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- EMDB-51540: Adeno-associated Virus 9 at 2.8A imaged on Falcon C -

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Basic information

Entry
Database: EMDB / ID: EMD-51540
TitleAdeno-associated Virus 9 at 2.8A imaged on Falcon C
Map data
Sample
  • Virus: Adeno-associated virus 9
KeywordsI symmetry / Tundra / Falcon C / VIRUS
Biological speciesAdeno-associated virus 9
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKoh FA / Karia D / Yang W / Yu L / Kotecha A
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Other private Netherlands
CitationJournal: Structure / Year: 2025
Title: Sub-3 Å resolution protein structure determination by single-particle cryo-EM at 100 keV.
Authors: Dimple Karia / Adrian F Koh / Wen Yang / Victoria I Cushing / Benjamin Basanta / Daniel B Mihaylov / Sagar Khavnekar / Ondřej Vyroubal / Miloš Malínský / Ondřej Sháněl / Vojtěch ...Authors: Dimple Karia / Adrian F Koh / Wen Yang / Victoria I Cushing / Benjamin Basanta / Daniel B Mihaylov / Sagar Khavnekar / Ondřej Vyroubal / Miloš Malínský / Ondřej Sháněl / Vojtěch Doležal / Jürgen Plitzko / Lingbo Yu / Gabriel C Lander / A Radu Aricescu / Basil J Greber / Abhay Kotecha /
Abstract: Cryoelectron microscopy (cryo-EM) has transformed structural biology by providing high-resolution insights into biological macromolecules. We report sub-3 Å resolution structures using the 100 keV ...Cryoelectron microscopy (cryo-EM) has transformed structural biology by providing high-resolution insights into biological macromolecules. We report sub-3 Å resolution structures using the 100 keV Tundra cryo-TEM, equipped with the Falcon C direct electron detector (DED). This system combines advanced optics, extreme-brightness field emission gun (XFEG), and SP-TWIN lens to enhance coherence and resolution. The semi-automated loader reduced contamination and drift, enabling extended data collection, while the high detective quantum efficiency (DQE) of Falcon C improved signal-to-noise ratio. We validated performance by determining structures of biological samples, including apoferritin (2.1 Å), T20S proteasome (2.7 Å), GABA receptor (2.8 Å), hemoglobin (5.0 Å), transthyretin (3.5 Å), and AAV9 capsid (2.8 Å), spanning 50 kDa-3.9 MDa. This work highlights the potential of 100 keV transmission electron microscopes (TEMs) to make cryo-EM more accessible. It sets a precedent for using lower voltage TEMs not only for screening, but also for high-resolution protein structure determination.
History
DepositionSep 13, 2024-
Header (metadata) releaseSep 25, 2024-
Map releaseSep 25, 2024-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51540.png

Downloads & links

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Map

FileDownload / File: emd_51540.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 280 pix.
= 359.8 Å		1.29 Å/pix.
x 280 pix.
= 359.8 Å		1.29 Å/pix.
x 280 pix.
= 359.8 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.285 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.08669228 - 0.16165227
Average (Standard dev.)0.0011286921 (±0.011078056)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 359.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51540_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51540_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Adeno-associated virus 9

EntireName: Adeno-associated virus 9
Components
  • Virus: Adeno-associated virus 9

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Supramolecule #1: Adeno-associated virus 9

SupramoleculeName: Adeno-associated virus 9 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 235455 / Sci species name: Adeno-associated virus 9 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS TUNDRA
Image recordingFilm or detector model: OTHER / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.6 µm / Nominal defocus min: 0.2 µm

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Image processing

DetailsFalcon C
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 89673
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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