS ROTAVIRUS VP5 ANTIGEN DOMAIN TRIMER
 
Authors :  J. D. Yoder, P. R. Dormitzer
Date :  24 Sep 05  (Deposition) - 18 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C
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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OUTER CAPSID PROTEIN VP4
    Chains: A, B, C
    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

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2B4I)

(-) Sites  (0, 0)

(no "Site" information available for 2B4I)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B4I)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:434 -Pro A:435
2Glu B:434 -Pro B:435
3Glu C:434 -Pro C:435

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B4I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B4I)

(-) Exons   (0, 0)

(no "Exon" information available for 2B4I)

(-) 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:232
 aligned with VP4_ROTRH | P12473 from UniProtKB/Swiss-Prot  Length:776

    Alignment length:232
                                   255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475  
            VP4_ROTRH   246 HRAQANEDIVVSKTSLWKEMQYNRDITIRFKFASSIVKSGGLGYKWSEISFKPANYQYTYTRDGEDVTAHTTCSVNGMNDFNFNGGSLPTDFIISRYEVIKENSYVYVDYWDDSQAFRNMVYVRSLAANLNSVICTGGDYSFALPVGQWPVMTGGAVSLHSAGVTLSTQFTDFVSFNSLRFRFRLTVEEPSFSITRTRVGGLYGLPAAYPNNGKEYYEVAGRLSLISLVPSN 477
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee...eeeeeeeeeeeeee..eeeeee......eeeeeeee.eeeeeeeee..eeeeeeeeeeee..eeeeee........eeeeeeee....eeeeeeee.hhhhh....eeeeeeee..eeee...ee.........eeee.eeeeeeeeeeeeeee....eeeeeeeeeeeee....eee..........ee..........eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b4i A 246 MRAQANEDIVVSKTSLWKEMQYNRDITIRFKFASSIVKSGGLGYKWSEISFKPANYQYTYTRDGEEVTAHTTCSVNGMNDFNFNGGSLPTDFVISRYEVIKENSYVYVDYWDDSQAFRNMVYVRSLAANLNSVICTGGDYSFALPVGQWPVMTGGAVSLHSAGVTLSTQFTDFVSLNSLRFRFRLTVEEPSFSITRTRVSRLYGLPAANPNNGKEYYEVAGRFSLISLVPSN 477
                                   255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475  


Chain B from PDB  Type:PROTEIN  Length:234
 aligned with VP4_ROTRH | P12473 from UniProtKB/Swiss-Prot  Length:776

    Alignment length:234
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473    
            VP4_ROTRH   244 ISHRAQANEDIVVSKTSLWKEMQYNRDITIRFKFASSIVKSGGLGYKWSEISFKPANYQYTYTRDGEDVTAHTTCSVNGMNDFNFNGGSLPTDFIISRYEVIKENSYVYVDYWDDSQAFRNMVYVRSLAANLNSVICTGGDYSFALPVGQWPVMTGGAVSLHSAGVTLSTQFTDFVSFNSLRFRFRLTVEEPSFSITRTRVGGLYGLPAAYPNNGKEYYEVAGRLSLISLVPSN 477
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeee...eeeeeeeeeeeeee..eeeeee......eeeeeeee.eeeeeeeee..eeeeeeeeeeee..eeeeee........eeeeeeee....eeeeeeee.hhhhh....eeeeeeee..eeee...ee.........eeee.eeeeeeeeeeeeeee....eeeeeeeeeeeee....eee..........ee..........eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2b4i B 244 SHMRAQANEDIVVSKTSLWKEMQYNRDITIRFKFASSIVKSGGLGYKWSEISFKPANYQYTYTRDGEEVTAHTTCSVNGMNDFNFNGGSLPTDFVISRYEVIKENSYVYVDYWDDSQAFRNMVYVRSLAANLNSVICTGGDYSFALPVGQWPVMTGGAVSLHSAGVTLSTQFTDFVSLNSLRFRFRLTVEEPSFSITRTRVSRLYGLPAANPNNGKEYYEVAGRFSLISLVPSN 477
                                   253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473    


Chain C from PDB  Type:PROTEIN  Length:232
 aligned with VP4_ROTRH | P12473 from UniProtKB/Swiss-Prot  Length:776

    Alignment length:232
                                   255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475  
            VP4_ROTRH   246 HRAQANEDIVVSKTSLWKEMQYNRDITIRFKFASSIVKSGGLGYKWSEISFKPANYQYTYTRDGEDVTAHTTCSVNGMNDFNFNGGSLPTDFIISRYEVIKENSYVYVDYWDDSQAFRNMVYVRSLAANLNSVICTGGDYSFALPVGQWPVMTGGAVSLHSAGVTLSTQFTDFVSFNSLRFRFRLTVEEPSFSITRTRVGGLYGLPAAYPNNGKEYYEVAGRLSLISLVPSN 477
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee...eeeeeeeeeeeeee..eeeeee......eeeeeeee.eeeeeeeee..eeeeeeeeeeee..eeeeee........eeeeeeee....eeeeeeee.hhhhh...eeeeeeeee..eeee...ee.........eeee.eeeeeeeeeeeeeee....eeeeeeeeeeeee....eee..........ee..........eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b4i C 246 MRAQANEDIVVSKTSLWKEMQYNRDITIRFKFASSIVKSGGLGYKWSEISFKPANYQYTYTRDGEEVTAHTTCSVNGMNDFNFNGGSLPTDFVISRYEVIKENSYVYVDYWDDSQAFRNMVYVRSLAANLNSVICTGGDYSFALPVGQWPVMTGGAVSLHSAGVTLSTQFTDFVSLNSLRFRFRLTVEEPSFSITRTRVSRLYGLPAANPNNGKEYYEVAGRFSLISLVPSN 477
                                   255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475
   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 2B4I)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2B4I)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B4I)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (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.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2b4i)
 
  Sites
(no "Sites" information available for 2b4i)
 
  Cis Peptide Bonds
    Glu A:434 - Pro A:435   [ RasMol ]  
    Glu B:434 - Pro B:435   [ RasMol ]  
    Glu C:434 - Pro C:435   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2b4i
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  VP4_ROTRH | P12473
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  VP4_ROTRH | P12473
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        VP4_ROTRH | P12473: 1kqr 1kri 1slq 2b4h 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 DIMER