Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  ZINC-BOUND RPN11 IN COMPLEX WITH RPN8
 
Authors :  E. J. Worden, C. Padovani, A. Martin
Date :  30 Dec 13  (Deposition) - 22 Jan 14  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mpn, Jamm, Deubiquitinase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Worden, C. Padovani, A. Martin
Structure Of The Rpn11-Rpn8 Dimer Reveals Mechanisms Of Substrate Deubiquitination During Proteasomal Degradation.
Nat. Struct. Mol. Biol. V. 21 220 2014
PubMed-ID: 24463465  |  Reference-DOI: 10.1038/NSMB.2771

(-) Compounds

Molecule 1 - 26S PROTEASOME REGULATORY SUBUNIT RPN8
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2-178
    Gene: RPN8, YOR261C, O5360
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
 
Molecule 2 - 26S PROTEASOME REGULATORY SUBUNIT RPN11
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2-239
    Gene: RPN11, MPR1, YFR004W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 32)

Asymmetric/Biological Unit (2, 32)
No.NameCountTypeFull Name
1EDO31Ligand/Ion1,2-ETHANEDIOL
2ZN1Ligand/IonZINC ION

(-) Sites  (32, 32)

Asymmetric Unit (32, 32)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:81 , ILE A:83 , ASN A:84 , ALA A:85 , HOH A:377BINDING SITE FOR RESIDUE EDO A 201
02AC2SOFTWARETYR A:22 , GLU A:29 , LYS A:31 , ARG A:32 , SER A:95 , GLY A:96BINDING SITE FOR RESIDUE EDO A 202
03AC3SOFTWAREPRO A:55 , PHE A:67BINDING SITE FOR RESIDUE EDO A 203
04AC4SOFTWAREARG A:100 , ALA A:101 , ASP A:103 , LEU A:104 , HOH A:398 , HOH A:409 , GLN B:145 , HOH B:454BINDING SITE FOR RESIDUE EDO A 204
05AC5SOFTWAREASN A:50 , SER A:51 , HOH A:338 , HOH A:405BINDING SITE FOR RESIDUE EDO A 205
06AC6SOFTWAREGLU A:29 , ASN A:30 , GLU A:60 , EDO A:210BINDING SITE FOR RESIDUE EDO A 206
07AC7SOFTWAREASP A:20 , GLU A:23 , HOH A:307 , HOH A:333 , GLU B:209 , HOH B:449BINDING SITE FOR RESIDUE EDO A 207
08AC8SOFTWAREASP A:40 , ASN A:42 , LYS A:88 , HOH A:337 , ASP B:101BINDING SITE FOR RESIDUE EDO A 208
09AC9SOFTWAREGLU A:78 , MET A:79 , LYS A:82 , HOH A:346 , HOH B:493BINDING SITE FOR RESIDUE EDO A 209
10BC1SOFTWAREASN A:30 , LYS A:31 , GLU A:60 , ARG A:100 , EDO A:206BINDING SITE FOR RESIDUE EDO A 210
11BC2SOFTWAREGLU A:29 , GLN A:128 , LEU B:118 , HIS B:195 , HOH B:418BINDING SITE FOR RESIDUE EDO A 211
12BC3SOFTWAREASP A:64 , TRP A:66BINDING SITE FOR RESIDUE EDO A 212
13BC4SOFTWAREGLU A:58 , ASP A:59 , ASN A:62 , PHE A:67BINDING SITE FOR RESIDUE EDO A 213
14BC5SOFTWARELYS A:82 , PRO B:72 , GLN B:73BINDING SITE FOR RESIDUE EDO A 214
15BC6SOFTWAREGLU A:108 , LYS A:111 , ASN A:117 , ALA A:139 , LYS A:152 , HOH A:375BINDING SITE FOR RESIDUE EDO A 215
16BC7SOFTWARETYR A:137 , PHE A:154 , HOH A:398BINDING SITE FOR RESIDUE EDO A 216
17BC8SOFTWAREALA A:41 , ASN A:42 , SER A:43 , HOH A:380 , MET B:103 , VAL B:104 , LEU B:132 , EDO B:304BINDING SITE FOR RESIDUE EDO A 217
18BC9SOFTWAREILE A:83 , HIS B:40 , ALA B:43 , GLY B:44 , GLN B:73 , HOH B:457BINDING SITE FOR RESIDUE EDO B 301
19CC1SOFTWARELYS A:111 , LYS A:112 , THR A:114 , GLN A:115 , PHE B:57 , VAL B:58 , ARG B:135BINDING SITE FOR RESIDUE EDO B 302
20CC2SOFTWAREPRO B:72 , GLN B:73 , SER B:74 , GLY B:77 , VAL B:78 , HOH B:402BINDING SITE FOR RESIDUE EDO B 303
21CC3SOFTWAREEDO A:217 , VAL B:83 , GLN B:88 , LEU B:132BINDING SITE FOR RESIDUE EDO B 304
22CC4SOFTWARELYS A:86 , LYS B:96 , ASP B:101 , HOH B:446 , HOH B:447BINDING SITE FOR RESIDUE EDO B 305
23CC5SOFTWAREVAL B:151 , VAL B:152 , ILE B:153 , HOH B:407 , HOH B:441BINDING SITE FOR RESIDUE EDO B 306
24CC6SOFTWAREGLU A:165 , ALA A:166 , ARG B:42 , PRO B:143 , HOH B:443 , HOH B:494BINDING SITE FOR RESIDUE EDO B 307
25CC7SOFTWAREASN A:75 , HOH A:339 , ASP B:93 , MET B:94 , GLN B:97BINDING SITE FOR RESIDUE EDO B 308
26CC8SOFTWARELYS A:98 , ASP A:124 , HOH A:396 , TYR B:196 , HOH B:458BINDING SITE FOR RESIDUE EDO B 309
27CC9SOFTWAREHOH A:351 , LYS B:96BINDING SITE FOR RESIDUE EDO B 310
28DC1SOFTWAREARG B:194BINDING SITE FOR RESIDUE EDO B 311
29DC2SOFTWAREMET B:214 , LEU B:216BINDING SITE FOR RESIDUE EDO B 312
30DC3SOFTWAREHIS A:173 , ILE B:201 , TYR B:203 , HOH B:503BINDING SITE FOR RESIDUE EDO B 313
31DC4SOFTWAREGLN A:128 , HOH A:354 , ASN B:193 , LYS B:211BINDING SITE FOR RESIDUE EDO B 314
32DC5SOFTWAREHIS B:109 , HIS B:111 , ASP B:122 , HOH B:492BINDING SITE FOR RESIDUE ZN B 315

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4O8X)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:96 -Pro A:97
2Val B:45 -Pro B:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4O8X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4O8X)

(-) Exons   (0, 0)

(no "Exon" information available for 4O8X)

(-) Sequences/Alignments

Asymmetric/Biological 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:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeehhhhhhhhhhhhhhh........eeeeeee....eeeeeeeee..eeee..eeeeeeehhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhh.......eeeee..........eeeeeeee...eeeeee.eee..hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4o8x A   2 SLQHEKVTIAPLVLLSALDHYERTQTKENKRCVGVILGDANSSTIRVTNSFALPFEEDEKNSDVWFLDHNYIENMNEMCKKINAKEKLIGWYHSGPKLRASDLKINELFKKYTQNNPLLLIVDVKQQGVGLPTDAYVAIEQTEKTFLHLPCTIEAEEAEEIGVEHLLRDVLEVL 182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141||     158       168       178    
                                                                                                                                                                      142|                                
                                                                                                                                                                       150                                


Chain B from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeehhhhhhhhhhhhhhh....eeeeeeeeee..eeeeeeeee........hhhhhhhhhhhhhhhhhhh.....eeeeeeee........hhhhhhhhhhhhhhh...eeeee...........eeeeee......eee.eeeee.hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4o8x B  24 KETVYISSIALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVNVVDVFAMPQSGTGVSVEAVDDVFQAKMMDMLKQTGRDQMVVGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRAVAVVVDPIQSVKGKVVIDAFRLIDLNRHYYSLNIDYHKTAKETKMLMNLHKEQ 220
                                    33        43        53        63        73        83        93       103       113       123       133       143       153      |194       204       214      
                                                                                                                                                                  160|                            
                                                                                                                                                                   192
   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 4O8X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4O8X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4O8X)

(-) Gene Ontology  (21, 26)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
    CC1  [ RasMol ]  +environment [ RasMol ]
    CC2  [ RasMol ]  +environment [ RasMol ]
    CC3  [ RasMol ]  +environment [ RasMol ]
    CC4  [ RasMol ]  +environment [ RasMol ]
    CC5  [ RasMol ]  +environment [ RasMol ]
    CC6  [ RasMol ]  +environment [ RasMol ]
    CC7  [ RasMol ]  +environment [ RasMol ]
    CC8  [ RasMol ]  +environment [ RasMol ]
    CC9  [ RasMol ]  +environment [ RasMol ]
    DC1  [ RasMol ]  +environment [ RasMol ]
    DC2  [ RasMol ]  +environment [ RasMol ]
    DC3  [ RasMol ]  +environment [ RasMol ]
    DC4  [ RasMol ]  +environment [ RasMol ]
    DC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:96 - Pro A:97   [ RasMol ]  
    Val B:45 - Pro B:46   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4o8x
    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
  RPN11_YEAST | P43588
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  RPN8_YEAST | Q08723
    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
  RPN11_YEAST | P43588
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  RPN8_YEAST | Q08723
    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
        RPN11_YEAST | P43588: 3j47 3jck 3jco 3jcp 4cr2 4cr3 4cr4 4o8y 4ocl 4ocm 4ocn 4owp 5a5b 5mpb 5mpc 5mpd 5mpe 5wvi 5wvk
        RPN8_YEAST | Q08723: 3j47 3jck 3jco 3jcp 4cr2 4cr3 4cr4 4o8y 4ocl 4ocm 4ocn 4owp 5a5b 5mpb 5mpc 5mpd 5mpe 5wvi 5wvk

(-) Related Entries Specified in the PDB File

4o8y