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- EMDB-76415: Human 19S proteasome regulatory particle bound to TXNL1 PITH doma... -

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Basic information

Entry
Database: EMDB / ID: EMD-76415
TitleHuman 19S proteasome regulatory particle bound to TXNL1 PITH domain and p28
Map data
Sample
  • Complex: Human proteasome from HCT116 cells
    • Protein or peptide: 19S RP
KeywordsProteasome / 19S / RP / TXNL1 / PSMD5 / HYDROLASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.35 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: To Be Published
Title: Structures of dynamic interactors at native proteasomes by PhIX-MS and cryoelectron microscopy
Authors: Lee K / Negi H / Chen X / Atallah-Yunes K / Truslow S / Castelino RE / Guest M / Ciancone AM / Tarasov SG / Chari R / Walters KJ / O'Reilly FJ
History
DepositionApr 3, 2026-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76415.png

Downloads & links

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Map

FileDownload / File: emd_76415.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.073844105 - 0.1983526
Average (Standard dev.)-0.0002034054 (±0.009888123)
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_76415_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_76415_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_76415_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human proteasome from HCT116 cells

EntireName: Human proteasome from HCT116 cells
Components
  • Complex: Human proteasome from HCT116 cells
    • Protein or peptide: 19S RP

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Supramolecule #1: Human proteasome from HCT116 cells

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

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Macromolecule #1: 19S RP

MacromoleculeName: 19S RP / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MVGVKPVGSD PDFQPELSGA GSRLAVVKFT MRGCGPCLRI APAFSSMSNK YPQAVFLEVD VHQCQGTAA TNNISATPTF LFFRNKVRID QYQGADAVGL EEKIKQHLEN DPGSNEDTDI P KGYMDLMP FINKAGCECL NESDEHGFDN CLRKDTTFLE SDCDEQLLIT ...String:
MVGVKPVGSD PDFQPELSGA GSRLAVVKFT MRGCGPCLRI APAFSSMSNK YPQAVFLEVD VHQCQGTAA TNNISATPTF LFFRNKVRID QYQGADAVGL EEKIKQHLEN DPGSNEDTDI P KGYMDLMP FINKAGCECL NESDEHGFDN CLRKDTTFLE SDCDEQLLIT VAFNQPVKLY SM KFQGPDN GQGPKYVKIF INLPRSMDFE EAERSEPTQA LELTEDDIKE DGIVPLRYVK FQN VNSVTI FVQSNQGEEE TTRISYFTFI GTPVQATNMN DFKRVVGKKG ESH

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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 / Pretreatment - Pressure: 0.038 kPa / Details: 20 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: 5.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.3) / Number images used: 11036
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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Atomic model buiding 1

Initial model
PDB IDChain

7wsi

chain_id: A, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: B, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: C, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: D, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: E, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: F, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: U, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: V, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: W, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: X, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: Y, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: Z, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: a, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: b, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: c, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: d, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: e, source_name: PDB, initial_model_type: experimental model

7wsi

chain_id: f, source_name: PDB, initial_model_type: experimental model

1wwy

chain_id: g, source_name: PDB, initial_model_type: experimental model
chain_id: f, source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Overall B value: 51 / Target criteria: Cross-correlation coefficient

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