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- EMDB-54648: Cryo-EM structure of endogenous yeast EMC in complex with Spf1 in... -

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Basic information

Entry
Database: EMDB / ID: EMD-54648
TitleCryo-EM structure of endogenous yeast EMC in complex with Spf1 in digitonin: EMC locally refined
Map data
Sample
  • Complex: endogenous yeast EMC bound to Spf1
KeywordsER membrane protein complex / protein translocation / protein folding / chaperone / membrane proteins / MEMBRANE PROTEIN
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsKlose CJ / Prabu JR / Schulman BA
Funding support Germany, European Union, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)FE 1581/5-1 Germany
European Research Council (ERC)101098161European Union
German Research Foundation (DFG)SCHU 3196/1-1 Germany
Max Planck Society Germany
CitationJournal: To Be Published
Title: Structural basis of an endoplasmic reticulum EMC:Spf1 insertase-dislocase complex
Authors: Klose CJ / Prabu JR / Fenech EJ / Braeuning B / Baydar I / Steigenberger S / von Gronau S / Arad S / Langlois C / Schuldiner M / Schulman BA / Feige MJ
History
DepositionAug 5, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54648.png

Downloads & links

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Map

FileDownload / File: emd_54648.map.gz / Format: CCP4 / Size: 155.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 344 pix.
= 648.44 Å		1.89 Å/pix.
x 344 pix.
= 648.44 Å		1.89 Å/pix.
x 344 pix.
= 648.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.885 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.252
Minimum - Maximum-1.037546 - 1.1858119
Average (Standard dev.)0.0000844501 (±0.017032307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions344344344
Spacing344344344
CellA=B=C: 648.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54648_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_54648_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54648_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : endogenous yeast EMC bound to Spf1

EntireName: endogenous yeast EMC bound to Spf1
Components
  • Complex: endogenous yeast EMC bound to Spf1

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Supramolecule #1: endogenous yeast EMC bound to Spf1

SupramoleculeName: endogenous yeast EMC bound to Spf1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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

Concentration1.4 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 80281
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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