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- EMDB-7788: Insulin Receptor ectodomain in complex with two insulin molecules... -

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Basic information

Entry
Database: EMDB / ID: EMD-7788
TitleInsulin Receptor ectodomain in complex with two insulin molecules plunged with a spot-to-plunge time of 200 ms
Map dataCryoSPARC auto-generated sharpened full map from the last iteration of independent refinement.
Sample
  • Complex: Insulin Receptor Ectodomain in complex with two insulin molecules
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.93 Å
AuthorsNoble AJ / Wei H / Dandey VP / Zhang Z / Potter CS / Carragher B
CitationJournal: Nat Methods / Year: 2018
Title: Reducing effects of particle adsorption to the air-water interface in cryo-EM.
Authors: Alex J Noble / Hui Wei / Venkata P Dandey / Zhening Zhang / Yong Zi Tan / Clinton S Potter / Bridget Carragher /
Abstract: Most protein particles prepared in vitreous ice for single-particle cryo-electron microscopy (cryo-EM) are adsorbed to air-water or substrate-water interfaces, which can cause the particles to adopt ...Most protein particles prepared in vitreous ice for single-particle cryo-electron microscopy (cryo-EM) are adsorbed to air-water or substrate-water interfaces, which can cause the particles to adopt preferred orientations. By using a rapid plunge-freezing robot and nanowire grids, we were able to reduce some of the deleterious effects of the air-water interface by decreasing the dwell time of particles in thin liquid films. We demonstrated this by using single-particle cryo-EM and cryo-electron tomography (cryo-ET) to examine hemagglutinin, insulin receptor complex, and apoferritin.
History
DepositionApr 15, 2018-
Header (metadata) releaseMay 23, 2018-
Map releaseMay 23, 2018-
UpdateOct 10, 2018-
Current statusOct 10, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.614
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.614
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7788.png

Downloads & links

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Map

FileDownload / File: emd_7788.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoSPARC auto-generated sharpened full map from the last iteration of independent refinement.
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.614 / Movie #1: 0.614
Minimum - Maximum-0.3421783 - 1.3880165
Average (Standard dev.)0.0053676306 (±0.050904404)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z316.800316.800316.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.3421.3880.005

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Supplemental data

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Mask #1

Fileemd_7788_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoSPARC auto-generated half-map from the last iteration of...

Fileemd_7788_half_map_1.map
AnnotationCryoSPARC auto-generated half-map from the last iteration of independent refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoSPARC auto-generated half-map from the last iteration of...

Fileemd_7788_half_map_2.map
AnnotationCryoSPARC auto-generated half-map from the last iteration of independent refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Insulin Receptor Ectodomain in complex with two insulin molecules

EntireName: Insulin Receptor Ectodomain in complex with two insulin molecules
Components
  • Complex: Insulin Receptor Ectodomain in complex with two insulin molecules

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Supramolecule #1: Insulin Receptor Ectodomain in complex with two insulin molecules

SupramoleculeName: Insulin Receptor Ectodomain in complex with two insulin molecules
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Ovis aries (sheep)
Molecular weightExperimental: 215 KDa

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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

BufferpH: 7.5
GridModel: Homemade
VitrificationCryogen name: ETHANE / Instrument: OTHER
Details: 200 ms spot-to-plunge time. The value given for _emd_vitrification.instrument is SPOTITON. This is not in a list of allowed values set(['LEICA EM CPC', 'GATAN CRYOPLUNGE 3', 'LEICA PLUNGER', ...Details: 200 ms spot-to-plunge time. The value given for _emd_vitrification.instrument is SPOTITON. This is not in a list of allowed values set(['LEICA EM CPC', 'GATAN CRYOPLUNGE 3', 'LEICA PLUNGER', 'FEI VITROBOT MARK II', 'HOMEMADE PLUNGER', 'REICHERT-JUNG PLUNGER', 'FEI VITROBOT MARK I', 'LEICA KF80', 'FEI VITROBOT MARK III', 'LEICA EM GP', 'OTHER', 'FEI VITROBOT MARK IV']) so OTHER is written into the XML file.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal magnification: 105000
Specialist opticsSpherical aberration corrector: Corrected so that Cs is as close to 0 as possible.
Energy filter - Name: GIF Bioquantum
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average exposure time: 10.0 sec. / Average electron dose: 66.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 83513
CTF correctionSoftware - Name: Gctf
Startup modelType of model: INSILICO MODEL / In silico model: CryoSPARC ab-initio
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 0.6.5) / Details: CryoSPARC SGD
Final 3D classificationSoftware - Name: cryoSPARC (ver. 0.6.5)
Details: The best-looking class was used for full refinement.
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 0.6.5) / Details: CryoSPARC SGD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 0.6.5) / Number images used: 40390

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