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 A PROTEASOME RELATED SUBUNIT C TERMINAL DOMAIN
 
Authors :  Y. Wu, Y. Hu, C. Jin
Date :  06 Jul 14  (Deposition) - 04 Feb 15  (Release) - 12 Apr 17  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Hydrolase, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Hu, Y. Wu, Q. Li, W. Zhang, C. Jin
Solution Structure Of Yeast Rpn9: Insights Into Proteasome Lid Assembly.
J. Biol. Chem. V. 290 6878 2015
PubMed-ID: 25631053  |  Reference-DOI: 10.1074/JBC.M114.626762

(-) Compounds

Molecule 1 - 26S PROTEASOME REGULATORY SUBUNIT RPN9
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET21A
    Expression System Vector Type: VECTOR
    Fragment: UNP RESIDUES 181-356
    Gene: RPN9, NAS7, YDR427W, D9461.14
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE S288C
    Organism Taxid: 559292
    Synonym: PROTEASOME NON-ATPASE SUBUNIT 7

 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 2MRI)

(-) Sites  (0, 0)

(no "Site" information available for 2MRI)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2MRI)

(-) 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:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh......hhhhhhh..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeehhhhhhh...hhhhhhhhhhhhhhh..eeeeeehhh.eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mri A 181 FKNDFNSFYYTSLLYLSTLEPSTSITLAERQQLAYDLSISALLGDKIYNFGELLHHPIMETIVNDSNYDWLFQLLNALTVGDFDKFDSLIKVQISKIPILAQHESFLRQKICLMTLIETVFVKNIRMLSFEDISKATHLPKDNVEHLVMRAISLGLLKGSIDQVNELVTISWVQPR 356
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350
   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 2MRI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)

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

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models 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
  2mri
    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
  RPN9_YEAST | Q04062
    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
  RPN9_YEAST | Q04062
    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
        RPN9_YEAST | Q04062: 2mqw 2mr3 3j47 3jck 3jco 3jcp 4cr2 4cr3 4cr4 5a5b 5mpb 5mpc 5mpd 5mpe 5wvi 5wvk

(-) Related Entries Specified in the PDB File

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