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- EMDB-30745: Liganded EGFR averaged cluster 5 -

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Basic information

Entry
Database: EMDB / ID: EMD-30745
TitleLiganded EGFR averaged cluster 5
Map data
Sample
  • Complex: Liganded EGFR averaged cluster 5
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM / Resolution: 15.0 Å
AuthorsPurba ER / Saita EI / Akhouri RR / Ofverstedt LG / Wilken G / Skoglund U / Maruyama IN
CitationJournal: Front Endocrinol / Year: 2022
Title: Allosteric activation of preformed EGF receptor dimers by a single ligand binding event.
Authors: Purba ER / Saita EI / Akhouri RR / Ofverstedt LG / Wilken G / Skoglund U / Maruyama IN
History
DepositionDec 3, 2020-
Header (metadata) releaseDec 30, 2020-
Map releaseDec 30, 2020-
UpdateDec 14, 2022-
Current statusDec 14, 2022Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30745.png

Downloads & links

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Map

FileDownload / File: emd_30745.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.26 Å/pix.
x 110 pix.
= 248.38 Å		2.26 Å/pix.
x 110 pix.
= 248.38 Å		2.26 Å/pix.
x 110 pix.
= 248.38 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.258 Å
Density

Histogram

Histogram (log scale)
Contour LevelMovie #1: 0.5
Minimum - Maximum0.12534176 - 0.75793755
Average (Standard dev.)0.41072318 (±0.065927364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions110110110
Spacing110110110
CellA=B=C: 248.38002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.2582.2582.258
M x/y/z110110110
origin x/y/z0.0000.0000.000
length x/y/z248.380248.380248.380
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ558558558
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS110110110
D min/max/mean0.1250.7580.411

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Supplemental data

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Sample components

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Entire : Liganded EGFR averaged cluster 5

EntireName: Liganded EGFR averaged cluster 5
Components
  • Complex: Liganded EGFR averaged cluster 5

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Supramolecule #1: Liganded EGFR averaged cluster 5

SupramoleculeName: Liganded EGFR averaged cluster 5 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Location in cell: membrane cell
Molecular weightTheoretical: 300 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 8
Component:
ConcentrationName
20.0 mMTris-HCL
200.0 mMSodium chloride
0.2 mMDodecyl maltocide
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 277.0 K / Instrument: FEI VITROBOT MARK IV
Detailsthe sample was monodisperse
Cryo protectantNo
SectioningOther: NO SECTIONING

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 135 / Average exposure time: 1.8 sec. / Average electron dose: 90.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 1.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 37000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 37000
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 reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: OTHER / Number images used: 141

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Atomic model buiding 1

Initial model
PDB IDChain

3njp

chain_id: A, residue_range: 1-614

3njp

chain_id: B, residue_range: 1-614

2m20

chain_id: A, residue_range: 1-60

2m20

chain_id: B, residue_range: 61-120

2gs6

chain_id: A, residue_range: 669-995

2gs6

chain_id: B, residue_range: 669-995
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient

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