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- EMDB-71583: NUB1/FAT10-processing human 26S proteasome bound to TXNL1 with Rp... -

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Basic information

Entry
Database: EMDB / ID: EMD-71583
TitleNUB1/FAT10-processing human 26S proteasome bound to TXNL1 with Rpt6 at top of spiral staircase
Map data
Sample
  • Complex: Human 26S proteasome degrading FAT10-Eos with Nub1 and TXNL1 bound, RPT6 at the top
Keywords26S Proteasome / MOTOR PROTEIN / HYDROLASE-PROTEIN BINDING complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsArkinson C / Gee CL / Martin A
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural landscape of the degrading 26S proteasome reveals conformation-specific binding of TXNL1.
Authors: Connor Arkinson / Christine L Gee / Zeyuan Zhang / Ken C Dong / Andreas Martin /
Abstract: The 26S proteasome targets many cellular proteins for degradation during homeostasis and quality control. Proteasome-interacting cofactors modulate these functions and aid in substrate degradation. ...The 26S proteasome targets many cellular proteins for degradation during homeostasis and quality control. Proteasome-interacting cofactors modulate these functions and aid in substrate degradation. Here we solve high-resolution structures of the redox active cofactor TXNL1 bound to the human 26S proteasome at saturating and substoichiometric concentrations by time-resolved cryo-electron microscopy (cryo-EM). We identify distinct binding modes of TXNL1 that depend on the proteasome conformation and ATPase motor states. Together with biophysical and biochemical experiments, we show that the resting-state proteasome binds TXNL1 with low affinity and in variable positions on top of the Rpn11 deubiquitinase. In contrast, in the actively degrading proteasome, TXNL1 uses additional interactions for high-affinity binding, whereby its C-terminal tail covers the catalytic groove of Rpn11 and coordinates the active-site Zn. Furthermore, these cryo-EM structures of the degrading proteasome capture the ATPase hexamer in several spiral-staircase arrangements that indicate 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 β-barrel mEos3.2 substrate while the ATPase hexamer is in a particular staircase register. Our findings advance current models for protein translocation through hexameric AAA+ motors and reveal how the proteasome uses its distinct conformational states to coordinate cofactor binding and substrate processing.
History
DepositionJul 2, 2025-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71583.png

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Map

FileDownload / File: emd_71583.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 340 pix.
= 356.32 Å		1.05 Å/pix.
x 340 pix.
= 356.32 Å		1.05 Å/pix.
x 340 pix.
= 356.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.20224194 - 0.45054772
Average (Standard dev.)0.0026051172 (±0.025376584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 356.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened

Fileemd_71583_additional_1.map
AnnotationSharpened
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Half map: #1

Fileemd_71583_half_map_1.map
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Half map: #2

Fileemd_71583_half_map_2.map
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Sample components

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Entire : Human 26S proteasome degrading FAT10-Eos with Nub1 and TXNL1 boun...

EntireName: Human 26S proteasome degrading FAT10-Eos with Nub1 and TXNL1 bound, RPT6 at the top
Components
  • Complex: Human 26S proteasome degrading FAT10-Eos with Nub1 and TXNL1 bound, RPT6 at the top

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Supramolecule #1: Human 26S proteasome degrading FAT10-Eos with Nub1 and TXNL1 boun...

SupramoleculeName: Human 26S proteasome degrading FAT10-Eos with Nub1 and TXNL1 bound, RPT6 at the top
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.6 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Details: 30 mM HEPES pH7.4, 25 mM NaCl, 25 mM KCl, 3% (v/v) glycerol, 5 mM MgCl2 2 mM ATP and 0.5 mM TCEP
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 24203
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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