9RLT | pdb_00009rlt

dimerised 13S-13S+Beta5 proteasome precursor complexes


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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Literature

Structural transitions in the stepwise assembly of proteasome core particles.

Mark, E.Ramos, P.C.Nunes, M.M.Matias, A.C.Jurgen Dohmen, R.Wendler, P.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-70525-w
  • Primary Citation Related Structures: 
    9RL3, 9RLA, 9RLT, 9RLZ, 9RM0, 9RM1

  • PubMed Abstract: 

    20S catalytic core particles (CP) of eukaryotic 26S proteasomes are composed of two identical halves comprising 14 distinct subunits. 15S precursor complexes (PC) represent detectable half-CPs assembly intermediates lacking the β7-subunit but containing assembly chaperones Ump1 and Pba1-Pba2. Incorporation of β7 drives 15S-PC dimerisation and further CP maturation. Our cryo-EM structures of the yeast 15S-PC and all 13S-PC-derived intermediates suggest that assembly in yeast is not restricted to a single trajectory, but instead involves alternative, and potentially simultaneous pathways. Comparison of the intermediates reveals how Ump1 and β-subunits become structured with each additionally incorporated β-subunit, and how this prepares peptidase sites for auto-activation. We identify two transient interactions of Pba1 with the α-ring, which are important for an ordered progression of maturation. Pba1 loop 81-117 intercalates between subunits α3 and α4 in 13S-15S-PCs and is displaced upon 15S-PC dimerisation. The second interaction involves the α1 N-terminus, deletion of which leads to a defect in Pba1-Pba2 release. These findings indicate how changes in α-ring subunit conformations coordinate CP maturation with Pba1‑Pba2 release.


  • Organizational Affiliation
    • Institute of Biochemistry and Biology, Department of Biochemistry, University of Potsdam, Potsdam-Golm, Germany.

Macromolecule Content 

  • Total Structure Weight: 735.41 kDa 
  • Atom Count: 47,532 
  • Modeled Residue Count: 6,098 
  • Deposited Residue Count: 6,617 
  • Unique protein chains: 14

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1A,
L [auth O]
252Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4B [auth D],
M [auth R]
254Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5C [auth E],
N [auth S]
260Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6D [auth F],
O [auth T]
234Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome maturation factor UMP1E [auth 3],
P [auth 6]
162Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: UMP1YBR173CYBR1234
UniProt
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2F [auth B],
Q [auth P]
250Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3G [auth C],
R [auth Q]
258Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7H [auth G],
S [auth U]
288Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2I,
T [auth W]
261Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: PUP1YOR157C
EC: 3.4.25.1
UniProt
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3J,
U [auth X]
205Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4K,
V [auth Y]
198Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5W [auth Z]287Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome chaperone 1X [auth 7],
Z [auth 4]
276Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q05778 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome assembly chaperone 2AA [auth 5],
Y [auth 8]
267Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P36040 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC4.7.0

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany406260942
German Research Foundation (DFG)Germany442219341

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-18
    Type: Initial release
  • Version 1.1: 2026-04-01
    Changes: Data collection, Database references