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- EMDB-71791: Human 19S proteasome regulatory particle (RP) without observing T... -

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Basic information

Entry
Database: EMDB / ID: EMD-71791
TitleHuman 19S proteasome regulatory particle (RP) without observing TXNL1 PITH domain bound
Map data
Sample
  • Complex: Human proteasome purified from HCT116 cells
KeywordsProteasome / 19S / RP / HYDROLASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.92 Å
AuthorsChen X / Negi H / Walters KJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1 ZIABC011490 United States
CitationJournal: Mol Cell / Year: 2026
Title: Structures of dynamic interactors at native proteasomes by PhIX-MS and cryo-electron microscopy.
Authors: Kitaik Lee / Hitendra Negi / Xiang Chen / Katerina Atallah-Yunes / Sophia Truslow / Rithik E Castelino / Mary R Guest / Anthony M Ciancone / Xiuxiu Lu / Sergey G Tarasov / Raj Chari / Kylie ...Authors: Kitaik Lee / Hitendra Negi / Xiang Chen / Katerina Atallah-Yunes / Sophia Truslow / Rithik E Castelino / Mary R Guest / Anthony M Ciancone / Xiuxiu Lu / Sergey G Tarasov / Raj Chari / Kylie J Walters / Francis J O'Reilly /
Abstract: Molecular machines rely on dynamic, low-affinity interactions to perform their functional roles. We developed PhIX-MS (photo-induced in situ crosslinking-mass spectrometry), a structural proteomics ...Molecular machines rely on dynamic, low-affinity interactions to perform their functional roles. We developed PhIX-MS (photo-induced in situ crosslinking-mass spectrometry), a structural proteomics workflow to capture topological information for such transient interactions in cells by UV-activated crosslinking. Applying PhIX-MS with cryo-electron microscopy (cryo-EM) to proteasomes, we mapped the redox sensor TXNL1 at the proteasome regulatory particle (RP), including its dynamic thioredoxin-like domain near RPN2/PSMD1 and RPN13/ADRM1, where it is ideal for reducing substrates prior to proteolysis. RPs without the proteolytic core particle (CP) were structurally resolved while bound to TXNL1 and/or the chaperone PSMD5/S5b, which inserts its C terminus into the ATPase pore, causing extensive structural rearrangements. Additionally, PhIX-MS and AlphaFold identified the ubiquitin ligase UBE3C/Hul5 at RPN2, RPN3, and a dynamic RPN10 region, tethering UBE3C above the substrate entry channel. Our integrative approach enables the localization of native, low-affinity protein interactions and is broadly applicable to dynamic macromolecular assemblies.
History
DepositionJul 23, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71791.png

Downloads & links

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Map

FileDownload / File: emd_71791.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 432 pix.
= 349.92 Å		0.81 Å/pix.
x 432 pix.
= 349.92 Å		0.81 Å/pix.
x 432 pix.
= 349.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.08780113 - 0.2052532
Average (Standard dev.)0.00003519099 (±0.008512646)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 349.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_71791_additional_1.map
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Half map: #1

Fileemd_71791_half_map_1.map
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Half map: #2

Fileemd_71791_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human proteasome purified from HCT116 cells

EntireName: Human proteasome purified from HCT116 cells
Components
  • Complex: Human proteasome purified from HCT116 cells

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Supramolecule #1: Human proteasome purified from HCT116 cells

SupramoleculeName: Human proteasome purified from HCT116 cells / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1 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

Concentration0.75 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMC4H12NO3ClTris(hydroxymethyl)aminomethane hydrochloride
50.0 mMNaClSodium Chloride
1.5 mMC10H12N5O12P3SATP-gamma-S
5.0 mMMgCl2Magnesium chloride
2.0 mM(CH(OH)CH2SH)2Dithiothreitol

Details: 50 mM Tris [pH7.5], 50 mM NaCl, 1.5 mM ATP-gamma-S, 5 mM MgCl2 and 2 mM DTT
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 295.15 K / Instrument: LEICA EM GP
DetailsQuantifoil copper R 1.2/1.3 holey carbon 300 mesh grids (#Q3100CR1.3; Electron Microscopy Sciences).

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number real images: 40 / Average exposure time: 2.5 sec. / Average electron dose: 55.6 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1504498
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7wsi

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 102897
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5.3)
FSC plot (resolution estimation)

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