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- EMDB-44949: TXNL1-bound proteasome (focused on TXNL1) -

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Basic information

Entry
Database: EMDB / ID: EMD-44949
TitleTXNL1-bound proteasome (focused on TXNL1)
Map datasharpened map
Sample
  • Complex: 26 proteasome with degron-fused midnolin
Keywordsproteasome / NUCLEAR PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGao J / Yip MCJ / Shao S
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)R01AG073277 United States
David and Lucile Packard Foundation2019-69660 United States
Richard and Susan Smith Family Foundation United States
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structure of the TXNL1-bound proteasome.
Authors: Jingjing Gao / Christopher Nardone / Matthew C J Yip / Haruka Chino / Xin Gu / Zachary Mirman / Michael J Rale / Joao A Paulo / Stephen J Elledge / Sichen Shao /
Abstract: Proteasomes degrade diverse proteins in different cellular contexts through incompletely defined regulatory mechanisms. Here we report the cryo-EM structure of human thioredoxin-like protein 1 (TXNL1) ...Proteasomes degrade diverse proteins in different cellular contexts through incompletely defined regulatory mechanisms. Here we report the cryo-EM structure of human thioredoxin-like protein 1 (TXNL1) bound to the 19S regulatory particle of proteasomes via interactions with PSMD1 (Rpn2), PSMD4 (Rpn10) and PSMD14 (Rpn11). Proteasome binding is necessary for the ubiquitin-independent degradation of TXNL1 upon cellular exposure to metal- or metalloid-containing oxidative agents, thereby establishing a structural requirement for the stress-induced degradation of TXNL1.
History
DepositionMay 20, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44949.png

Downloads & links

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Map

FileDownload / File: emd_44949.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 440 pix.
= 363. Å		0.83 Å/pix.
x 440 pix.
= 363. Å		0.83 Å/pix.
x 440 pix.
= 363. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.92641324 - 1.3064485
Average (Standard dev.)0.000080021615 (±0.03514009)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 363.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44949_msk_1.map
Projections & Slices
AxesZYX

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Additional map: unsharpened map

Fileemd_44949_additional_1.map
Annotationunsharpened map
Projections & Slices
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Half map: half map 1

Fileemd_44949_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

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Half map: half map 2

Fileemd_44949_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : 26 proteasome with degron-fused midnolin

EntireName: 26 proteasome with degron-fused midnolin
Components
  • Complex: 26 proteasome with degron-fused midnolin

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Supramolecule #1: 26 proteasome with degron-fused midnolin

SupramoleculeName: 26 proteasome with degron-fused midnolin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#40
Source (natural)Organism: Homo sapiens (human)

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 53.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 103163
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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