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- EMDB-53883: EGFR(1-672) fused to CD82 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53883
TitleEGFR(1-672) fused to CD82
Map dataFusion protein of EGFR(1-672) and CD82 solubilized in DDM/CHS.
Sample
  • Complex: Complex EGFR and CD82 expressed as a fusion protein with a long, flexible linker
KeywordsFusion protein / tetraspanin / complex / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsLamottke E / Brondijk THC / Gros P
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO) Netherlands
CitationJournal: To Be Published
Title: Mechanistic implications on EGFR regulation by tetraspanin CD82
Authors: Lamottke E / Brondijk THC / Gros P
History
DepositionMay 21, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53883.png

Downloads & links

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Map

FileDownload / File: emd_53883.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFusion protein of EGFR(1-672) and CD82 solubilized in DDM/CHS.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.22 Å/pix.
x 196 pix.
= 434.885 Å		2.22 Å/pix.
x 196 pix.
= 434.885 Å		2.22 Å/pix.
x 196 pix.
= 434.885 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2188 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-0.08232233 - 1.2437093
Average (Standard dev.)0.00056080543 (±0.034359712)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions196196196
Spacing196196196
CellA=B=C: 434.88483 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53883_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_53883_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local refinement of transmembrane helices and interaction site.

Fileemd_53883_additional_2.map
AnnotationLocal refinement of transmembrane helices and interaction site.
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_53883_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_53883_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex EGFR and CD82 expressed as a fusion protein with a long, ...

EntireName: Complex EGFR and CD82 expressed as a fusion protein with a long, flexible linker
Components
  • Complex: Complex EGFR and CD82 expressed as a fusion protein with a long, flexible linker

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Supramolecule #1: Complex EGFR and CD82 expressed as a fusion protein with a long, ...

SupramoleculeName: Complex EGFR and CD82 expressed as a fusion protein with a long, flexible linker
type: complex / ID: 1 / Parent: 0
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

Concentration5 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 13848
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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