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- EMDB-60690: cryo-EM structure of incomplete acetyl-CoA carboxyltransferase di... -

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Basic information

Entry
Database: EMDB / ID: EMD-60690
Titlecryo-EM structure of incomplete acetyl-CoA carboxyltransferase dimer from Shewanella without BCCP domain
Map dataThe filtered map corrected by spIsoNet.
Sample
  • Complex: incomplete Acetyl-CoA carboxyltransferase dimer without BCCP domain
Keywordsacetyl-CoA carboxyltransferase / LIGASE
Biological speciesShewanella oneidensis MR-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.28 Å
AuthorsWang W / Han SR / Xu YY / Gao HC
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: cryo-EM structure of incomplete acetyl-CoA carboxyltransferase dimer from Shewanella without BCCP domain
Authors: Wang W / Han SR / Xu YY / Gao HC
History
DepositionJul 3, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60690.png

Downloads & links

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Map

FileDownload / File: emd_60690.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe filtered map corrected by spIsoNet.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å		0.93 Å/pix.
x 256 pix.
= 238.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.08
Minimum - Maximum-3.5302258 - 14.660757
Average (Standard dev.)-0.07481644 (±0.75882554)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: The sharpened full map generated by the half-maps uploaded.

Fileemd_60690_additional_1.map
AnnotationThe sharpened full map generated by the half-maps uploaded.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: The original full map generated by the half-maps uploaded.

Fileemd_60690_additional_2.map
AnnotationThe original full map generated by the half-maps uploaded.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half-map A generated by homogeneous refinement of cryoSPARC.

Fileemd_60690_half_map_1.map
AnnotationThe half-map A generated by homogeneous refinement of cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half-map B generated by homogeneous refinement of cryoSPARC.

Fileemd_60690_half_map_2.map
AnnotationThe half-map B generated by homogeneous refinement of cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : incomplete Acetyl-CoA carboxyltransferase dimer without BCCP domain

EntireName: incomplete Acetyl-CoA carboxyltransferase dimer without BCCP domain
Components
  • Complex: incomplete Acetyl-CoA carboxyltransferase dimer without BCCP domain

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Supramolecule #1: incomplete Acetyl-CoA carboxyltransferase dimer without BCCP domain

SupramoleculeName: incomplete Acetyl-CoA carboxyltransferase dimer without BCCP domain
type: complex / ID: 1 / Parent: 0
Details: The complex lacks BC and BCCP domains due to the flexibility of it.
Source (natural)Organism: Shewanella oneidensis MR-1 (bacteria)

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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

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMNaClSodium chloride
20.0 mMHEPESN-2-Hydroxyethylpiperazine-N-2-Ethane Sulfonic Acid
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER / Details: model from AlphaFold2
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Software - details: Homogeneous Refinement / Number images used: 162227
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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