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

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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: Nat Commun / Year: 2026
Title: The prokaryotic origins of the COMMD protein family involved in eukaryotic membrane trafficking.
Authors: Meihan Liu / Edmund R R Moody / Farrah Blades / Caroline Puente-Lelievre / Kai-En Chen / Ella J Stephens / Katharine A Michie / Rosemary J Cater / Tom A Williams / Brett M Collins / Michael D Healy /
Abstract: The ten eukaryotic COMMD proteins are core components of the Commander complex, with central roles in endosomal membrane trafficking and signalling. Each protein has an α-helical N-terminal (HN) ...The ten eukaryotic COMMD proteins are core components of the Commander complex, with central roles in endosomal membrane trafficking and signalling. Each protein has an α-helical N-terminal (HN) domain with a C-terminal copper metabolism gene MURR1 (COMM) domain. These ten family members assemble into a heterodecameric ring composed of five specific heterodimers. In this work we have combined structural homology searches with genome-wide predicted structures to identify ancestral COMMD-like proteins that exist as single genes in Bacteria and Archaea. Although there is limited sequence similarity to the eukaryotic proteins the bacterial and archaeal COMMD-like proteins are predicted to form homomeric ring-shaped assemblies like their eukaryotic counterparts. Our biophysical studies, crystal and cryo-EM structures confirm COMMD-like proteins readily form homooligomeric rings composed of eight or ten subunits assembled from core dimeric building blocks and inter-dimer interactions that are analogous to the heterodecameric core structure of the eukaryotic Commander complex. Phylogenetic analyses using amino acid sequences and FoldSeek structural alphabet (3Di) infer that the closest identified relatives to the eukaryotic COMMD proteins are found in Myxococcota bacteria. These findings indicate that COMMD genes emerged early in eukaryotic evolution through multiple rounds of duplication from a single ancestral gene likely acquired from bacteria.
History
DepositionAug 22, 2025-
Header (metadata) releaseOct 1, 2025-
Map releaseOct 1, 2025-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing 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

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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
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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
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Half map: #1

Fileemd_72267_half_map_1.map
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Half map: #2

Fileemd_72267_half_map_2.map
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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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