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- EMDB-49404: Subtomogram Averaging of Liganded EGFR Dimer from Extracellular V... -

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Basic information

Entry
Database: EMDB / ID: EMD-49404
TitleSubtomogram Averaging of Liganded EGFR Dimer from Extracellular Vesicle
Map data
Sample
  • Complex: the EGFR extracellular region in extracellular vesicles
    • Other: Liganded EGFR dimer extracellular region
KeywordsEGFR / Receptor Tyrosine Kinase / Extracellular Vesicle / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 15.0 Å
AuthorsKe Z / Liu C / Gonzalez-Magaldi M / Leahy DJ
Funding support United States, 4 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR160023 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR230050 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122480 United States
Welch FoundationF-1515 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structure and organization of full-length epidermal growth factor receptor in extracellular vesicles by cryo-electron tomography.
Authors: Monica Gonzalez-Magaldi / Anuradha Gullapalli / Ophelia Papoulas / Chang Liu / Adelaide Y-H Leung / Luqiang Guo / Axel F Brilot / Edward M Marcotte / Zunlong Ke / Daniel J Leahy /
Abstract: We report here transport of full-length epidermal growth factor receptor (EGFR), Insulin Receptor, 7-pass transmembrane receptor Smoothened, and 13-pass Sodium-iodide symporter to extracellular ...We report here transport of full-length epidermal growth factor receptor (EGFR), Insulin Receptor, 7-pass transmembrane receptor Smoothened, and 13-pass Sodium-iodide symporter to extracellular vesicles (EVs) for structural and functional studies. Mass spectrometry confirmed the transported proteins are the most abundant in EV membranes, and the presence of many receptor-interacting proteins in EVs demonstrates their utility for characterizing membrane protein interactomes. Cryo-electron tomography of EGFR-containing EVs reveals that EGFR forms clusters in both the presence and absence of EGF with a ~3 nm gap between the inner membrane and cytoplasmic density. EGFR extracellular region (ECR) dimers do not form regular arrays in these clusters. Subtomogram averaging of the 150 kDa EGF-bound EGFR ECR dimer yielded a 15 Å map into which the crystal structure of the ligand-bound EGFR ECR dimer fits well. These findings refine our understanding of EGFR activation, clustering, and signaling and establish EVs as a versatile platform for structural and functional characterization of human membrane proteins in cell-derived membranes.
History
DepositionFeb 24, 2025-
Header (metadata) releaseMay 21, 2025-
Map releaseMay 21, 2025-
UpdateJun 18, 2025-
Current statusJun 18, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49404.png

Downloads & links

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Map

FileDownload / File: emd_49404.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 192 pix.
= 324.48 Å		1.69 Å/pix.
x 192 pix.
= 324.48 Å		1.69 Å/pix.
x 192 pix.
= 324.48 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.69 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.08629393 - 0.20161733
Average (Standard dev.)-0.00023751064 (±0.015267028)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 324.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_49404_msk_1.map
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Additional map: #1

Fileemd_49404_additional_1.map
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Half map: #1

Fileemd_49404_half_map_1.map
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Half map: #2

Fileemd_49404_half_map_2.map
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Sample components

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Entire : the EGFR extracellular region in extracellular vesicles

EntireName: the EGFR extracellular region in extracellular vesicles
Components
  • Complex: the EGFR extracellular region in extracellular vesicles
    • Other: Liganded EGFR dimer extracellular region

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Supramolecule #1: the EGFR extracellular region in extracellular vesicles

SupramoleculeName: the EGFR extracellular region in extracellular vesicles
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Liganded EGFR dimer extracellular region

MacromoleculeName: Liganded EGFR dimer extracellular region / type: other / ID: 1 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString: LEEKKVCQGT SNKLTQLGTF EDHFLSLQRM FNNCEVVLGN LEITYVQRNY DLSFLKTIQE VAGYVLIALN TVERIPLENL QIIRGNMYYE NSYALAVLSN YDANKTGLKE LPMRNLQEIL HGAVRFSNNP ALCNVESIQW RDIVSSDFLS NMSMDFQNHL GSCQKCDPSC ...String:
LEEKKVCQGT SNKLTQLGTF EDHFLSLQRM FNNCEVVLGN LEITYVQRNY DLSFLKTIQE VAGYVLIALN TVERIPLENL QIIRGNMYYE NSYALAVLSN YDANKTGLKE LPMRNLQEIL HGAVRFSNNP ALCNVESIQW RDIVSSDFLS NMSMDFQNHL GSCQKCDPSC PNGSCWGAGE ENCQKLTKII CAQQCSGRCR GKSPSDCCHN QCAAGCTGPR ESDCLVCRKF RDEATCKDTC PPLMLYNPTT YQMDVNPEGK YSFGATCVKK CPRNYVVTDH GSCVRACGAD SYEMEEDGVR KCKKCEGPCR KVCNGIGIGE FKDSLSINAT NIKHFKNCTS ISGDLHILPV AFRGDSFTHT PPLDPQELDI LKTVKEITGF LLIQAWPENR TDLHAFENLE IIRGRTKQHG QFSLAVVSLN ITSLGLRSLK EISDGDVIIS GNKNLCYANT INWKKLFGTS GQKTKIISNR GENSCKATGQ VCHALCSPEG CWGPEPRDCV SCRNVSRGRE CVDKCKLLEG EPREFVENSE CIQCHPECLP QAMNITCTGR GPDNCIQCAH YIDGPHCVKT CPAGVMGENN TLVWKYADAG HVCHLCHPNC TYGCTGPGLE GCPT
Recombinant expressionOrganism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number subtomograms used: 843
ExtractionNumber tomograms: 20 / Number images used: 1602
CTF correctionSoftware - Name: RELION (ver. 5.0) / Software - details: CTF estimation / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0) / Software - details: Refine3D
FSC plot (resolution estimation)

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