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- EMDB-45794: MmCpn in closed state wit D9 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-45794
TitleMmCpn in closed state wit D9 symmetry
Map dataDy symmetry reconstruction of MmCpn by subtomogram averaging
Sample
  • Complex: MmCpn
KeywordsArchaea chaperonin in closed state with ATP/AlFx / CHAPERONE
Biological speciesArchaea (unknown)
Methodsubtomogram averaging / cryo EM / Resolution: 3.6 Å
AuthorsYanyan Z
Funding support United States, 3 items
OrganizationGrant numberCountry
Chan Zuckerberg Initiative2021-234593 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM139166 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129541 United States
CitationJournal: To Be Published
Title: Cost-benefit analysis of cryogenic electron tomography subtomogram averaging of chaperonin MmCpn at near atomic resolution
Authors: Yanyan Z
History
DepositionJul 17, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45794.png

Downloads & links

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Map

FileDownload / File: emd_45794.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDy symmetry reconstruction of MmCpn by subtomogram averaging
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å		1.08 Å/pix.
x 300 pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-16.101500999999999 - 34.922980000000003
Average (Standard dev.)0.15668114 (±1.7123686)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_45794_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45794_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 : MmCpn

EntireName: MmCpn
Components
  • Complex: MmCpn

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Supramolecule #1: MmCpn

SupramoleculeName: MmCpn / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Archaea (unknown)
Molecular weightTheoretical: 1 MDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: D9 (2x9 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 11000
ExtractionNumber tomograms: 500 / Number images used: 170000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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