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- PDB-9q6c: Cryo-EM structure of octameric COMMD-like protein MBK5214510 from... -

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Basic information

Entry
Database: PDB / ID: 9q6c
TitleCryo-EM structure of octameric 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: 4.22 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: To Be Published
Title: The prokaryotic origins of the COMMD protein family involved in eukaryotic membrane trafficking
Authors: Collins, B.M. / Healy, M.D. / Liu, M.
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
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 1, 2025Data 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: 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


Theoretical massNumber of molelcules
Total (without water)222,0128
Polymers222,0128
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
d_1ens_1chain "A"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"

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_1AA
d_2BB
d_3CC
d_4DD
d_5EE
d_6FF
d_7GG
d_8HH

NCS oper:
IDCodeMatrixVector
1given(-0.0439972486507, -0.998828504141, 0.0201460027336), (-0.998772501551, 0.0435176055989, -0.0236581518599), (0.0227537306316, -0.0211621671364, -0.999517098615)232.971018431, 227.856531476, 228.304362182
2given(0.0244381139445, 0.999695829982, -0.00332055775082), (-0.999695408514, 0.024426387501, -0.00352729198773), (-0.00344510986092, 0.00340574670072, 0.999988265985)-2.6659241083, 227.530312318, 0.127018737958
3given(-0.999333063421, 0.0327893886003, 0.0160712273431), (0.0326555680574, 0.999430352413, -0.00851965669755), (-0.0163414267414, -0.00798915956859, -0.999834551864)224.323263947, -3.56158021731, 232.728201949
4given(-0.998935412853, 0.0437419529215, -0.0146520477408), (-0.0439670919043, -0.99891407692, 0.0154130386463), (-0.0139619403332, 0.0160408380531, 0.999773852297)226.931626309, 233.794837324, 0.320205293625
5given(-0.0139858976073, 0.99963738727, 0.0230106201689), (0.999879909455, 0.0141355178929, -0.00635246420302), (-0.00667542775176, 0.0229190118971, -0.999715038177)-0.883113467392, -0.430751023224, 228.138014922
6given(-0.0307094804652, -0.999444840778, 0.0129204509322), (0.999476218064, -0.0305732876225, 0.0106095998411), (-0.0102086891613, 0.0132394987324, 0.999860239403)232.29819456, 2.17337717176, 0.0934583718245
7given(0.999826769047, -0.0177440936392, -0.00561952289706), (-0.017747859884, -0.999842301451, -0.000621046310962), (-0.00560761680256, 0.00072067323151, -0.999984017504)2.7283009348, 231.997418159, 230.043489126

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Components

#1: Protein
COMMD-like protein MBK5214510


Mass: 27751.531 Da / Num. of mol.: 8
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: Homooctamer of the MBK5214510 COMMD-like protein / 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: 4.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 72675 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 1.11 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.007614528
ELECTRON MICROSCOPYf_angle_d0.819319440
ELECTRON MICROSCOPYf_chiral_restr0.04252200
ELECTRON MICROSCOPYf_plane_restr0.00582520
ELECTRON MICROSCOPYf_dihedral_angle_d6.38121848
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints8.08125600136E-13
ens_1d_3AAELECTRON MICROSCOPYNCS constraints5.38079136685E-12
ens_1d_4AAELECTRON MICROSCOPYNCS constraints1.24229732873E-13
ens_1d_5AAELECTRON MICROSCOPYNCS constraints4.24308810531E-13
ens_1d_6AAELECTRON MICROSCOPYNCS constraints7.74764156638E-12
ens_1d_7AAELECTRON MICROSCOPYNCS constraints4.14869116182E-13
ens_1d_8AAELECTRON MICROSCOPYNCS constraints2.98653430047E-10

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