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- PDB-9q6a: Crystal structure of octameric COMMD-like protein MBK5214510 from... -

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Basic information

Entry
Database: PDB / ID: 9q6a
TitleCrystal structure of octameric COMMD-like protein MBK5214510 from Flavobacteriaceae bacterium
ComponentsCOMMD-like protein MBK5214510
KeywordsUNKNOWN FUNCTION / COMMD / homooligomer
Biological speciesFlavobacteriaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsCollins, B.M. / Healy, M.D. / Liu, M.
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 21, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COMMD-like protein MBK5214510
B: COMMD-like protein MBK5214510


Theoretical massNumber of molelcules
Total (without water)55,5032
Polymers55,5032
Non-polymers00
Water27015
1
A: COMMD-like protein MBK5214510
B: COMMD-like protein MBK5214510

A: COMMD-like protein MBK5214510
B: COMMD-like protein MBK5214510

A: COMMD-like protein MBK5214510
B: COMMD-like protein MBK5214510

A: COMMD-like protein MBK5214510
B: COMMD-like protein MBK5214510


Theoretical massNumber of molelcules
Total (without water)222,0128
Polymers222,0128
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_755-x+2,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area36620 Å2
ΔGint-214 kcal/mol
Surface area82180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.343, 96.013, 115.614
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

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Components

#1: Protein COMMD-like protein MBK5214510


Mass: 27751.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacteriaceae bacterium (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 10% DMSO, 0.1 M sodium chloride, 25% PE5/4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.58→45.7 Å / Num. obs: 16103 / % possible obs: 98.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 57.72 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.022 / Net I/σ(I): 14.8
Reflection shellResolution: 2.58→2.66 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 1127 / CC1/2: 0.919 / Rpim(I) all: 0.146

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Processing

Software
NameVersionClassification
PHENIX1.21refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.58→45.67 Å / SU ML: 0.2868 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.5961
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2923 1617 10.04 %
Rwork0.2392 14486 -
obs0.2452 16103 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.23 Å2
Refinement stepCycle: LAST / Resolution: 2.58→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3477 0 0 15 3492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083513
X-RAY DIFFRACTIONf_angle_d1.47014705
X-RAY DIFFRACTIONf_chiral_restr0.1015537
X-RAY DIFFRACTIONf_plane_restr0.0096611
X-RAY DIFFRACTIONf_dihedral_angle_d22.7881373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.660.34091100.28811017X-RAY DIFFRACTION84.74
2.66-2.740.30311410.26381206X-RAY DIFFRACTION100
2.74-2.840.33251240.27751220X-RAY DIFFRACTION100
2.84-2.960.4481310.30921191X-RAY DIFFRACTION100
2.96-3.090.38431380.29421198X-RAY DIFFRACTION100
3.09-3.250.28551420.25811220X-RAY DIFFRACTION100
3.25-3.460.33531250.25861207X-RAY DIFFRACTION99.92
3.46-3.720.30981370.26631220X-RAY DIFFRACTION100
3.72-4.10.29691420.22081218X-RAY DIFFRACTION99.85
4.1-4.690.27561390.21451227X-RAY DIFFRACTION99.78
4.69-5.90.26811360.21791256X-RAY DIFFRACTION99.86
5.91-45.670.23581520.21651306X-RAY DIFFRACTION99.86

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