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- EMDB-42882: Amylin 1 receptor bound to salmon calcitonin (Amy1R:sCT) reconstr... -

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Basic information

Entry
Database: EMDB / ID: EMD-42882
TitleAmylin 1 receptor bound to salmon calcitonin (Amy1R:sCT) reconstructed from cryo-EM datasets recorded using a rectangular aperture
Map dataAmylin 1 receptor bound to salmon calcitonin (Amy2R:sCT) reconstructed from a dataset recorded using a rectangular beam
Sample
  • Complex: Human Amylin1 Receptor in complex with Gs and salmon calcitonin peptide
    • Complex: Receptor activity-modifying protein 1
KeywordsHuman Amylin 1 Receptor in complex with Gs and salmon calcitonin peptide / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBrown HG / Hanssen E
Funding support1 items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Nat Methods / Year: 2024
Title: Square condenser apertures for square cameras in low-dose transmission electron microscopy.
Authors: Hamish G Brown / Dan Smith / Benjamin C Wardle / Eric Hanssen /
Abstract: In transmission electron microscopy (TEM), cameras are square or rectangular but beams are round so the circular lobes irradiate adjacent areas, precluding further neighboring acquisition for beam- ...In transmission electron microscopy (TEM), cameras are square or rectangular but beams are round so the circular lobes irradiate adjacent areas, precluding further neighboring acquisition for beam-sensitive samples. We present condenser aperture plates with square and rectangular shapes that improve the efficiency of area usage by 70% and enhance montage imaging for beam-sensitive specimens. We demonstrate the compatibility of these condenser aperture plates with high-resolution cryogenic TEM by reconstructing a 1.8-Å map of equine apo-ferritin.
#1: Journal: BioRxiv / Year: 2023
Title: Fitting a square beam in a square camera: Novel condenser apertures for low-dose transmission electron microscopy
Authors: Brown HG / Hanssen E
History
DepositionNov 19, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42882.png

Downloads & links

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Map

FileDownload / File: emd_42882.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAmylin 1 receptor bound to salmon calcitonin (Amy2R:sCT) reconstructed from a dataset recorded using a rectangular beam
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 333.2 Å		0.83 Å/pix.
x 400 pix.
= 333.2 Å		0.83 Å/pix.
x 400 pix.
= 333.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.19
Minimum - Maximum-1.1912746 - 1.747444
Average (Standard dev.)-0.00016130444 (±0.03524672)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 333.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_42882_msk_1.map
Projections & Slices
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Half map: Half map B

Fileemd_42882_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_42882_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human Amylin1 Receptor in complex with Gs and salmon calcitonin p...

EntireName: Human Amylin1 Receptor in complex with Gs and salmon calcitonin peptide
Components
  • Complex: Human Amylin1 Receptor in complex with Gs and salmon calcitonin peptide
    • Complex: Receptor activity-modifying protein 1

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Supramolecule #1: Human Amylin1 Receptor in complex with Gs and salmon calcitonin p...

SupramoleculeName: Human Amylin1 Receptor in complex with Gs and salmon calcitonin peptide
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 189 KDa

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Supramolecule #2: Receptor activity-modifying protein 1

SupramoleculeName: Receptor activity-modifying protein 1 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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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

Concentration4 mg/mL
BufferpH: 7.4
GridMaterial: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 3333 / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 1.5 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.4000000000000001 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 1441511
Details: Template picking using 2D classes from initial blob picking
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 138105
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Avg.num./class: 105074 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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