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- EMDB-63526: Subtomogram average of GEM-mCherry-nanobody labeled EGFR on A549 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-63526
TitleSubtomogram average of GEM-mCherry-nanobody labeled EGFR on A549 cell membranes
Map dataThe map was processed using ChimeraX's "vop flip" command to ensure it matched the correct handedness.
Sample
  • Organelle or cellular component: Native membranes derived from A549 cells expressing GEM-mCherry-nanobody
KeywordsTag / Agonist / Icosahedron / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 38.0 Å
AuthorsZou T / Zhang J / Zhang Y / Zhang M / Wang H / Pan Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22327808 China
CitationJournal: Acs Chem.Biol. / Year: 2026
Title: Visualization of EGFR Assembly and Activation Induced by a Protein Nanocage Using Cryo-Electron Tomography
Authors: Zou T / Zhang J / Zhang Y / Zhang M / Wang H / Pan Y / Wang H
History
DepositionFeb 21, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63526.png

Downloads & links

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Map

FileDownload / File: emd_63526.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe map was processed using ChimeraX's "vop flip" command to ensure it matched the correct handedness.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.88 Å/pix.
x 64 pix.
= 568.32 Å		8.88 Å/pix.
x 64 pix.
= 568.32 Å		8.88 Å/pix.
x 64 pix.
= 568.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.8253965 - 2.197665
Average (Standard dev.)0.047900446 (±0.31108937)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 568.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: The map was processed using ChimeraX's "vop flip"...

Fileemd_63526_half_map_1.map
AnnotationThe map was processed using ChimeraX's "vop flip" command to ensure it matched the correct handedness.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The map was processed using ChimeraX's "vop flip"...

Fileemd_63526_half_map_2.map
AnnotationThe map was processed using ChimeraX's "vop flip" command to ensure it matched the correct handedness.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Native membranes derived from A549 cells expressing GEM-mCherry-n...

EntireName: Native membranes derived from A549 cells expressing GEM-mCherry-nanobody
Components
  • Organelle or cellular component: Native membranes derived from A549 cells expressing GEM-mCherry-nanobody

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Supramolecule #1: Native membranes derived from A549 cells expressing GEM-mCherry-n...

SupramoleculeName: Native membranes derived from A549 cells expressing GEM-mCherry-nanobody
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4 / Details: phosphate-buffered saline (PBS)
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-10 / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.4 µm / Nominal magnification: 64000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 38.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number subtomograms used: 336
ExtractionNumber tomograms: 11 / Number images used: 336 / Reference model: ab initio / Method: manually picked particles / Software - Name: Warp (ver. 1.1.0)
Details: IsoNet-corrected tomograms were used for particle picking
CTF correctionSoftware - Name: Warp (ver. 1.1.0)
Details: Per-particle ctf estimation was performed with Warp
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model
Details: The initial model was generated with direct reconstruction by relion_reconstruction using predetermined orientations
RefinementProtocol: AB INITIO MODEL

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