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- PDB-9za2: cryoEM structure of COMMD-like protein S4Y171 octamer -

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Basic information

Entry
Database: PDB / ID: 9za2
TitlecryoEM structure of COMMD-like protein S4Y171 octamer
ComponentsCOMM domain-containing protein
KeywordsUNKNOWN FUNCTION / Commd-like / octamer / bacterial / Commd / Commander
Function / homologyCOMM domain-containing protein
Function and homology information
Biological speciesSorangium cellulosum So0157-2 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsHealy, M.D. / Collins, B.M. / Liu, M. / Cater, R.J. / Blades, F.
Funding support Australia, France, 3items
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 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 10, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COMM domain-containing protein
B: COMM domain-containing protein
C: COMM domain-containing protein
D: COMM domain-containing protein
E: COMM domain-containing protein
F: COMM domain-containing protein
G: COMM domain-containing protein
H: COMM domain-containing protein


Theoretical massNumber of molelcules
Total (without water)238,5308
Polymers238,5308
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
COMM domain-containing protein


Mass: 29816.225 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum So0157-2 (bacteria)
Gene: SCE1572_19075 / Production host: Escherichia coli (E. coli) / References: UniProt: S4XVP2
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: 2D ARRAY / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: S4XVP2 Homo-octameric assembly / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.197 MDa / Experimental value: YES
Source (natural)Organism: Sorangium cellulosum So0157-2 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28401 / Symmetry type: POINT

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