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- EMDB-63504: Refinement of Cdc37-PINK1 in Hsp90-Cdc37-PINK1 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-63504
TitleRefinement of Cdc37-PINK1 in Hsp90-Cdc37-PINK1 complex
Map data
Sample
  • Complex: Refinement of Cdc37-PINK1 in Hsp90-Cdc37-PINK1 complex
KeywordsHsp90 / PINK1 / Cdc37 / CYTOSOLIC PROTEIN / CHAPERONE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsTian XY / Su JY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071192 China
CitationJournal: To Be Published
Title: Refinement of Cdc37-PINK1 in Hsp90-Cdc37-PINK1 complex
Authors: Tian XY / Su JY
History
DepositionFeb 19, 2025-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63504.png

Downloads & links

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Map

FileDownload / File: emd_63504.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 280 pix.
= 243.516 Å		0.87 Å/pix.
x 280 pix.
= 243.516 Å		0.87 Å/pix.
x 280 pix.
= 243.516 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8697 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-1.1681337 - 2.1908042
Average (Standard dev.)-0.00049249677 (±0.027359813)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 243.516 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63504_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_63504_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 : Refinement of Cdc37-PINK1 in Hsp90-Cdc37-PINK1 complex

EntireName: Refinement of Cdc37-PINK1 in Hsp90-Cdc37-PINK1 complex
Components
  • Complex: Refinement of Cdc37-PINK1 in Hsp90-Cdc37-PINK1 complex

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Supramolecule #1: Refinement of Cdc37-PINK1 in Hsp90-Cdc37-PINK1 complex

SupramoleculeName: Refinement of Cdc37-PINK1 in Hsp90-Cdc37-PINK1 complex
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 277 KDa

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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
GridModel: Quantifoil R0.6/1 / Material: GOLD / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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: 1.8 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1324869
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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