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- EMDB-32612: Structure of apo-ferritin with Hybrid electron counting at 120 kV -

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Basic information

Entry
Database: EMDB / ID: EMD-32612
TitleStructure of apo-ferritin with Hybrid electron counting at 120 kV
Map data
Sample
  • Complex: apo-ferritin
KeywordsCoxsackievirus A10 / VIRUS
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsZhu DJ / Zhang XZ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31930069 China
CitationJournal: Commun Biol / Year: 2022
Title: An electron counting algorithm improves imaging of proteins with low-acceleration-voltage cryo-electron microscope.
Authors: Dongjie Zhu / Huigang Shi / Chunling Wu / Xinzheng Zhang /
Abstract: Relative to the 300-kV accelerating field, electrons accelerated under lower voltages are potentially scattered more strongly. Lowering the accelerate voltage has been suggested to enhance the signal- ...Relative to the 300-kV accelerating field, electrons accelerated under lower voltages are potentially scattered more strongly. Lowering the accelerate voltage has been suggested to enhance the signal-to-noise ratio (SNR) of cryo-electron microscopy (cryo-EM) images of small-molecular-weight proteins (<100 kD). However, the detection efficient of current Direct Detection Devices (DDDs) and temporal coherence of cryo-EM decrease at lower voltage, leading to loss of SNR. Here, we present an electron counting algorithm to improve the detection of low-energy electrons. The counting algorithm increased the SNR of 120-kV and 200-kV cryo-EM image from a Falcon III camera by 8%, 20% at half the Nyquist frequency and 21%, 80% at Nyquist frequency, respectively, resulting in a considerable improvement in resolution of 3D reconstructions. Our results indicate that with further improved temporal coherence and a dedicated designed camera, a 120-kV cryo-electron microscope has potential to match the 300-kV microscope at imaging small proteins.
History
DepositionJan 15, 2022-
Header (metadata) releaseApr 13, 2022-
Map releaseApr 13, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_32612.png

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Map

FileDownload / File: emd_32612.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 224 pix.
= 224. Å		1 Å/pix.
x 224 pix.
= 224. Å		1 Å/pix.
x 224 pix.
= 224. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
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Contour LevelBy AUTHOR: 0.0443
Minimum - Maximum-0.11791298 - 0.18498023
Average (Standard dev.)0.0000026107002 (±0.012495696)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-112-112-112
Dimensions224224224
Spacing224224224
CellA=B=C: 224.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_32612_msk_1.map
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Half map: #2

Fileemd_32612_half_map_1.map
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Half map: #1

Fileemd_32612_half_map_2.map
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Sample components

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Entire : apo-ferritin

EntireName: apo-ferritin
Components
  • Complex: apo-ferritin

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Supramolecule #1: apo-ferritin

SupramoleculeName: apo-ferritin / type: complex / ID: 1 / Parent: 0
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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: OTHER / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 19.6 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1mfr

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 88485
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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