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- EMDB-45793: Closed state MmCpn under ATP/AlFx condition by subtomogram averaging -

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Basic information

Entry
Database: EMDB / ID: EMD-45793
TitleClosed state MmCpn under ATP/AlFx condition by subtomogram averaging
Map dataReconstructed with D8 symmetry by subtomogram averaging
Sample
  • Complex: MmCpn
KeywordsArchaea chaperonin in closed state with ATP/AlFx / CHAPERONE
Function / homology
Function and homology information


ATP-dependent protein folding chaperone / unfolded protein binding / ATP hydrolysis activity / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
Thermosome, archaeal / : / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily ...Thermosome, archaeal / : / Chaperonins TCP-1 signature 1. / : / Chaperonins TCP-1 signature 2. / Chaperonin TCP-1, conserved site / Chaperonins TCP-1 signature 3. / Chaperone tailless complex polypeptide 1 (TCP-1) / GroEL-like equatorial domain superfamily / TCP-1-like chaperonin intermediate domain superfamily / GroEL-like apical domain superfamily / TCP-1/cpn60 chaperonin family / Chaperonin Cpn60/GroEL/TCP-1 family
Similarity search - Domain/homology
Biological speciesArchaea (unknown)
Methodsubtomogram averaging / cryo EM / Resolution: 2.56 Å
AuthorsYanyan Z
Funding support United States, 3 items
OrganizationGrant numberCountry
Chan Zuckerberg InitiativeSilicon Valley Community Foundation CZI Imaging Initiative (2021-234593) 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_45793.png

Downloads & links

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Map

FileDownload / File: emd_45793.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstructed with D8 symmetry by subtomogram averaging
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 Å		1.08 Å/pix.
x 280 pix.
= 302.4 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: 10.699999999999999
Minimum - Maximum-24.130882 - 41.818820000000002
Average (Standard dev.)0.20424068 (±2.2226372)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 302.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: total dose of 3 electron per angstrom square

Fileemd_45793_additional_1.map
Annotationtotal dose of 3 electron per angstrom square
Projections & Slices
AxesZYX

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Additional map: total dose of 12 electron per angstrom square

Fileemd_45793_additional_2.map
Annotationtotal dose of 12 electron per angstrom square
Projections & Slices
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Additional map: total dose of 21 electron per angstrom square

Fileemd_45793_additional_3.map
Annotationtotal dose of 21 electron per angstrom square
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: total dose of 30 electron per angstrom square

Fileemd_45793_additional_4.map
Annotationtotal dose of 30 electron per angstrom square
Projections & Slices
AxesZYX

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Additional map: total dose of 39 electron per angstrom square

Fileemd_45793_additional_5.map
Annotationtotal dose of 39 electron per angstrom square
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_45793_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: #1

Fileemd_45793_half_map_2.map
Projections & Slices
AxesZYX

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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: D8 (2x8 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.56 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 170000
ExtractionNumber tomograms: 500 / Number images used: 170000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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