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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RHESUS ROTAVIRUS VP4 SIALIC ACID BINDING DOMAIN IN COMPLEX WITH 2-O-METHYL-ALPHA-D-N-ACETYL NEURAMINIC ACID
 
Authors :  P. R. Dormitzer, Z. -Y. J. Sun, G. Wagner, S. C. Harrison
Date :  07 Jan 02  (Deposition) - 27 Mar 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Rotavirus, Vp4, Vp8*, Spike Protein, Outer Capsid, Sialic Acid, Hemagglutinin, Cell Attachment, Neutralization Antigen, Lectin, Galectin Fold, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. R. Dormitzer, Z. -Y. J. Sun, G. Wagner, S. C. Harrison
The Rhesus Rotavirus Vp4 Sialic Acid Binding Domain Has A Galectin Fold With A Novel Carbohydrate Binding Site
Embo J. V. 21 885 2002
PubMed-ID: 11867517  |  Reference-DOI: 10.1093/EMBOJ/21.5.885
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VP4
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-VP8(62-224)
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SIALIC ACID BINDING DOMAIN (RESIDUES 62-224)
    Gene: SEGMENT 4
    Organism Scientific: RHESUS ROTAVIRUS
    Organism Taxid: 10969

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2MNA1Ligand/Ion2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:134 , GLN A:135 , THR A:136 , HOH A:2080BINDING SITE FOR RESIDUE SO4 A 3000
2AC2SOFTWAREARG A:101 , THR A:113 , ASN A:132 , ALA A:133 , THR A:146 , TYR A:155 , LYS A:187 , TYR A:188 , TYR A:189 , SER A:190 , HOH A:2003 , HOH A:2028 , HOH A:2034 , HOH A:2035 , HOH A:2038 , HOH A:2127 , HOH A:2183BINDING SITE FOR RESIDUE MNA A 1000
3AC3SOFTWAREMET A:168 , HIS A:170 , TYR A:175 , THR A:186 , ARG A:210 , GLU A:213BINDING SITE FOR RESIDUE GOL A 4000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KQR)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:67 -Pro A:68
2Gly A:156 -Pro A:157
3Thr A:181 -Pro A:182

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_VP4_ROTRH_001 *T146SVP4_ROTRH  ---  ---AT146S
2UniProtVAR_VP4_ROTRH_002 *A166GVP4_ROTRH  ---  ---AA166G
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1KQR)

(-) Exons   (0, 0)

(no "Exon" information available for 1KQR)

(-) 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_ROTRH | P12473 from UniProtKB/Swiss-Prot  Length:776

    Alignment length:160
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224
            VP4_ROTRH    65 LDGPYQPTSFNPPVDYWMLLAPTAAGVVVEGTNNTDRWLATILVEPNVTSETRSYTLFGTQEQITIANASQTQWKFIDVVKTTQNGSYSQYGPLQSTPKLYAVMKHNGKIYTYNGETPNVTTKYYSTTNYDSVNMTAFCDFYIIPREEESTCTEYINNGL 224
               SCOP domains d1kqra_ A: vp4 sialic acid binding domain                                                                                                                        SCOP domains
               CATH domains 1kqrA00 A:65-224  [code=2.60.120.200, no name defined]                                                                                                           CATH domains
               Pfam domains VP4_haemagglut-1kqrA01 A:65-224                                                                                                                                  Pfam domains
         Sec.struct. author .......eeee....eeeeee....eeeeeeee...eeeeeeee.....eeeeeeee..eeeeeeee......eeeeeeee.......eeeeeeee...eeeeeee..eeeeeeeee...eeeeeee.hhhhh.eeee.eeeee...hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------S-------------------G---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1kqr A  65 LDGPYQPTTFNPPVDYWMLLAPTAAGVVVEGTNNTDRWLATILVEPNVTSETRSYTLFGTQEQITIANASQTQWKFIDVVKTTQNGSYSQYGPLQSTPKLYAVMKHNGKIYTYNGETPNVTTKYYSTTNYDSVNMTAFCDFYIIPREEESTCTEYINNGL 224
                                    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: VP4_haemagglut] (5)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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: 1kri 1slq 2b4h 2b4i 2p3i 2p3j 2p3k 3tb0

(-) Related Entries Specified in the PDB File

1kri NMR SOLUTION STRUCTURES OF THE RHESUS ROTAVIRUS VP4 SIALIC ACID BINDING DOMAIN WITHOUT LIGAND