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 :  X-RAY STRUCTURE OF THE MURINE NOROVIRUS (MNV)-1 CAPSID PROTEIN PROTRUDING (P) DOMAIN
 
Authors :  J. R. Rubin, J. A. Stuckey
Date :  09 Feb 10  (Deposition) - 21 Apr 10  (Release) - 19 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Viral Capsid Protein, Protruding (P) Domain, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Taube, J. R. Rubin, U. Katpally, T. J. Smith, A. Kendall, J. A. Stuckey, C. E. Wobus
High-Resolution X-Ray Structure And Functional Analysis Of The Murine Norovirus 1 Capsid Protein Protruding Domain.
J. Virol. V. 84 5695 2010
PubMed-ID: 20335262  |  Reference-DOI: 10.1128/JVI.00316-10

(-) Compounds

Molecule 1 - CAPSID PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PROTRUDING (P) DOMAIN, RESIDUES 228-540
    Gene: 223997 [NCBI]
    Organism Scientific: MURINE NOROVIRUS 1
    Organism Taxid: 223997
    Strain: MNV-1

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3LQE)

(-) Sites  (0, 0)

(no "Site" information available for 3LQE)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LQE)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:421 -Pro A:422

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LQE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LQE)

(-) Exons   (0, 0)

(no "Exon" information available for 3LQE)

(-) 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 Q2V8W4_9CALI | Q2V8W4 from UniProtKB/TrEMBL  Length:541

    Alignment length:313
                                   237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537   
         Q2V8W4_9CALI   228 RMVDLPVIQPRLCTHARWPAPVYGLLVDPSLPSNPQWQNGRVHVDGTLLGTTPISGSWVSCFAAEAAYEFQSGTGEVATFTLIEQDGSAYVPGDRAAPLGYPDFSGQLEIEVQTETTKTGDKLKVTTFEMILGPTTNADQAPYQGRVFASVTAAASLDLVDGRVRAVPRSIYGFQDTIPEYNDGLLVPLAPPIGPFLPGEVLLRFRTYMRQIDTADAAAEAIDCALPQEFVSWFASNAFTVQSEALLLRYRNTLTGQLLFECKLYNEGYIALSYSGSGPLTFPTDGIFEVVSWVPRLYQLASVGSLATGRMLK 540
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Calici_coat-3lqeA01 A:228-292                                    ----------------Calici_coat_C-3lqeA02 A:309-538                                                                                                                                                                                                       -- Pfam domains
         Sec.struct. author ........hhhhh..........eeee...........................hhhhh..eeeeeeeeee...eeeeeeeee.....................eeeeeeeeee..........eeeeeee..............eeeeee..........eeeeeeeeeeeeee........................eee.eeeeeeee......eeeeeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee......ee.....eeeeeeee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqe A 228 RMVDLPVIQPRLCTHARWPAPVYGLLVDPSLPSNPQWQNGRVHVDGTLLGTTPISGSWVSCFAAEAAYEFQSGTGEVATFTLIEQDGSAYVPGDRAAPLGYPDFSGQLEIEVQTETTKTGDKLKVTTFEMILGPTTNADQAPYQGRVFASVTAAASLDLVDGRVRAVPRSIYGFQDTIPEYNDGLLVPLAPPIGPFLPGEVLLRFRTYMRQIDTADAAAEAIDCALPQEFVSWFASNAFTVQSEALLLRYRNTLTGQLLFECKLYNEGYIALSYSGSGPLTFPTDGIFEVVSWVPRLYQLASVGSLATGRMLK 540
                                   237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537   


Chain A from PDB  Type:PROTEIN  Length:313
 aligned with Q80J94_9CALI | Q80J94 from UniProtKB/TrEMBL  Length:541

    Alignment length:313
                                   237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537   
         Q80J94_9CALI   228 RMVDLPVIQPRLCTHARWPAPVYGLLVDPSLPSNPQWQNGRVHVDGTLLGTTPISGSWVSCFAAEAAYKFQSGTGEVATFTLIEQDGSAYVPGDRAAPLGYPDFSGQLEIEVQTETTKTGDKLKVTTFEMILGPTTNADQAPYQGRVFASVTAAASLDLVDGRVRAVPRSIYGFQDTIPEYNDGLLVPLAPPIGPFLPGEVLLRFRTYMRQIDTADAAAEAIDCALPQEFVSWFASNAFTVQSEALLLRYRNTLTGQLLFECKLYNEGYIALSYSGSGPLTFPTDGIFEVVSWVPRLYQLASVGSLATGRMLK 540
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Calici_coat-3lqeA01 A:228-292                                    ----------------Calici_coat_C-3lqeA02 A:309-538                                                                                                                                                                                                       -- Pfam domains
         Sec.struct. author ........hhhhh..........eeee...........................hhhhh..eeeeeeeeee...eeeeeeeee.....................eeeeeeeeee..........eeeeeee..............eeeeee..........eeeeeeeeeeeeee........................eee.eeeeeeee......eeeeeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee......ee.....eeeeeeee................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lqe A 228 RMVDLPVIQPRLCTHARWPAPVYGLLVDPSLPSNPQWQNGRVHVDGTLLGTTPISGSWVSCFAAEAAYEFQSGTGEVATFTLIEQDGSAYVPGDRAAPLGYPDFSGQLEIEVQTETTKTGDKLKVTTFEMILGPTTNADQAPYQGRVFASVTAAASLDLVDGRVRAVPRSIYGFQDTIPEYNDGLLVPLAPPIGPFLPGEVLLRFRTYMRQIDTADAAAEAIDCALPQEFVSWFASNAFTVQSEALLLRYRNTLTGQLLFECKLYNEGYIALSYSGSGPLTFPTDGIFEVVSWVPRLYQLASVGSLATGRMLK 540
                                   237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537
   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 3LQE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LQE)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Viral_ssRNA_CP (106)
(-)
Clan: no clan defined [family: Calici_coat_C] (19)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q80J94_9CALI | Q80J94)

Chain A   (Q2V8W4_9CALI | Q2V8W4)
biological process
    GO:0019049    evasion or tolerance of host defenses by virus    Any process, either active or passive, by which a virus avoids or tolerates the effects of its host organism's defense(s). Host defenses may be induced by the presence of the virus or may be preformed (e.g. physical barriers). The host is defined as the larger of the organisms involved in a symbiotic interaction.

 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 3lqe)
 
  Sites
(no "Sites" information available for 3lqe)
 
  Cis Peptide Bonds
    Gly A:421 - Pro A:422   [ RasMol ]  
 
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
  3lqe
    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
  Q2V8W4_9CALI | Q2V8W4
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  Q80J94_9CALI | Q80J94
    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
  Q2V8W4_9CALI | Q2V8W4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q80J94_9CALI | Q80J94
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q2V8W4_9CALI | Q2V8W4: 3lq6

(-) Related Entries Specified in the PDB File

3lq6