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 DOUBLE-STRANDED RNA BINDING DOMAIN OF S. CEREVISIAE RNASE III (RNT1P) IN COMPLEX WITH AAGU TETRALOOP HAIRPIN
 
Authors :  Z. Wang, E. Hartman, K. Roy, G. Chanfreau, J. Feigon
Date :  06 Apr 11  (Deposition) - 31 Aug 11  (Release) - 31 Aug 11  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (16x)
NMR Structure *:  A,B  (1x)
Keywords :  Dsrbd, Aagu Tetraloop, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Wang, E. Hartman, K. Roy, G. Chanfreau, J. Feigon
Structure Of A Yeast Rnase Iii Dsrbd Complex With A Noncanonical Rna Substrate Provides New Insights Into Binding Specificity Of Dsrbds.
Structure V. 19 999 2011
PubMed-ID: 21742266  |  Reference-DOI: 10.1016/J.STR.2011.03.022
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RNA (32-MER)
    ChainsA
    EngineeredYES
    SyntheticYES
 
Molecule 2 - RIBONUCLEASE 3
    ChainsB
    EC Number3.1.26.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorPGEX-2T
    FragmentDRBM DOMAIN RESIDUES 366-453
    GeneRNT1, YM9408.01C, YM9959.21, YMR239C
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymRIBONUCLEASE III, RNASE III

 Structural Features

(-) Chains, Units

  12
NMR Structure (16x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2LBS)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.RNT1_YEAST369-437  1B:369-437
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DS_RBDPS50137 Double stranded RNA-binding domain (dsRBD) profile.RNT1_YEAST369-437  1B:369-437

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YMR239C1YMR239C.1XIII:749676-7482611416RNT1_YEAST1-4714711B:364-45390

(-) 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:RNA  Length:32
                                                                
                 2lbs A   1 GGGAUACCAUGUUCAAGUGAACGUGGUAUCUC  32
                                    10        20        30  

Chain B from PDB  Type:PROTEIN  Length:90
 aligned with RNT1_YEAST | Q02555 from UniProtKB/Swiss-Prot  Length:471

    Alignment length:90
                                   373       383       393       403       413       423       433       443       453
           RNT1_YEAST   364 DKLDMNAKRQLYSLIGYASLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAAENALRDKKMLDFYAKQRAAIPRSES 453
               SCOP domains d2lbsb_ B: automated matches                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh........eeeeee.........eeeeeee...eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----DS_RBD  PDB: B:369-437 UniProt: 369-437                              ---------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:364-453 UniProt: 1-471 [INCOMPLETE]                                       Transcript 1
                 2lbs B 364 GSLDMNAKRQLYSLIGYASLRLHYVTVKKPTAVDPNSIVECRVGDGTVLGTGVGRNIKIAGIRAAENALRDKKMLDFYAKQRAAIPRSES 453
                                   373       383       393       403       413       423       433       443       453

   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, 1)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

NMR Structure(hide GO term definitions)
Chain B   (RNT1_YEAST | Q02555)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    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:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    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).
    GO:0004525    ribonuclease III activity    Catalysis of the endonucleolytic cleavage of RNA with 5'-phosphomonoesters and 3'-OH termini; makes two staggered cuts in both strands of dsRNA, leaving a 3' overhang of 2 nt.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
    GO:0006396    RNA processing    Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
    GO:0034473    U1 snRNA 3'-end processing    Any process involved in forming the mature 3' end of a U1 snRNA molecule.
    GO:0034475    U4 snRNA 3'-end processing    Any process involved in forming the mature 3' end of a U4 snRNA molecule.
    GO:0034476    U5 snRNA 3'-end processing    Any process involved in forming the mature 3' end of a U5 snRNA molecule.
    GO:0034963    box C/D snoRNA processing    Any process involved in the conversion of a primary box C/D type small nucleolar RNA (snoRNA) transcript into a mature box C/D snoRNA.
    GO:0034964    box H/ACA snoRNA processing    Any process involved in the conversion of a primary box H/ACA type small nucleolar RNA (snoRNA) transcript into a mature box H/ACA snoRNA.
    GO:0006325    chromatin organization    Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic chromatin.
    GO:0000294    nuclear-transcribed mRNA catabolic process, endonucleolytic cleavage-dependent decay    A minor degradation pathway nuclear-transcribed mRNAs that begins with an endonucleolytic cleavage to generate unprotected ends.
    GO:0090305    nucleic acid phosphodiester bond hydrolysis    The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
    GO:0031054    pre-miRNA processing    Any process involved in the conversion of a pre-microRNA transcript into a mature microRNA molecule.
    GO:0031053    primary miRNA processing    Any process involved in the conversion of a primary microRNA transcript into a pre-microRNA molecule.
    GO:0030422    production of siRNA involved in RNA interference    Cleavage of double-stranded RNA to form small interfering RNA molecules (siRNAs) of 21-23 nucleotides, in the context of RNA interference.
    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:0009303    rRNA transcription    The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template.
    GO:0060237    regulation of fungal-type cell wall organization    Any process that modulates the rate, frequency or extent of the formation, arrangement of constituent parts, or disassembly of the fungal-type cell wall.
    GO:0030847    termination of RNA polymerase II transcription, exosome-dependent    The process in which transcription of nonpolyadenylated RNA polymerase II transcripts is terminated; coupled to the maturation of the RNA 3'-end.
cellular component
    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:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.

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

(-) 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
  2lbs
    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
  RNT1_YEAST | Q02555
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.26.3
    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
  RNT1_YEAST | Q02555
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        RNT1_YEAST | Q025551t4l 1t4n 1t4o 2lup 2luq 4oog 5t16

(-) Related Entries Specified in the PDB File

1t4l RELATED ID: 17574 RELATED DB: BMRB