3JCK Hydrolase date Dec 20, 2015
title Structure Of The Yeast 26s Proteasome Lid Sub-Complex
authors M.A.Herzik Jr., C.M.Dambacher, E.J.Worden, A.Martin, G.C.Lander
compound source
Molecule: 26s Proteasome Regulatory Subunit Rpn3
Chain: A
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Cellular_location: Cytoplasm
Gene: Rpn3, Sun2, Yer021w
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet, Pcola, Pacyc

Molecule: 26s Proteasome Regulatory Subunit Rpn5
Chain: B
Synonym: Proteasome Non-Atpase Subunit 5
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Cellular_location: Cytoplasm
Gene: Rpn5, Nas5, Ydl147w, D1572
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet, Pcola, Pacyc

Molecule: 26s Proteasome Regulatory Subunit Rpn6
Chain: C
Synonym: Proteasome Non-Atpase Subunit 4
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Cellular_location: Cytoplasm
Gene: Rpn6, Nas4, Ydl097c, D2381
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet, Pcola, Pacyc

Molecule: 26s Proteasome Regulatory Subunit Rpn7
Chain: D
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Cellular_location: Cytoplasm
Gene: Rpn7, Ypr108w, P8283.8
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet, Pcola, Pacyc

Molecule: 26s Proteasome Regulatory Subunit Rpn8
Chain: E
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Cellular_location: Cytoplasm
Gene: Rpn8, Yor261c, O5360
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet, Pcola, Pacyc

Molecule: 26s Proteasome Regulatory Subunit Rpn9
Chain: F
Synonym: Proteasome Non-Atpase Subunit 7
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Cellular_location: Cytoplasm
Gene: Rpn9, Nas7, Ydr427w, D9461.14
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet, Pcola, Pacyc

Molecule: Ubiquitin Carboxyl-Terminal Hydrolase Rpn11
Chain: G
Synonym: 26s Proteasome Regulatory Subunit Rpn11, Protein M
Ec: 3.4.19.12
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Cellular_location: Cytoplasm
Gene: Rpn11, Mpr1, Yfr004w
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet, Pcola, Pacyc

Molecule: 26s Proteasome Regulatory Subunit Rpn12
Chain: H
Synonym: Nuclear Integrity Protein 1
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Cellular_location: Cytoplasm
Gene: Rpn12, Nin1, Yfr052w
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet, Pcola, Pacyc

Molecule: 26s Proteasome Complex Subunit Sem1
Chain: I
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Atcc 204508 S288c
Cellular_location: Cytoplasm
Gene: Sem1, Dsh1, Ydr363w-A
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet, Pcola, Pacyc
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.50 Å
ligand ZN enzyme Hydrolase E.C.3.4.19.12 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D
  • enzyme regulator activity


  • E


    F


    G


    H


    I


    Primary referenceAtomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition., Dambacher CM, Worden EJ, Herzik MA, Martin A, Lander GC, Elife. 2016 Jan 8;5. pii: e13027. doi: 10.7554/eLife.13027. PMID:26744777
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2055 Kb) [Save to disk]
  • Biological Unit Coordinates (3jck.pdb1.gz) 416 Kb
  • LPC: Ligand-Protein Contacts for 3JCK
  • CSU: Contacts of Structural Units for 3JCK
  • Retrieve 3JCK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3JCK from S2C, [Save to disk]
  • View 3JCK in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3JCK
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 3jck from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3jck_G] [3jck] [3jck_F] [3jck_H] [3jck_D] [3jck_C] [3jck_I] [3jck_E] [3jck_A] [3jck_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3JCK: [DSS1_SEM1] [JAB_MPN] [PAM] [PINT ] by SMART
  • Other resources with information on 3JCK
  • Community annotation for 3JCK at PDBWiki (http://pdbwiki.org)

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