6EPE | pdb_00006epe

Substrate processing state 26S proteasome (SPS2)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.8 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation 3D Report Full Report

Validation slider image for 6EPE

This is version 1.4 of the entry. See complete history

Literature

In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment.

Guo, Q.Lehmer, C.Martinez-Sanchez, A.Rudack, T.Beck, F.Hartmann, H.Perez-Berlanga, M.Frottin, F.Hipp, M.S.Hartl, F.U.Edbauer, D.Baumeister, W.Fernandez-Busnadiego, R.

(2018) Cell 172: 696-705.e12

  • DOI: https://doi.org/10.1016/j.cell.2017.12.030
  • Primary Citation Related Structures: 
    6EPC, 6EPD, 6EPE, 6EPF

  • PubMed Abstract: 

    Protein aggregation and dysfunction of the ubiquitin-proteasome system are hallmarks of many neurodegenerative diseases. Here, we address the elusive link between these phenomena by employing cryo-electron tomography to dissect the molecular architecture of protein aggregates within intact neurons at high resolution. We focus on the poly-Gly-Ala (poly-GA) aggregates resulting from aberrant translation of an expanded GGGGCC repeat in C9orf72, the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. We find that poly-GA aggregates consist of densely packed twisted ribbons that recruit numerous 26S proteasome complexes, while other macromolecules are largely excluded. Proximity to poly-GA ribbons stabilizes a transient substrate-processing conformation of the 26S proteasome, suggesting stalled degradation. Thus, poly-GA aggregates may compromise neuronal proteostasis by driving the accumulation and functional impairment of a large fraction of cellular proteasomes.


  • Organizational Affiliation
    • Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.

Macromolecule Content 

  • Total Structure Weight: 1,284 kDa 
  • Atom Count: 82,758 
  • Modeled Residue Count: 10,504 
  • Deposited Residue Count: 11,447 
  • Unique protein chains: 32

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6246Rattus norvegicusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for P60901 (Rattus norvegicus)
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2234Rattus norvegicusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for P17220 (Rattus norvegicus)
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4261Rattus norvegicusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for P21670 (Rattus norvegicus)
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7254Rattus norvegicusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for P48004 (Rattus norvegicus)
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5241Rattus norvegicusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for P34064 (Rattus norvegicus)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1263Rattus norvegicusMutation(s): 0 
EC: 3.4.25.1
UniProt
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3255Rattus norvegicusMutation(s): 0 
EC: 3.4.25.1
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6H [auth 1]238Rattus norvegicusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for P28073 (Rattus norvegicus)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7I [auth 2]277Rattus norvegicusMutation(s): 0 
EC: 3.4.25.1
UniProt
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3J [auth 3]205Rattus norvegicusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for P40112 (Rattus norvegicus)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2K [auth 4]201Rattus norvegicusMutation(s): 0 
EC: 3.4.25.1
UniProt
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5L [auth 5]263Rattus norvegicusMutation(s): 0 
EC: 3.4.25.1
UniProt
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1M [auth 6]240Rattus norvegicusMutation(s): 0 
EC: 3.4.25.1
UniProt
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4N [auth 7]263Rattus norvegicusMutation(s): 0 
EC: 3.4.25.1
UniProt
Find proteins for P34067 (Rattus norvegicus)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome subunit S5aO [auth W]377Rattus norvegicusMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 14P [auth V]310Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome 26S subunit, non-ATPase 8Q [auth T]353Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
RCG28037R [auth Y]70Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for D3ZHW9 (Rattus norvegicus)
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 2S [auth Z]908Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q4FZT9 (Rattus norvegicus)
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1T [auth N]953Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for O88761 (Rattus norvegicus)
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Reference Sequence
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 3U [auth S]530Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for A6HIT6 (Rattus norvegicus)
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Reference Sequence
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 12V [auth P]456Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q5XIC6 (Rattus norvegicus)
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11W [auth Q]422Rattus norvegicusMutation(s): 0 
UniProt
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Reference Sequence
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 6X [auth R]389Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q6PCT9 (Rattus norvegicus)
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 7 (Predicted)Y [auth U]320Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for D4AEH3 (Rattus norvegicus)
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13Z [auth O]376Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7AA [auth H]433Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4BA [auth I]440Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6BCA [auth K]418Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome 26S subunit, ATPase 6DA [auth L]403Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6AEA [auth M]442Rattus norvegicusMutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 8FA [auth J]406Rattus norvegicusMutation(s): 0 
UniProt
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 12.8 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION1.4

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionGermanyFP7 GA ERC-2012-SyG_318987-ToPAG
European CommissionGermanyFP7 GA ERC-2013-CoG_617198 DPR-MODELS
German Research FoundationGermanySFB-1035/Project A01
National Institutes of HealthUnited States9P41GM104601

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-14
    Changes: Database references
  • Version 1.2: 2018-02-21
    Changes: Database references
  • Version 1.3: 2019-12-11
    Changes: Other
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references