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- EMDB-53933: EGF-bound EGFR(1-672) dimer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53933
TitleEGF-bound EGFR(1-672) dimer
Map dataGlobal map of EGF-bound EGFR(1-672) dimer in DDM/CHS.
Sample
  • Complex: 2:2 complex of EGF-bound EGFR(1-672) dimer
KeywordsComplex / Ligand-bound / detergent-solubilized / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 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
DepositionJun 2, 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_53933.png

Downloads & links

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Map

FileDownload / File: emd_53933.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGlobal map of EGF-bound EGFR(1-672) dimer in DDM/CHS.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 320 pix.
= 434.88 Å		1.36 Å/pix.
x 320 pix.
= 434.88 Å		1.36 Å/pix.
x 320 pix.
= 434.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.359 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.133
Minimum - Maximum-0.03835888 - 0.40355498
Average (Standard dev.)0.0011896623 (±0.01698264)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 434.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53933_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Local refinement excluding the micelle.

Fileemd_53933_additional_1.map
AnnotationLocal refinement excluding the micelle.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Global, sharpened map.

Fileemd_53933_additional_2.map
AnnotationGlobal, sharpened map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A.

Fileemd_53933_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_53933_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 : 2:2 complex of EGF-bound EGFR(1-672) dimer

EntireName: 2:2 complex of EGF-bound EGFR(1-672) dimer
Components
  • Complex: 2:2 complex of EGF-bound EGFR(1-672) dimer

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Supramolecule #1: 2:2 complex of EGF-bound EGFR(1-672) dimer

SupramoleculeName: 2:2 complex of EGF-bound EGFR(1-672) dimer / 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

Concentration3 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
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: 57.0 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: 6.5 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Number images used: 56818
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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