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(-) Description

Title :  STRUCTURE OF THE EXTENDED DIARRHEA-INDUCING DOMAIN OF ROTAVIRUS ENTEROTOXIGENIC PROTEIN NSP4
 
Authors :  R. Deepa, K. Suguna, C. Durga Rao
Date :  29 Nov 06  (Deposition) - 26 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Rotavirus Enterotoxin, Nonstructural Protein, Nsp4, Tetrameric Coiled-Coil, Virulence, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Deepa, C. Durga Rao, K. Suguna
Structure Of The Extended Diarrhea-Inducing Domain Of Rotavirus Enterotoxigenic Protein
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NON-STRUCTURAL GLYCOPROTEIN NSP4
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET22(B)+
    Expression System Strain: BL21 DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: DIARRHEA-INDUCING DOMAIN (RESIDUES 95-146)
    Gene: G10
    Organism Scientific: SIMIAN ROTAVIRUS A/SA11
    Organism Taxid: 10923
    Strain: SA11
    Synonym: NS28

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:123 , GLU B:120 , GLN B:123BINDING SITE FOR RESIDUE CA B 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O1K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O1K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O1K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O1K)

(-) Exons   (0, 0)

(no "Exon" information available for 2O1K)

(-) 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:43
 aligned with NSP4_ROTS1 | P04512 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:43
                                   104       114       124       134   
           NSP4_ROTS1    95 IEKQMDRVVKEMRRQLEMIDKLTTREIEQVELLKRIYDKLTVQ 137
               SCOP domains d2o1ka_ A: automated matches                SCOP domains
               CATH domains 2o1kA00 A:95-137                            CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 2o1k A  95 IEKQMDRVVKEMRRQLEMIDKLTTREIEQVELLKRIYDKLTVQ 137
                                   104       114       124       134   


Chain A from PDB  Type:PROTEIN  Length:43
 aligned with O92323_9REOV | O92323 from UniProtKB/TrEMBL  Length:175

    Alignment length:43
                                   104       114       124       134   
         O92323_9REOV    95 IEKQMDRVVKEMRRQLEMIDKLTTREIEQVELLKRIYDKLTVQ 137
               SCOP domains d2o1ka_ A: automated matches                SCOP domains
               CATH domains 2o1kA00 A:95-137                            CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 2o1k A  95 IEKQMDRVVKEMRRQLEMIDKLTTREIEQVELLKRIYDKLTVQ 137
                                   104       114       124       134   


Chain B from PDB  Type:PROTEIN  Length:43
 aligned with NSP4_ROTS1 | P04512 from UniProtKB/Swiss-Prot  Length:175

    Alignment length:43
                                   104       114       124       134   
           NSP4_ROTS1    95 IEKQMDRVVKEMRRQLEMIDKLTTREIEQVELLKRIYDKLTVQ 137
               SCOP domains d2o1kb_ B: automated matches                SCOP domains
               CATH domains 2o1kB00 B:95-137                            CATH domains
           Pfam domains (1) Rota_NSP4-2o1kB01 B:95-137                  Pfam domains (1)
           Pfam domains (2) Rota_NSP4-2o1kB02 B:95-137                  Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 2o1k B  95 IEKQMDRVVKEMRRQLEMIDKLTTREIEQVELLKRIYDKLTVQ 137
                                   104       114       124       134   


Chain B from PDB  Type:PROTEIN  Length:43
 aligned with O92323_9REOV | O92323 from UniProtKB/TrEMBL  Length:175

    Alignment length:43
                                   104       114       124       134   
         O92323_9REOV    95 IEKQMDRVVKEMRRQLEMIDKLTTREIEQVELLKRIYDKLTVQ 137
               SCOP domains d2o1kb_ B: automated matches                SCOP domains
               CATH domains 2o1kB00 B:95-137                            CATH domains
           Pfam domains (1) Rota_NSP4-2o1kB01 B:95-137                  Pfam domains (1)
           Pfam domains (2) Rota_NSP4-2o1kB02 B:95-137                  Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 2o1k B  95 IEKQMDRVVKEMRRQLEMIDKLTTREIEQVELLKRIYDKLTVQ 137
                                   104       114       124       134
   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: Coiled coil proteins (689)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Rota_NSP4] (3)

(-) Gene Ontology  (10, 12)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NSP4_ROTS1 | P04512)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0044155    host caveola    A small pit, depression, or invagination, such as any of the minute pits or incuppings of the host cell membrane formed during pinocytosis, that communicates with the outside of a host cell and extends inward, indenting the host cytoplasm and the host cell membrane. Such caveolae may be pinched off to form free vesicles within the host cytoplasm. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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:0033644    host cell membrane    Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0044169    host cell rough endoplasmic reticulum membrane    The lipid bilayer surrounding the host cell rough endoplasmic reticulum.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Chain A,B   (O92323_9REOV | O92323)
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NSP4_ROTS1 | P04512: 1g1i 1g1j
        O92323_9REOV | O92323: 1g1i 1g1j
UniProtKB/TrEMBL
        O92323_9REOV | O92323: 4wb4 4wba

(-) Related Entries Specified in the PDB File

2o1j NONSTRUCTURAL PROTEIN NSP4(SIMILAR PROTEIN)