Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  NON STRUCTURAL PROTEIN ENCODED BY GENE SEGMENT 8 OF ROTAVIRUS (NSP2), AN NTPASE, SSRNA BINDING AND NUCLEIC ACID HELIX-DESTABILIZING PROTEIN
 
Authors :  H. Jayaram, Z. Taraporewala, J. T. Patton, B. V. Prasad
Date :  26 Mar 02  (Deposition) - 05 Jun 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (8x)
Keywords :  Alpha/Beta Protein, Hit-Like Fold, Octamer, Two Domain Protein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Jayaram, Z. Taraporewala, J. T. Patton, B. V. Prasad
Rotavirus Protein Involved In Genome Replication And Packaging Exhibits A Hit-Like Fold.
Nature V. 417 311 2002
PubMed-ID: 12015608  |  Reference-DOI: 10.1038/417311A

(-) Compounds

Molecule 1 - ROTAVIRUS-NSP2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE60 (QIAGEN)
    Expression System Strain: M15[PREP5]
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NSP2 OF ROTAVIRUS
    Gene: GENE SEGMENT 8
    Organism Scientific: SIMIAN 11 ROTAVIRUS (SEROTYPE 3 / STRAIN SA11- RAMIG)
    Organism Taxid: 36435
    Strain: SA11-RAMIG

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (8x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1L9V)

(-) Sites  (0, 0)

(no "Site" information available for 1L9V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1L9V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1L9V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L9V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1L9V)

(-) Exons   (0, 0)

(no "Exon" information available for 1L9V)

(-) 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:313
 aligned with NSP2_ROTSR | Q03243 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:313
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310   
           NSP2_ROTSR     1 MAELACFCYPHLENDSYKFIPFNNLAIKAMLTAKVDKKDMDKFYDSIIYGIAPPPQFKKRYNTNDNSRGMNFETIMFTKVAMLICEALNSLKVTQANVSNVLSRVVSIRHLENLVIRKENPQDILFHSKDLLLKSTLIAIGQSKEIETTITAEGGEIVFQNAAFTMWKLTYLEHQLMPILDQNFIEYKVTLNEDKPISDVHVKELVAELRWQYNKFAVITHGKGHYRIVKYSSVANHADRVYATFKSNVKTGVNNDFNLLDQRIIWQNWYAFTSSMKQGNTLDVCKRLLFQKMKPEKNPFKGLSTDRKMDEVS 313
               SCOP domains d1l9va2 A:1-143 Rotavirus NSP2 fragment, N-terminal domain                                                                                     d1l9va1 A:144-313 Rotavirus NSP2 fragment, C-terminal domain                                                                                                               SCOP domains
               CATH domains 1l9vA01 A:1-145 Rotavirus NSP2 fragment, N-terminal domain                                                                                       ------1l9vA02 A:152-312  [code=3.30.428.20, no name defined]                                                                                                           - CATH domains
               Pfam domains Rota_NS35-1l9vA01 A:1-313                                                                                                                                                                                                                                                                                                 Pfam domains
         Sec.struct. author ..hhhh.eeeeee..eeeeee.hhhhhhhhh....hhhhh...ee.....ee.hhhhhhhh............hhhhhhhhhhhhhhhh....hhhhhhhhhhh..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...............eeeee...eeeee.hhhhh...........eeeeee......hhhhhhhhhhhhhhhh..eeeee.....eeeeehhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhh.hhhhhhhhhhh..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l9v A   1 MAELACFCYPHLENDSYKFIPFNNLAIKAMLTAKVDKKDMDKFYDSIIYGIAPPPQFKKRYNTNDNSRGMNFETIMFTKVAMLICEALNSLKVTQANVSNVLSRVVSIRHLENLVIRKENPQDILFHSKDLLLKSTLIAIGQSKEIETTITAEGGEIVFQNAAFTMWKLTYLEHQLMPILDQNFIEYKVTLNEDKPISDVHVKELVAELRWQYNKFAVITHGKGHYRIVKYSSVANHADRVYATFKSNVKTGVNNDFNLLDQRIIWQNWYAFTSSMKQGNTLDVCKRLLFQKMKPEKNPFKGLSTDRKMDEVS 313
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310
   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  (2, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Rota_NS35] (5)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (NSP2_ROTSR | Q03243)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016817    hydrolase activity, acting on acid anhydrides    Catalysis of the hydrolysis of any acid anhydride.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0019079    viral genome replication    Any process involved directly in viral genome replication, including viral nucleotide metabolism.
cellular component
    GO:0030430    host cell cytoplasm    The cytoplasm of a host cell.

 Visualization

(-) Interactive Views

Asymmetric 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 1l9v)
 
  Sites
(no "Sites" information available for 1l9v)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1l9v)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 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
  1l9v
    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
  NSP2_ROTSR | Q03243
    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
  NSP2_ROTSR | Q03243
    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
        NSP2_ROTSR | Q03243: 2r7c 2r7j 2r7p 2r8f 4g0a 4g0j

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1L9V)