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- PDB-9uk9: CryoEM structure of Brucella melitensis CobN with cobalt ion -

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Basic information

Entry
Database: PDB / ID: 9uk9
TitleCryoEM structure of Brucella melitensis CobN with cobalt ion
ComponentsCobaltochelatase subunit CobN
KeywordsLIGASE / Cobalt chelatase / CobN / Cobalt ion
Function / homologyCobaltochelatase, CobN subunit / CobN/magnesium chelatase / CobN/Magnesium Chelatase / cobaltochelatase / cobaltochelatase activity / cobalamin biosynthetic process / : / Cobaltochelatase subunit CobN
Function and homology information
Biological speciesBrucella melitensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.49 Å
AuthorsZhou, Y.L. / Chen, X. / Liu, L.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32471323 China
National Natural Science Foundation of China (NSFC)32371270 China
CitationJournal: Biorxiv / Year: 2026
Title: Assembly of the ATP-driven cobalt chelatase
Authors: Zhou, Y.L. / Yuan, H. / Wu, Y.C. / Wang, J. / Chen, H. / Yao, L. / Wang, M. / Wang, X. / Wang, J. / He, C. / Chen, X. / Liu, L.
History
DepositionApr 17, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 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: Cobaltochelatase subunit CobN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,0413
Polymers136,9231
Non-polymers1182
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 Cobaltochelatase subunit CobN


Mass: 136922.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: BI318_15330 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AB36PS61
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: CobN / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Brucella melitensis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
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: 2000 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
Image processingDetails: cryosparc
CTF correctionType: NONE
Particle selectionDetails: cryosparc
3D reconstructionResolution: 3.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 207001 / Symmetry type: POINT
RefinementHighest resolution: 3.49 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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