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- EMDB-72267: CryoEM structure of decameric COMMD-like protein MBK5214510 from ... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-72267
TitleCryoEM structure of decameric COMMD-like protein MBK5214510 from Flavobacteriaceae bacterium
Map data
Sample
  • Complex: Decameric cryoEM structure of MBK5214510
    • Protein or peptide: COMMD-like protein MBK5214510
KeywordsCOMMD / homooligomer / UNKNOWN FUNCTION
Biological speciesFlavobacteriaceae bacterium (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.77 Å
AuthorsCollins BM / Healy MD / Liu M / Cater RJ
Funding support Australia, 1 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: To Be Published
Title: The prokaryotic origins of the COMMD protein family involved in eukaryotic membrane trafficking
Authors: Collins BM / Healy MD / Liu M
History
DepositionAug 22, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72267.png

Downloads & links

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Map

FileDownload / File: emd_72267.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 280 pix.
= 229.6 Å		0.82 Å/pix.
x 280 pix.
= 229.6 Å		0.82 Å/pix.
x 280 pix.
= 229.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0381
Minimum - Maximum-0.15944228 - 0.29265526
Average (Standard dev.)0.0007690471 (±0.013564755)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 229.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_72267_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_72267_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_72267_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 : Decameric cryoEM structure of MBK5214510

EntireName: Decameric cryoEM structure of MBK5214510
Components
  • Complex: Decameric cryoEM structure of MBK5214510
    • Protein or peptide: COMMD-like protein MBK5214510

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Supramolecule #1: Decameric cryoEM structure of MBK5214510

SupramoleculeName: Decameric cryoEM structure of MBK5214510 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Flavobacteriaceae bacterium (bacteria)

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Macromolecule #1: COMMD-like protein MBK5214510

MacromoleculeName: COMMD-like protein MBK5214510 / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Flavobacteriaceae bacterium (bacteria)
Molecular weightTheoretical: 27.751531 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MKYKIPKNFL SGFQILSQLD KKEIEELAKL LGELPVGSNV QEFQSAIQTN KELSENALKS ADTIFSLGG LLLEIKADDS LNQVAEDLTN AYAKEGEEEI GTEQREQLIH NLLIVLQKAE NLKKTFKAYR LLFENTRSFR K SRVMTDMR ...String:
MGSSHHHHHH SSGLVPRGSH MKYKIPKNFL SGFQILSQLD KKEIEELAKL LGELPVGSNV QEFQSAIQTN KELSENALKS ADTIFSLGG LLLEIKADDS LNQVAEDLTN AYAKEGEEEI GTEQREQLIH NLLIVLQKAE NLKKTFKAYR LLFENTRSFR K SRVMTDMR MIFDDDFQKK NQTGLIIHQL KLEYIEDNTS KEFFISLDND DVLKLSEELK RSLEKEECIK RDFDQVQFIN IK

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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

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.77 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: PHENIX / Number images used: 48201
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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