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- EMDB-30712: Cryo-Molecular electron tomography of epidermal growth factor rec... -

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Basic information

Entry
Database: EMDB / ID: EMD-30712
TitleCryo-Molecular electron tomography of epidermal growth factor receptor (averaged cluster 1)
Map dataUnliganded EGFR, averaged cluster 1
Sample
  • Complex: Unliganded EGFR
Biological speciesEGFR (human)
Methodsubtomogram averaging / cryo EM / Resolution: 15.0 Å
AuthorsPurba ER / Saita E-I / Akhouri RR / Ofverstedt LG / Wilken G / Skoglund U / Maruyama IN
CitationJournal: To Be Published
Title: Conformational flexibility transitions of the epidermal growth factor receptor dimer upon activation
Authors: Purba ER / Saita E-I / Akhouri RR / Ofverstedt LG / Wilken G / Skoglund U / Maruyama IN
History
DepositionNov 30, 2020-
Header (metadata) releaseDec 30, 2020-
Map releaseDec 30, 2020-
UpdateDec 30, 2020-
Current statusDec 30, 2020Processing 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_30712.png

Downloads & links

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Map

FileDownload / File: emd_30712.map.gz / Format: CCP4 / Size: 5.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnliganded EGFR, averaged cluster 1
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 LevelBy AUTHOR: 0.5 / Movie #1: 0.5
Minimum - Maximum0.19260542 - 0.7802467
Average (Standard dev.)0.3929175 (±0.065753855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions110110110
Spacing110110110
CellA=B=C: 248.37999 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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS110110110
D min/max/mean0.1930.7800.393

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Supplemental data

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Sample components

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Entire : Unliganded EGFR

EntireName: Unliganded EGFR
Components
  • Complex: Unliganded EGFR

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Supramolecule #1: Unliganded EGFR

SupramoleculeName: Unliganded EGFR / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Unliganded EGFR, subtomogram averaged cluster 1
Source (natural)Organism: EGFR (human)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: DH5a / Recombinant cell: E. coli / Recombinant plasmid: pIRES2-ZsGreen1-Thr-His8
Molecular weightTheoretical: 300 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 8 / Component - Concentration: 20.0 0.5 / Component - Name: Tris-HCL
Details: Solutions were made fresh from concentrated to avoid microbial contamination.
GridModel: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK I / Details: Blot for 5.5 seconds before plunging.
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsPhase plate: OTHER
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: OTHER / Digitization - Dimensions - Width: 2258 pixel / Digitization - Dimensions - Height: 2258 pixel / 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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: -2.0 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 reconstructionNumber classes used: 25 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: OTHER / Software - Name: UCSF Chimera (ver. 1.15) / Number subtomograms used: 15
ExtractionNumber tomograms: 15 / Number images used: 474
Final 3D classificationNumber classes: 25 / Avg.num./class: 40
Final angle assignmentType: ANGULAR RECONSTITUTION
Crystal parametersUnit cell - A: 60.7 Å / Unit cell - B: 9.3 Å / Unit cell - C: 14.4 Å / Unit cell - γ: 120 ° / Unit cell - α: 120 ° / Unit cell - β: 120 ° / Space group: P1

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Atomic model buiding 1

Initial modelPDB ID:

1nql

RefinementProtocol: FLEXIBLE FIT / Target criteria: Correlation coefficient

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Atomic model buiding 2

Initial modelPDB ID:

2m0b

RefinementProtocol: FLEXIBLE FIT / Target criteria: Correlation coefficient

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Atomic model buiding 3

Initial modelPDB ID:

3gt8

RefinementProtocol: FLEXIBLE FIT / Target criteria: Correlation coefficient

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