Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE CORE DOMAIN (11-85) OF THE MURINE NOROVIRUS VPG PROTEIN
 
Authors :  E. N. Leen, R. Kwok, J. R. Birtley, S. N. Prater, P. J. Simpson, S. Matthew J. Marchant, S. Curry
Date :  05 Feb 13  (Deposition) - 27 Mar 13  (Release) - 08 May 13  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Vpg, Viral Protein, Ns5 (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. N. Leen, K. Y. Kwok, J. R. Birtley, P. J. Simpson, C. V. Subba-Reddy, Y. Chaudhry, S. V. Sosnovtsev, K. Y. Green, S. N. Prater, M. Tong, J. C. Young, L. M. Chung, J. Marchant, L. O. Roberts, C. C. Kao, S. Matthews, I. G. Goodfellow, S. Curry
Structures Of The Compact Helical Core Domains Of Feline Calicivirus And Murine Norovirus Vpg Proteins.
J. Virol. V. 87 5318 2013
PubMed-ID: 23487472  |  Reference-DOI: 10.1128/JVI.03151-12

(-) Compounds

Molecule 1 - MURINE NOROVIRUS VPG PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPETM11
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantROSETTA
    Expression System Vector TypePLASMID
    FragmentCORE DOMAIN
    GeneVPG
    Organism ScientificMURINE NOROVIRUS 1
    Organism Taxid223997

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2M4G)

(-) Sites  (0, 0)

(no "Site" information available for 2M4G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2M4G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2M4G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2M4G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2M4G)

(-) Exons   (0, 0)

(no "Exon" information available for 2M4G)

(-) Sequences/Alignments

NMR Structure
   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:75
 aligned with Q80J95_9CALI | Q80J95 from UniProtKB/TrEMBL  Length:1687

    Alignment length:75
                                   890       900       910       920       930       940       950     
         Q80J95_9CALI   881 GRPGVFRTRGLTDEEYDEFKKRRESRGGKYSIDDYLADREREEELLERDEEEAIFGDGFGLKATRRSRKAERAKL 955
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhh....hhhhhhhhhhhhh...............hhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 2m4g A  11 GRPGVFRTRGLTDEEYDEFKKRRESRGGKYSIDDYLADREREEELLERDEEEAIFGDGFGLKATRRSRKAERAKL  85
                                    20        30        40        50        60        70        80     

   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 2M4G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2M4G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2M4G)

(-) Gene Ontology  (18, 18)

NMR Structure(hide GO term definitions)
Chain A   (Q80J95_9CALI | Q80J95)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003724    RNA helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a RNA helix.
    GO:0003968    RNA-directed 5'-3' RNA polymerase activity    Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1); uses an RNA template, i.e. the catalysis of RNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time.
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0017111    nucleoside-triphosphatase activity    Catalysis of the reaction: a nucleoside triphosphate + H2O = nucleoside diphosphate + phosphate.
    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.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0044419    interspecies interaction between organisms    Any process in which an organism has an effect on an organism of a different species.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001172    transcription, RNA-templated    The cellular synthesis of RNA on a template of RNA.
    GO:0039694    viral RNA genome replication    The replication of a viral RNA genome.

 Visualization

(-) Interactive Views

NMR Structure
  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 2m4g)
 
  Sites
(no "Sites" information available for 2m4g)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2m4g)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2m4g
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q80J95_9CALI | Q80J95
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  Q80J95_9CALI | Q80J95
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q80J95_9CALI | Q80J952mcd 2mch 3nah 3nai 3qid 3sfg 3sfu 3upf 3uqs 3ur0 4ash 4nru 4o4r 4x2v 4x2w 4x2x 4x2y

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2M4G)