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- EMDB-52196: Hsp70-NBD:Bag1:Rpn1 ternary complex class 2 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-52196
TitleHsp70-NBD:Bag1:Rpn1 ternary complex class 2
Map dataDeepemhancer processed map
Sample
  • Complex: Hsp70-NBD:Bag1:Rpn1 ternary complex class 2
KeywordsHsp70 / Chaperone / cochaperone / proteasome / protein degradation
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsCheng TC / Sakata E / Muntaner J / Maestro-Lopez M / Cuellar J / Valpuesta JM
Funding support Germany, Spain, 6 items
OrganizationGrant numberCountry
German Research Foundation (DFG)154113120 Germany
German Research Foundation (DFG)EXC 2067/1-390729940 Germany
German Research Foundation (DFG)448415290 Germany
Spanish Ministry of Science, Innovation, and UniversitiesPID2022-137175NB-I00 Spain
Spanish Ministry of Science, Innovation, and UniversitiesAEI/10.13039/501100011033 Spain
Spanish Ministry of Science, Innovation, and UniversitiesCEX2023-001386-S Spain
CitationJournal: To Be Published
Title: Structures of the 26S proteasome in complex with cochaperone Bag1
Authors: Maestro-Lopez M / Cheng TC / Muntaner J / Menendez M / Alonso M / Schweitzer A / Cuellar J / Valpuesta JM / Sakata E
History
DepositionNov 27, 2024-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52196.png

Downloads & links

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Map

FileDownload / File: emd_52196.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepemhancer processed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.59 Å/pix.
x 140 pix.
= 222.6 Å		1.59 Å/pix.
x 140 pix.
= 222.6 Å		1.59 Å/pix.
x 140 pix.
= 222.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.59 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.17
Minimum - Maximum-0.002630825 - 1.4852804
Average (Standard dev.)0.0013828535 (±0.027904103)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 222.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: B-factor sharpened map

Fileemd_52196_additional_1.map
AnnotationB-factor sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52196_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_52196_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 : Hsp70-NBD:Bag1:Rpn1 ternary complex class 2

EntireName: Hsp70-NBD:Bag1:Rpn1 ternary complex class 2
Components
  • Complex: Hsp70-NBD:Bag1:Rpn1 ternary complex class 2

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Supramolecule #1: Hsp70-NBD:Bag1:Rpn1 ternary complex class 2

SupramoleculeName: Hsp70-NBD:Bag1:Rpn1 ternary complex class 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#33
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: 7.6
Component:
ConcentrationFormulaName
20.0 mMHepesHepes
150.0 mMKClPotassium chloride
1.0 mMDTTDithiothreitol
GridModel: UltrAuFoil R1.2/1.3 / Mesh: 200 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 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: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.4000000000000001 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30256
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Details: Cryosparc Ab-Initio Reconstruction
Final angle assignmentType: MAXIMUM LIKELIHOOD

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