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- PDB-36bl: yeast 26S proteasome base assembly intermediate, base-Nas2-Rpn14-... -

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Basic information

Entry
Database: PDB / ID: 36bl
Titleyeast 26S proteasome base assembly intermediate, base-Nas2-Rpn14-Hsm3-Nas6
Components
  • (26S proteasome regulatory subunit ...) x 9
  • 26S proteasome subunit RPT4
  • DNA mismatch repair protein HSM3
  • Probable 26S proteasome regulatory subunit p28
KeywordsMOTOR PROTEIN / proteasome / chaperone / base / 26S / AAA / motor / assembly
Function / homology
Function and homology information


Regulation of PTEN stability and activity / proteasome regulatory particle binding / proteasome regulatory particle assembly / protein-containing complex localization / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / regulation of protein catabolic process / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway ...Regulation of PTEN stability and activity / proteasome regulatory particle binding / proteasome regulatory particle assembly / protein-containing complex localization / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / regulation of protein catabolic process / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Proteasome assembly / nonfunctional rRNA decay / Ub-specific processing proteases / peptide catabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome storage granule / mismatch repair / proteasome assembly / proteasome complex / enzyme regulator activity / ERAD pathway / Neutrophil degranulation / protein folding chaperone / ubiquitin binding / positive regulation of transcription elongation by RNA polymerase II / nucleotide-excision repair / positive regulation of protein catabolic process / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / chromatin remodeling / protein domain specific binding / ubiquitin protein ligase binding / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
DNA mismatch repair protein HSM3, C-terminal domain / DNA mismatch repair protein HSM3, N-terminal domain / DNA mismatch repair protein HSM3, C terminal domain / DNA mismatch repair protein HSM3, N terminal domain / : / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain / Pru (pleckstrin-like receptor for ubiquitin) domain profile. ...DNA mismatch repair protein HSM3, C-terminal domain / DNA mismatch repair protein HSM3, N-terminal domain / DNA mismatch repair protein HSM3, C terminal domain / DNA mismatch repair protein HSM3, N terminal domain / : / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / : / 26S proteasome subunit RPN2, N-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / : / 26S proteasome regulatory subunit 7, OB domain / : / HEAT repeats / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / Ankyrin repeat / ATPase, AAA-type, conserved site / AAA-protein family signature. / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / ATPase family associated with various cellular activities (AAA) / Ankyrin repeat-containing domain superfamily / ATPase, AAA-type, core / Armadillo-like helical / WD domain, G-beta repeat / Armadillo-type fold / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / 26S proteasome regulatory subunit RPN13 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 6B homolog / 26S proteasome regulatory subunit 7 homolog / DNA mismatch repair protein HSM3 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit 4 homolog / Probable 26S proteasome regulatory subunit p28 ...ADENOSINE-5'-TRIPHOSPHATE / 26S proteasome regulatory subunit RPN13 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 6B homolog / 26S proteasome regulatory subunit 7 homolog / DNA mismatch repair protein HSM3 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit 4 homolog / Probable 26S proteasome regulatory subunit p28 / 26S proteasome regulatory subunit RPN14 / 26S proteasome subunit RPT4 / 26S proteasome regulatory subunit 8 homolog
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.91 Å
AuthorsHsieh, H.H. / Martin, A.
Funding support United States, 2items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM094497 United States
Citation
Journal: bioRxiv / Year: 2026
Title: Chaperones shape the conformational landscape of 26S-proteasome-base assembly for allosteric ATPase motor activation.
Authors: Hao-Hsuan Hsieh / Andreas Martin /
Abstract: Protein homeostasis depends on the 26S proteasome, the most complex ATP-dependent protease in eukaryotic cells. The proteasome base subcomplex is responsible for mechanical substrate unfolding and ...Protein homeostasis depends on the 26S proteasome, the most complex ATP-dependent protease in eukaryotic cells. The proteasome base subcomplex is responsible for mechanical substrate unfolding and translocation into an internal degradation chamber. It contains three non-ATPase subunits, Rpn1, Rpn2, and Rpn13, and a heterohexameric AAA+ motor with six distinct ATPases, Rpt1 - Rpt6. Correct base assembly requires four dedicated chaperones that initially form the Hsm3 module (Hsm3-Rpt1-Rpt2-Rpn1), the Rpn14/Nas6 module (Rpn14-Rpt6-Nas6-Rpt3-Rpn2-Rpn13), and the Nas2 module (Nas2-Rpt5-Rpt4). However, the mechanisms underlying module assembly and formation of the mature base remain unknown. Here, we reconstitute the base subcomplex of the 26S proteasome from recombinant modules. Using biochemical assays, mass photometry, single-molecule fluorescence measurements, and single-particle cryo-EM, we reveal how the chaperones direct the conformational transitions through several intermediates toward the ATP-hydrolysis-active base. The Nas2 and Rpn14/Nas6 modules associate first, and binding of the Hsm3 module creates a state in which the chaperones stabilize an open ATPase ring that lacks hydrolysis activity. Sequential chaperone release then leads to a gradual ATPase-ring closure, whereby Hsm3's unstructured C-terminal tail mimics a substrate polypeptide in the central channel and induces a processing motor state with a spiral-staircase arrangement of Rpt subunits and a closed ATPase site at Rpt4. Inaugural ATP hydrolysis in Rpt4 is subsequently required to eject Hsm3 and transition to the Nas6-bound base that is ATPase active and competent for 26S-proteasome incorporation. Our studies thus provide exciting insights into how chaperones assure correct assembly, guide the complex through an intricate conformational landscape, and thereby prevent premature ATP-hydrolysis activation or incorporation of faulty assemblies into holoenzymes.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 28, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 26S proteasome regulatory subunit 7 homolog
B: 26S proteasome regulatory subunit 4 homolog
C: 26S proteasome regulatory subunit RPN1
D: DNA mismatch repair protein HSM3
I: 26S proteasome regulatory subunit 8 homolog
J: 26S proteasome regulatory subunit 6B homolog
K: 26S proteasome subunit RPT4
L: 26S proteasome regulatory subunit RPN13
M: 26S proteasome regulatory subunit RPN14
N: Probable 26S proteasome regulatory subunit p28
P: 26S proteasome regulatory subunit 6A
Z: 26S proteasome regulatory subunit RPN2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)654,64418
Polymers651,60112
Non-polymers3,0436
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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26S proteasome regulatory subunit ... , 9 types, 9 molecules ABCIJLMPZ

#1: Protein 26S proteasome regulatory subunit 7 homolog / Protein CIM5 / Tat-binding homolog 3


Mass: 52054.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPT1, CIM5, YTA3, YKL145W / Production host: Escherichia coli (E. coli) / References: UniProt: P33299
#2: Protein 26S proteasome regulatory subunit 4 homolog / Tat-binding homolog 5


Mass: 48898.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPT2, YHS4, YTA5, YDL007W, D2920 / Production host: Escherichia coli (E. coli) / References: UniProt: P40327
#3: Protein 26S proteasome regulatory subunit RPN1 / HMG-CoA reductase degradation protein 2 / Proteasome non-ATPase subunit 1


Mass: 109601.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPN1, HRD2, NAS1, RPD1, YHR027C / Production host: Escherichia coli (E. coli) / References: UniProt: P38764
#5: Protein 26S proteasome regulatory subunit 8 homolog / Protein CIM3 / Protein SUG1 / Tat-binding protein TBY1


Mass: 45342.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPT6, CIM3, CRL3, SUG1, TBPY, TBY1, YGL048C / Production host: Escherichia coli (E. coli) / References: UniProt: Q01939
#6: Protein 26S proteasome regulatory subunit 6B homolog / Protein YNT1 / Tat-binding homolog 2


Mass: 47953.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPT3, YNT1, YTA2, YDR394W, D9509.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P33298
#8: Protein 26S proteasome regulatory subunit RPN13 / Proteasome non-ATPase subunit 13


Mass: 17919.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPN13, DAQ1, YLR421C / Production host: Escherichia coli (E. coli) / References: UniProt: O13563
#9: Protein 26S proteasome regulatory subunit RPN14 / Proteasome non-ATPase subunit 14


Mass: 46433.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPN14, YGL004C / Production host: Escherichia coli (E. coli) / References: UniProt: P53196
#11: Protein 26S proteasome regulatory subunit 6A / Tat-binding protein homolog 1 / TBP-1


Mass: 48315.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPT5, YTA1, YOR117W, O3258, YOR3258W / Production host: Escherichia coli (E. coli) / References: UniProt: P33297
#12: Protein 26S proteasome regulatory subunit RPN2


Mass: 104351.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPN2, SEN3, YIL075C / Production host: Escherichia coli (E. coli) / References: UniProt: P32565

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Protein , 3 types, 3 molecules DKN

#4: Protein DNA mismatch repair protein HSM3 / Enhanced spontaneous mutability protein 3


Mass: 55601.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HSM3, YBR272C, YBR1740 / Production host: Escherichia coli (E. coli) / References: UniProt: P38348
#7: Protein 26S proteasome subunit RPT4 / 26S protease subunit SUG2 / Proteasomal cap subunit


Mass: 49479.152 Da / Num. of mol.: 1 / Mutation: E282Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPT4, CRL13, PCS1, SUG2, YOR259C / Production host: Escherichia coli (E. coli) / References: UniProt: P53549
#10: Protein Probable 26S proteasome regulatory subunit p28 / Proteasome non-ATPase subunit 6


Mass: 25648.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NAS6, YGR232W, G8564 / Production host: Escherichia coli (E. coli) / References: UniProt: P50086

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Non-polymers , 1 types, 6 molecules

#13: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: yeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2 (base-Hsm3-Nas6)
Type: COMPLEX / Entity ID: #1-#12 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC5particle selection
2PHENIX2.0_5936model refinement
13cryoSPARC53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208110 / Symmetry type: POINT

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