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 :  SEGMENTAL ISOTOPE LABELING OF NPL3P
 
Authors :  L. Skrisovska, F. H-T. Allain
Date :  25 Sep 07  (Deposition) - 18 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Protein, Rna Recognition Motif, Nucleus, Phosphorylation, Ribonucleoprotein, Ribosome Biogenesis, Rna-Binding, Rrna Processing, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Skrisovska, F. H. Allain
Improved Segmental Isotope Labeling Methods For The Nmr Study Of Multidomain Or Large Proteins: Application To The Rrms Of Npl3P And Hnrnp L
J. Mol. Biol. V. 375 151 2008
PubMed-ID: 17936301  |  Reference-DOI: 10.1016/J.JMB.2007.09.030
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEOLAR PROTEIN 3
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21 CODON+ RIL
    Expression System Taxid562
    Expression System VectorPET28A+
    Expression System Vector TypeVECTOR
    FragmentRNA RECOGNITION MOTIF 2 (RRM 2) DOMAIN
    GeneNOP3, MTS1, NAB1, NPL3
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymMITOCHONDRIAL TARGETING SUPPRESSOR 1 PROTEIN, NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN 1

 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 2JVR)

(-) Sites  (0, 0)

(no "Site" information available for 2JVR)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.NOP3_YEAST125-195
200-275
  1-
A:29-104
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RRMPS50102 Eukaryotic RNA Recognition Motif (RRM) profile.NOP3_YEAST125-195
200-275
  1-
A:29-104

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YDR432W1YDR432W.1IV:1328776-13300201245NOP3_YEAST1-4144141A:25-10480

(-) 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:80
 aligned with NOP3_YEAST | Q01560 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:80
                                   205       215       225       235       245       255       265       275
           NOP3_YEAST   196 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDN 275
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains ------RRM_1-2jvrA01 A:31-98                                               ------ Pfam domains
         Sec.struct. author ....eeeeee......hhhhhhhhhhhhh....eee.........eeeee.hhhhhhhhhhhh..eee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----RRM  PDB: A:29-104 UniProt: 200-275                                          PROSITE
               Transcript 1 Exon 1.1  PDB: A:25-104 UniProt: 1-414 [INCOMPLETE]                              Transcript 1
                 2jvr A  25 PAKRYRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDGTGALEFPSEEILVEALERLNNIEFRGSVITVERDDN 104
                                    34        44        54        64        74        84        94       104

   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 2JVR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: RRM (206)

(-) Gene Ontology  (21, 21)

NMR Structure(hide GO term definitions)
Chain A   (NOP3_YEAST | Q01560)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0000993    RNA polymerase II core binding    Interacting selectively and non-covalently with RNA polymerase II core enzyme, a multisubunit eukaryotic nuclear RNA polymerase typically composed of twelve subunits.
    GO:0031370    eukaryotic initiation factor 4G binding    Interacting selectively and non-covalently with eukaryotic initiation factor 4G, a polypeptide factor involved in the initiation of ribosome-mediated translation.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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:0008143    poly(A) binding    Interacting selectively and non-covalently with a sequence of adenylyl residues in an RNA molecule, such as the poly(A) tail, a sequence of adenylyl residues at the 3' end of eukaryotic mRNA.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    GO:0000398    mRNA splicing, via spliceosome    The joining together of exons from one or more primary transcripts of messenger RNA (mRNA) and the excision of intron sequences, via a spliceosomal mechanism, so that mRNA consisting only of the joined exons is produced.
    GO:2000805    negative regulation of termination of RNA polymerase II transcription, poly(A)-coupled    Any process that stops, prevents or reduces the frequency, rate or extent of termination of RNA polymerase II transcription, poly(A)-coupled.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0032968    positive regulation of transcription elongation from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
    GO:0006364    rRNA processing    Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
    GO:0042254    ribosome biogenesis    A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
    GO:0006415    translational termination    The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030529    intracellular ribonucleoprotein complex    An intracellular macromolecular complex containing both protein and RNA molecules.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 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 2jvr)
 
  Sites
(no "Sites" information available for 2jvr)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2jvr)
 

(-) 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
  2jvr
    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
  NOP3_YEAST | Q01560
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  NOP3_YEAST | Q01560
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NOP3_YEAST | Q015602jd5 2jvo 2osq 2osr

(-) Related Entries Specified in the PDB File

2jvo