9E8J

Nub1/Fat10-processing human 26S proteasome bound to Txnl1 with Rpt1 at top of spiral staircase


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural landscape of AAA+ ATPase motor states in the substrate-degrading human 26S proteasome reveals conformation-specific binding of TXNL1.

Arkinson, C.Gee, C.L.Zhang, Z.Dong, K.C.Martin, A.

(2024) bioRxiv 

  • DOI: https://doi.org/10.1101/2024.11.08.622731
  • Primary Citation of Related Structures:  
    9E8G, 9E8H, 9E8I, 9E8J, 9E8K, 9E8L, 9E8N, 9E8O, 9E8Q

  • PubMed Abstract: 

    The 26S proteasome targets many cellular proteins for degradation during general homeostasis, protein quality control, and the regulation of vital processes. A broad range of proteasome-interacting cofactors thereby modulates these functions and aids in substrate degradation. Here, we solved several high-resolution structures of the redox active cofactor TXNL1 bound to the human 26S proteasome at saturating and sub-stoichiometric concentrations by time resolved cryo-EM. We identified distinct binding modes of TXNL1 that depend on the proteasome conformational and ATPase motor states. Together with biophysical and biochemical experiments, our structural studies reveal that the resting-state proteasome prior to substrate engagement with the ATPase motor binds TXNL1 with low affinity and in variable positions on top of the Rpn11 deubiquitinase. In contrast, the actively degrading proteasome shows additional interactions leading to high-affinity TXNL1 binding, whereby TXNL1's C-terminal tail covers the catalytic groove of the Rpn11 deubiquitinase and coordinates the active-site Zn 2+ . Furthermore, these cryo-EM structures of the degrading proteasome capture the ATPase hexamer in all registers of spiral-staircase arrangements and thus visualize the complete ATP-hydrolysis cycle of the AAA+ motor, indicating temporally asymmetric hydrolysis and conformational changes in bursts during mechanical substrate unfolding and translocation. Remarkably, we catch the proteasome in the act of unfolding the beta-barrel mEos3.2 substrate while the ATPase hexamer is in a particular spiral staircase register. Our findings challenge current models for protein translocation through hexameric AAA+ motors and reveal how the proteasome uses its distinct but broad range of conformational states to coordinate cofactor binding and substrate processing.


  • Organizational Affiliation

    California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, CA 94720, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7433Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161057 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4440Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100764 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 8406Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087191 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6B418Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000013275 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 10B389Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100519 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6A439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165916 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6246Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100902 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000106588 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4261Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000041357 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101182 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5241Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000143106 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000129084 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3255Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100567 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1N [auth U]953Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173692 
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MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3O [auth V]534Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108344 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12P [auth W]456Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197170 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11Q [auth X]422Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108671 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6R [auth Y]389Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163636 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7S [auth Z]324Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000103035 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13T [auth a]376Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185627 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4U [auth b]377Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159352 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14V [auth c]424Homo sapiensMutation(s): 0 
Gene Names: PSMD14
EC: 3.4.19
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GTEx:  ENSG00000115233 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8W [auth d]350Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099341 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1X [auth e]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000127922 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 2Y [auth f]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175166 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 2 of NEDD8 ultimate buster 1Z [auth g]601Homo sapiensMutation(s): 0 
Gene Names: NUB1NYREN18
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GTEx:  ENSG00000013374 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin-like protein 1AA [auth u]289Homo sapiensMutation(s): 0 
Gene Names: TXNL1TRP32TXLTXNL
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GTEx:  ENSG00000091164 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
substrate peptideBA [auth v]12Homo sapiensMutation(s): 0 
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
CA [auth A],
EA [auth B],
GA [auth C],
LA [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
IA [auth D],
KA [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
NA [auth u]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
DA [auth A],
FA [auth B],
HA [auth C],
JA [auth D],
MA [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.47 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release