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- EMDB-36313: Cryo-EM structure of apoferritin with MSBP -

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Basic information

Entry
Database: EMDB / ID: EMD-36313
TitleCryo-EM structure of apoferritin with MSBP
Map data
Sample
  • Complex: Apoferritin with MSBP
KeywordsIron storage / Complex / METAL BINDING PROTEIN
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.16 Å
AuthorsXu Y / Qin Y / Wang L / Zhang Y / Wang Y / Dang S
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: Commun Biol / Year: 2024
Title: Metallo-supramolecular branched polymer protects particles from air-water interface in single-particle cryo-electron microscopy.
Authors: Yixin Xu / Yuqi Qin / Lang Wang / Yingyi Zhang / Yufeng Wang / Shangyu Dang /
Abstract: Recent technological breakthroughs in single-particle cryo-electron microscopy (cryo-EM) enable rapid atomic structure determination of biological macromolecules. A major bottleneck in the current ...Recent technological breakthroughs in single-particle cryo-electron microscopy (cryo-EM) enable rapid atomic structure determination of biological macromolecules. A major bottleneck in the current single particle cryo-EM pipeline is the preparation of good quality frozen cryo-EM grids, which is mostly a trial-and-error process. Among many issues, preferred particle orientation and sample damage by air-water interface (AWI) are common practical problems. Here we report a method of applying metallo-supramolecular branched polymer (MSBP) in the cryo-sample preparation for high-resolution single-particle cryo-EM. Our data shows that MSBP keeps a majority of particles away from air-water interface and mitigates preferred orientation as verified by the analyses of apoferritin, hemagglutinin) trimer and various sample proteins. The use of MSBP is a simple method to improve particle distribution for high-resolution structure determination in single-particle cryo-EM.
History
DepositionMay 26, 2023-
Header (metadata) releaseJan 17, 2024-
Map releaseJan 17, 2024-
UpdateJan 24, 2024-
Current statusJan 24, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36313.png

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Map

FileDownload / File: emd_36313.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.75
Minimum - Maximum-1.1759508 - 2.971001
Average (Standard dev.)0.00076345104 (±0.14083344)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36313_msk_1.map
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Half map: #1

Fileemd_36313_half_map_1.map
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Half map: #2

Fileemd_36313_half_map_2.map
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Sample components

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Entire : Apoferritin with MSBP

EntireName: Apoferritin with MSBP
Components
  • Complex: Apoferritin with MSBP

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Supramolecule #1: Apoferritin with MSBP

SupramoleculeName: Apoferritin with MSBP / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

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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: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 57.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 2.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 255785
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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