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
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF NOP9 RNA COMPLEX
 
Authors :  K. Ye, B. Wang
Date :  15 Dec 16  (Deposition) - 25 Jan 17  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B,D  (1x)
Biol. Unit 2:  A,C  (1x)
Keywords :  Pumilio Repeat-Containing Protein, Rna-Binding Protein, Rnp, Rna Binding Protein-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Wang, K. Ye
Nop9 Binds The Central Pseudoknot Region Of 18S Rrna
Nucleic Acids Res. V. 45 3559 2017
PubMed-ID: 28053123  |  Reference-DOI: 10.1093/NAR/GKW1323

(-) Compounds

Molecule 1 - NUCLEOLAR PROTEIN 9
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 53-634
    Gene: NOP9
    Organism Scientific: SACCHAROMYCES CEREVISIAE S288C
    Organism Taxid: 559292
    Strain: S288C
    Synonym: PUMILIO DOMAIN-CONTAINING PROTEIN NOP9
 
Molecule 2 - RNA (5'- R(*AP*AP*AP*GP*GP*AP*AP*UP*UP*GP*AP*CP*GP*GP*AP*AP*GP*G)-3')
    Chains: C, D
    Engineered: YES
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):  B D
Biological Unit 2 (1x): A C 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5WTY)

(-) Sites  (0, 0)

(no "Site" information available for 5WTY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5WTY)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:276 -Ala B:277

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5WTY)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5WTY)

(-) Exons   (0, 0)

(no "Exon" information available for 5WTY)

(-) 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:544
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhh..ee...ee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...hhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.......hhhhhh.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5wty A   51 ASFGVLDREELEYFKQAESTLQLDAFEAPEEKFQFVTSIIEEAKGKELKLVTSQITSKLMERVILECDETQLKDIFQSFNGVFFGLSCHKYASHVLETLFVRSAALVERELLTPVTMENMFLFMLNELKPHLKTMMNHQYASHVLRLLILILSSKTLPNNKVYQTPESFKSELRDIITTLYKGFTNGAESRSDISQSTITKFREYSVDKVASPVIQLIIQVEGIFDRDRSFWRLVFNTADEKDPKEESFLEYLLSDPVGSHFLENVIGSARLKYVERLYRLYMKDRIVKLAKRDTTGAFVVRALLEHLKEKDVKQILDAVVPELSMLLNSNMDFGTAIINASNKQGGYLRDDVIAQLIQKYYPEKSDAKNILESCLLLSASTLGNTRDDWPTAEERRRSVFLEQLIDYDDKFLNITIDSMLALPEERLIQMCYHGVFSHVVEHVLQTTRVDIIKRKMLLNILSKESVNLACNVYGSHIMDKLWEFTAKLTLYKERIARALVLETEKVKNSIYGRQVWKNWKLELYVRKMWDWKKLIKEQEFEIF  633
                                    60        70        80        90       100       110       120       130       140       150       160   ||  181       191       201       211       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629    
                                                                                                                                           164|                                         220|                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                            176                                          249                                                                                                                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:547
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.......hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5wty B   48 GPEASFGVLDREELEYFKQAESTLQLDAFEAPEEKFQFVTSIIEEAKGKELKLVTSQITSKLMERVILECDETQLKDIFQSFNGVFFGLSCHKYASHVLETLFVRSAALVERELLTPVTMENMFLFMLNELKPHLKTMMNHQYASHVLRLLILILSSKTLPNNKVYQTPESFKSELRDIITTLYKGFTNGAESRSDISQSTITKFREYSVDKVASPVIQLIIQVEGIFDRDRSFWRLVFNTADEKDPKEESFLEYLLSDPVGSHFLENVIGSARLKYVERLYRLYMKDRIVKLAKRDTTGAFVVRALLEHLKEKDVKQILDAVVPELSMLLNSNMDFGTAIINASNKQGGYLRDDVIAQLIQKYYPEKSDAKNILESCLLLSASTLGNTRDDWPTAEERRRSVFLEQLIDYDDKFLNITIDSMLALPEERLIQMCYHGVFSHVVEHVLQTTRVDIIKRKMLLNILSKESVNLACNVYGSHIMDKLWEFTAKLTLYKERIARALVLETEKVKNSIYGRQVWKNWKLELYVRKMWDWKKLIKEQEFEIF  633
                                    57        67        77        87        97       107       117       127       137       147       157      |178       188       198       208       218 ||    256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       
                                                                                                                                              164|                                         220|                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                               176                                          249                                                                                                                                                                                                                                                                                                                                                                                                


Chain C from PDB  Type:RNA  Length:11
                                            
                5wty C 1140 GGAAUUGACGG 1150
                                  1149 


Chain D from PDB  Type:RNA  Length:11
                                            
                5wty D 1140 GGAAUUGACGG 1150
                                  1149
   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 5WTY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5WTY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5WTY)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)

 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 5wty)
 
  Sites
(no "Sites" information available for 5wty)
 
  Cis Peptide Bonds
    Gly B:276 - Ala B:277   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  5wty
    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
  NOP9_YEAST | P47077
    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
  NOP9_YEAST | P47077
    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
        NOP9_YEAST | P47077: 5svd 5wtx

(-) Related Entries Specified in the PDB File

5wtx