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- PDB-9q6d: CryoEM structure of decameric COMMD-like protein MBK5214510 from ... -

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Basic information

Entry
Database: PDB / ID: 9q6d
TitleCryoEM structure of decameric COMMD-like protein MBK5214510 from Flavobacteriaceae bacterium
ComponentsCOMMD-like protein MBK5214510
KeywordsUNKNOWN FUNCTION / COMMD / homooligomer
Biological speciesFlavobacteriaceae bacterium (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.77 Å
AuthorsCollins, B.M. / Healy, M.D. / Liu, M. / Cater, R.J.
Funding support Australia, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COMMD-like protein MBK5214510
B: COMMD-like protein MBK5214510
C: COMMD-like protein MBK5214510
D: COMMD-like protein MBK5214510
E: COMMD-like protein MBK5214510
F: COMMD-like protein MBK5214510
G: COMMD-like protein MBK5214510
H: COMMD-like protein MBK5214510
I: COMMD-like protein MBK5214510
J: COMMD-like protein MBK5214510


Theoretical massNumber of molelcules
Total (without water)277,51510
Polymers277,51510
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "B"
d_2ens_1chain "A"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 1 - 220 / Label seq-ID: 21 - 240

Dom-IDAuth asym-IDLabel asym-ID
d_1BB
d_2AA
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH
d_9II
d_10JJ

NCS oper:
IDCodeMatrixVector
1given(0.809465176364, 0.587150588589, 0.00450716916928), (0.587154184907, -0.809474879778, 0.000618186668427), (0.00401140888767, 0.00214600265924, -0.999989651582)-46.0721708422, 140.185887474, 227.442301862
2given(0.307610497892, -0.951488151957, 0.0067880978475), (0.951449544364, 0.307500385321, -0.0136849390336), (0.0109337146471, 0.0106681635139, 0.999883315278)187.866645364, -28.1404801086, -1.95484332079
3given(-0.325663089637, 0.945480621819, -0.00315369841147), (0.945323773516, 0.325667205966, 0.0174308399975), (0.0175075775898, 0.0026953151257, -0.999843097692)43.328921859, -33.1243318445, 226.253940649
4given(-0.813567832596, -0.581348942103, 0.0118654659253), (0.58143440912, -0.813574446183, 0.00553610066778), (0.00643503360232, 0.0114029835905, 0.99991427748)273.63251262, 140.370195515, -1.6778328931
5given(-0.999973045462, -0.000166838338203, 0.0073403347965), (-0.000195082603287, 0.999992580203, -0.00384726928829), (-0.0073396384607, -0.00384859755855, -0.999965658412)228.599951993, 0.411196209287, 229.013126612
6given(-0.806885958806, 0.590706393273, -0.00100320917053), (-0.590698897181, -0.806864363177, 0.00668672592954), (0.00314043802813, 0.00598801981361, 0.999977140373)139.874337241, 274.561711828, -0.821862199139
7given(-0.304493431676, -0.952091223018, 0.0283910746135), (-0.951789296733, 0.305289270517, 0.029926508861), (-0.0371602568801, -0.0179098955587, -0.999148813215)255.890673879, 185.410839438, 232.615387408
8given(0.297896574585, 0.954390940849, -0.0198887625748), (-0.954240599054, 0.298290548019, 0.0211572228702), (0.0261248917287, 0.0126760004931, 0.999578315613)-26.9615476522, 187.10948827, -3.22849481254
9given(0.797708466356, -0.603043255945, -0.00018483294638), (-0.603002919616, -0.797658580551, 0.0113255378909), (-0.00697722283068, -0.00892302265528, -0.999935846956)91.7428887422, 274.010615803, 229.413097854

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Components

#1: Protein
COMMD-like protein MBK5214510


Mass: 27751.531 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacteriaceae bacterium (bacteria) / Production host: Escherichia coli (E. coli)
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Decameric cryoEM structure of MBK5214510 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Flavobacteriaceae bacterium (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: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.21.1_5286model refinement
13PHENIX3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48201 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 319.28 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002418160
ELECTRON MICROSCOPYf_angle_d0.556424300
ELECTRON MICROSCOPYf_chiral_restr0.03512750
ELECTRON MICROSCOPYf_plane_restr0.00193150
ELECTRON MICROSCOPYf_dihedral_angle_d5.68752310
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BBELECTRON MICROSCOPYNCS constraints5.19994980951E-13
ens_1d_3BBELECTRON MICROSCOPYNCS constraints3.68002801569E-10
ens_1d_4BBELECTRON MICROSCOPYNCS constraints3.82629249577E-13
ens_1d_5BBELECTRON MICROSCOPYNCS constraints4.67978007577E-13
ens_1d_6BBELECTRON MICROSCOPYNCS constraints4.25479328142E-13
ens_1d_7BBELECTRON MICROSCOPYNCS constraints5.23660617671E-13
ens_1d_8BBELECTRON MICROSCOPYNCS constraints4.59061263575E-13
ens_1d_9BBELECTRON MICROSCOPYNCS constraints5.50462899453E-13
ens_1d_10BBELECTRON MICROSCOPYNCS constraints2.06379236143E-11

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