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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RPN8-RPN11 MPN DOMAIN HETERODIMER, CRYSTAL FORM II
 
Authors :  G. R. Pathare, A. Bracher
Date :  09 Jan 14  (Deposition) - 29 Jan 14  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  26S Proteasome, Isopeptidase Activity, Regulatory Particle, Lid, Ubiquitin, Hydrolase, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. R. Pathare, I. Nagy, P. Sledz, D. J. Anderson, H. J. Zhou, E. Pardon, J. Steyaert, F. Forster, A. Bracher, W. Baumeister
Crystal Structure Of The Proteasomal Deubiquitylation Modul Rpn8-Rpn11.
Proc. Natl. Acad. Sci. Usa V. 111 2984 2014
PubMed-ID: 24516147  |  Reference-DOI: 10.1073/PNAS.1400546111

(-) Compounds

Molecule 1 - 26S PROTEASOME REGULATORY SUBUNIT RPN8
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSFDUET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-176
    Gene: O5360, RPN8, YOR261C
    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, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSFDUET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-220
    Gene: MPR1, RPN11, YFR004W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: PROTEIN MPR1
 
Molecule 3 - NB1
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMESY4
    Expression System Strain: WK6 SU
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: LLAMA
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844
    Synonym: NANOBODY 1

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4OCN)

(-) Sites  (0, 0)

(no "Site" information available for 4OCN)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1C:23 -C:97
2F:23 -F:97

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:96 -Pro A:97
2Val B:45 -Pro B:46
3Gly D:96 -Pro D:97
4Val E:45 -Pro E:46

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OCN)

(-) 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:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeehhhhhhhhhhhhhhh........eeeeeee....eeeeeeeee..eeee..eeeeeeehhhhhhhhhhhhhh.....eeeeeee.......hhhhhhhhhh.......eeeee..........eeeeeeeeeee....eeeeeeeee.eee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ocn A   3 LQHEKVTIAPLVLLSALDHYERTQTKENKRCVGVILGDANSSTIRVTNSFALPFEEDEKNSDVWFLDHNYIENMNEMCKKINAKEKLIGWYHSGPKLRASDLKINELFKKYTQNNPLLLIVDVKQQGVGLPTDAYVAIEQVKDDGTSTEKTFLHLPCTIEAEEAEEIGVEHLLR 176
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172    


Chain B from PDB  Type:PROTEIN  Length:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhhhhhhhh....eeeeeeee....eeeeeeeee......hhhhhhhhhhhhhh.....eeeeeeee........hhhhhhhhhhhhh.....eeeee...........eeeeee..............eeeeeeeee.hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ocn B  23 TKETVYISSIALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVNVVDVFAMPQSGVDDVFQAKMMDMLKQTGRDQMVVGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRAVAVVVDPIQSVKGKVVIDAFRLIDTGALINNLLNRHYYSLNIDYHKTAKETKMLMNLH 217
                                    32        42        52        62        72  ||    89        99       109       119       129       139       149       159       192       202       212     
                                                                               75|                                                                                  168|                         
                                                                                83                                                                                   192                         


Chain C from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains d4ocnc_ C: automated matches                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeee...eeeeeee.....eeeeeee......eeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeee.....hhhhh.ee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ocn C   3 VQLQESGGGLVPAGGSLRLSCVDSGRSTVMAWFRQAPGKEREFVATIRWSGGNTYYADSVKGRFTISRDNARNTVYLQMNSLKPEDTAVYYCAGGTYYGTLSYKYDFWGRGTQVTVSSHHHH 127
                                    12        22     || 35        45        55        65        75        85        95       105       115       125  
                                                    28|                                                                                               
                                                     32                                                                                               


Chain D from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhh........eeeeeee....eeeeeeeeee.eee.......eeehhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhh.......eeeee..........eeeeeeeeeee....eeeeeeeee.eee........hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ocn D   5 HEKVTIAPLVLLSALDHYERTQTKENKRCVGVILGDANSSTIRVTNSFALPFEEDEKNSDVWFLDHNYIENMNEMCKKINAKEKLIGWYHSGPKLRASDLKINELFKKYTQNNPLLLIVDVKQQGVGLPTDAYVAIEQVKDDGTSTEKTFLHLPCTIEAEEAEEIGVEHLLR 176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174  


Chain E from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeehhhhhhhhhhhhhhh....eeeeeeee....eeeeeeeeee.........hhhhhhhhhhhhhh.....eeeeeeee........hhhhhhhhhhhhhhh...eeeee...........eeeeee......eeeeeeeee.hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ocn E  22 DTKETVYISSIALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVNVVDVFAMPQSGTVEAVDDVFQAKMMDMLKQTGRDQMVVGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRAVAVVVDPIQSVKGKVVIDAFRLIDLNRHYYSLNIDYHKTAKETKMLMNLH 217
                                    31        41        51        61        71    ||  84        94       104       114       124       134       144       154     ||195       205       215  
                                                                                 76|                                                                             160|                         
                                                                                  80                                                                              192                         


Chain F from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains d4ocnf_ F: automated matches                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee....eeeeeee.......eeeeeee......eeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.....hhhhh.ee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ocn F   3 VQLQESGGGLVPAGGSLRLSCVDSGRFSSTVMAWFRQAPGKEREFVATIRWSGGNTYYADSVKGRFTISRDNARNTVYLQMNSLKPEDTAVYYCAGGTYYGTLSYKYDFWGRGTQVTVSSHHH 126
                                    12        22     || 33        43        53        63        73        83        93       103       113       123   
                                                    28|                                                                                                
                                                     30
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 26)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:96 - Pro A:97   [ RasMol ]  
    Gly D:96 - Pro D:97   [ RasMol ]  
    Val B:45 - Pro B:46   [ RasMol ]  
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  RPN11_YEAST | P43588
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  RPN8_YEAST | Q08723
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 Related Entries

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

UniProtKB/Swiss-Prot
        RPN11_YEAST | P43588: 3j47 3jck 3jco 3jcp 4cr2 4cr3 4cr4 4o8x 4o8y 4ocl 4ocm 4owp 5a5b 5mpb 5mpc 5mpd 5mpe 5wvi 5wvk
        RPN8_YEAST | Q08723: 3j47 3jck 3jco 3jcp 4cr2 4cr3 4cr4 4o8x 4o8y 4ocl 4ocm 4owp 5a5b 5mpb 5mpc 5mpd 5mpe 5wvi 5wvk

(-) Related Entries Specified in the PDB File

2c0v 4b4t 4ocl 4ocm