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- EMDB-73963: cryoEM structure of COMMD-like protein S4Y171 octamer -

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Basic information

Entry
Database: EMDB / ID: EMD-73963
TitlecryoEM structure of COMMD-like protein S4Y171 octamer
Map data
Sample
  • Complex: S4Y171 Homo-octameric assembly
    • Protein or peptide: COMM domain-containing protein
KeywordsCommd-like / octamer / bacterial / Commd / Commander / UNKNOWN FUNCTION
Function / homologyCOMM domain / COMM domain / COMM domain profile. / COMM domain-containing protein
Function and homology information
Biological speciesSorangium cellulosum So0157-2 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsHealy MD / Collins BM / Liu M / Cater RJ / Blades F
Funding support Australia, France, 3 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2016410 Australia
Australian Research Council (ARC)DP240101315 Australia
Human Frontier Science Program (HFSP)RGY0072/2021 France
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
DepositionNov 18, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 10, 2026-
Current statusJun 10, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73963.png

Downloads & links

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Map

FileDownload / File: emd_73963.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 256 pix.
= 192. Å		0.75 Å/pix.
x 256 pix.
= 192. Å		0.75 Å/pix.
x 256 pix.
= 192. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0527
Minimum - Maximum-0.43315718 - 0.6100459
Average (Standard dev.)0.0002708096 (±0.01891604)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 192.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73963_half_map_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: #1

Fileemd_73963_half_map_2.map
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Sample components

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Entire : S4Y171 Homo-octameric assembly

EntireName: S4Y171 Homo-octameric assembly
Components
  • Complex: S4Y171 Homo-octameric assembly
    • Protein or peptide: COMM domain-containing protein

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Supramolecule #1: S4Y171 Homo-octameric assembly

SupramoleculeName: S4Y171 Homo-octameric assembly / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Sorangium cellulosum So0157-2 (bacteria)
Molecular weightTheoretical: 211 KDa

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Macromolecule #1: COMM domain-containing protein

MacromoleculeName: COMM domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Sorangium cellulosum So0157-2 (bacteria)
Molecular weightTheoretical: 27.920113 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPMRSSMSTS AREAPSPRPE LASLGGAPPP PELAADLRRL LDLPEGARQR LWEALGPSLG EPVPAAVERL LDEFCRRHEV GSEALARVL KACRFLVREA SKRDLDRAAL AADLAALAPG EGAEEIQAIL LAGYDQARAV VRREIVRGAL LDHGKLLTGV D WRIDSIAA ...String:
GPMRSSMSTS AREAPSPRPE LASLGGAPPP PELAADLRRL LDLPEGARQR LWEALGPSLG EPVPAAVERL LDEFCRRHEV GSEALARVL KACRFLVREA SKRDLDRAAL AADLAALAPG EGAEEIQAIL LAGYDQARAV VRREIVRGAL LDHGKLLTGV D WRIDSIAA ASRGAKIAAP VVLLTLSYQE GDQRSRITLQ ATPDVLRELQ QICAQLLGEK GSVLTLRLRD GGRDERTTIY VA PPALGQI KEACDRIERM I

UniProtKB: COMM domain-containing protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 73912
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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