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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RPN8-RPN11 MPN DOMAIN HETERODIMER, CRYSTAL FORM IB
 
Authors :  G. R. Pathare, A. Bracher
Date :  09 Jan 14  (Deposition) - 29 Jan 14  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
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  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1K1Ligand/IonPOTASSIUM ION
2ZN2Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:109 , HIS B:111 , ASP B:122BINDING SITE FOR RESIDUE ZN B 401
2AC2SOFTWARELEU D:132 , THR D:134 , ASP D:135BINDING SITE FOR RESIDUE K D 301
3AC3SOFTWAREHIS E:109 , HIS E:111 , ASP E:122 , HOH E:507BINDING SITE FOR RESIDUE ZN E 401

(-) 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 4OCM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OCM)

(-) 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:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhh........eeeeeee....eeeeeeeee..eee.......eeehhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhh.......eeeee..........eeeeeee...eeeee.eee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ocm A   5 HEKVTIAPLVLLSALDHYERTQTKENKRCVGVILGDANSSTIRVTNSFALPFEEDEKNSDVWFLDHNYIENMNEMCKKINAKEKLIGWYHSGPKLRASDLKINELFKKYTQNNPLLLIVDVKQQGVGLPTDAYVAIEQKTFLHLPCTIEAEEAEEIGVEHLLRG 177
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       153       163       173    
                                                                                                                                                                   142|                         
                                                                                                                                                                    152                         


Chain B from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhhhhhhhh....eeeeeeee....eeeeeeeee......hhhhhhhhhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhhhh...eeeeee.hhhhhh..eeeeeee....eehhhhhhhhhhhhhhheeeeeeeee.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ocm B  23 TKETVYISSIALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVNVVDVFAMPQSGVSVEAVDDVFQAKMMDMLKQTGRDQMVVGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRAVAVVVDPIQSVKGKVVIDAFRLIDTGLLNKANIQALIHGLNRHYYSLNIDYHKTAKETKMLMNLH 217
                                    32        42        52        62        72 ||     84        94       104       114       124       134       144       154      |180       190       200       210       
                                                                              74|                                                                                 161|                                       
                                                                               77                                                                                  178                                       


Chain C from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains d4ocmc_ C: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeee...eeeeeee........eeeeeee......eeeeeee.....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee.....hhhhh.ee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ocm C   3 VQLQESGGGLVPAGGSLRLSCVDSGRTFSSTVMAWFRQAPGKEREFVATIRWSGGNTYYADSVKGRFTISRDNARNTVYLQMNSLKPEDTAVYYCAGGTYYGTLSYKYDFWGRGTQVTVSSHHHH 127
                                    12        22        32        42        52        62        72        82        92       102       112       122     


Chain D from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeehhhhhhhhhhhhhhh........eeeeeee....eeeeeeeee..eeee..eeeeeeehhhhhhhhhhhhhhhh...eeeeeee.......hhhhhhhhhhhhh....eeeee..........eeeeeeeee..eeeeeee.eee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ocm D   5 HEKVTIAPLVLLSALDHYERTQTKENKRCVGVILGDANSSTIRVTNSFALPFEEDEKNSDVWFLDHNYIENMNEMCKKINAKEKLIGWYHSGPKLRASDLKINELFKKYTQNNPLLLIVDVKQQGVGLPTDAYVAIEQVTEKTFLHLPCTIEAEEAEEIGVEHLLR 176
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       150       160       170      
                                                                                                                                                                    143|                          
                                                                                                                                                                     150                          


Chain E from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhhhhhhhh....eeeeeeeee...eeeeeeeee........hhhhhhhhhhhhhhhhhhhh....eeeeeeee........hhhhhhhhhhhhhhh...eeeee...........eeeeee.hhhhhhhh....hhhhhhhh....eeeeeeeee.hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ocm E  23 TKETVYISSIALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVNVVDVFAMPQSGTGVSVEAVDDVFQAKMMDMLKQTGRDQMVVGWYHSHPGFGCWLSSVDVNTQKSFEQLNSRAVAVVVDPIQSVKGKVVIDAFRLIDTGALINNLNKANIQALIHGLNRHYYSLNIDYHKTAKETKMLMNLHK 218
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162     ||184       194       204       214    
                                                                                                                                                                           168|                                     
                                                                                                                                                                            181                                     


Chain F from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains d4ocmf_ F: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eeee...eeeeeee........eeeeeee......eeeeeee.....eee.......eeeeeehhh.eeeeee...hhhhheeeeeeee.....hhhhh.ee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ocm F   3 VQLQESGGGLVPAGGSLRLSCVDSGRTFSSTVMAWFRQAPGKEREFVATIRWSGGNTYYADSVKGRFTISRDNARNTVYLQMNSLKPEDTAVYYCAGGTYYGTLSYKYDFWGRGTQVTVSSHHHH 127
                                    12        22        32        42        52        62        72        82        92       102       112       122
   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 4OCM)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 26)

Asymmetric Unit(hide GO term definitions)

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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 4ocn 4owp 5a5b 5mpb 5mpc 5mpd 5mpe 5wvi 5wvk
        RPN8_YEAST | Q08723: 3j47 3jck 3jco 3jcp 4cr2 4cr3 4cr4 4o8x 4o8y 4ocl 4ocn 4owp 5a5b 5mpb 5mpc 5mpd 5mpe 5wvi 5wvk

(-) Related Entries Specified in the PDB File

2c0v 4b4t 4ocl 4ocn