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- EMDB-62530: Cryo-EM map of carboxysomal midi-shell: T = 9 shell under C1 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-62530
TitleCryo-EM map of carboxysomal midi-shell: T = 9 shell under C1 symmetry
Map data
Sample
  • Complex: Cryo-EM map of carboxysomal midi-shell: T = 9 shell under C1 symmetry
KeywordsCarboxysome / shell / STRUCTURAL PROTEIN
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation / viral translational frameshifting
Similarity search - Function
Carboxysome assembly protein / Carboxysome shell peptide mid-region / Carboxysome shell vertex protein CsoS4A / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment vertex (BMV) domain profile. / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain ...Carboxysome assembly protein / Carboxysome shell peptide mid-region / Carboxysome shell vertex protein CsoS4A / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment vertex (BMV) domain profile. / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily
Similarity search - Domain/homology
Carboxysome assembly protein CsoS2B / Carboxysome shell vertex protein CsoS4A / Major carboxysome shell protein CsoS1A
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsLi JX / Li TP / Wang SM / Zhang YZ / Liu LN / Wang P
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070109 China
CitationJournal: Plant Physiol / Year: 2025
Title: Symmetry-adjusted cryo-EM analysis unveils the detailed linker protein CsoS2 interactions within the α-carboxysome shell.
Authors: Jianxun Li / Tianpei Li / Saimeng Wang / Yu-Zhong Zhang / Lu-Ning Liu / Peng Wang /
Abstract: Excessive symmetry in cryo-EM data processing can distort key structural details of bacterial microcompartments, highlighting the importance of balanced symmetry for accurate structural insights.
History
DepositionNov 28, 2024-
Header (metadata) releaseDec 3, 2025-
Map releaseDec 3, 2025-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_62530.png

Downloads & links

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Map

FileDownload / File: emd_62530.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 500 pix.
= 530. Å		1.06 Å/pix.
x 500 pix.
= 530. Å		1.06 Å/pix.
x 500 pix.
= 530. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.95633054 - 1.8133065
Average (Standard dev.)0.005904285 (±0.10195847)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 530.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62530_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62530_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM map of carboxysomal midi-shell: T = 9 shell under C1 symmetry

EntireName: Cryo-EM map of carboxysomal midi-shell: T = 9 shell under C1 symmetry
Components
  • Complex: Cryo-EM map of carboxysomal midi-shell: T = 9 shell under C1 symmetry

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Supramolecule #1: Cryo-EM map of carboxysomal midi-shell: T = 9 shell under C1 symmetry

SupramoleculeName: Cryo-EM map of carboxysomal midi-shell: T = 9 shell under C1 symmetry
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Halothiobacillus neapolitanus (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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 40177
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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