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- PDB-9ujx: CryoEM structure of Brucella melitensis CobS dodecamer 2 without ... -

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Basic information

Entry
Database: PDB / ID: 9ujx
TitleCryoEM structure of Brucella melitensis CobS dodecamer 2 without AMPPNP
ComponentsCobaltochelatase subunit CobS
KeywordsLIGASE / Cobalt chelatase / CobS / AAA+ / ATPase
Function / homology
Function and homology information


cobaltochelatase / cobaltochelatase activity / cobalamin biosynthetic process / ATP hydrolysis activity / ATP binding
Similarity search - Function
Cobaltochelatase subunit CobS / Cobaltochelatase subunit CobS N-terminal domain / Cobaltochelatase CobS subunit N terminal / : / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cobaltochelatase subunit CobS
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.02 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 CobS
B: Cobaltochelatase subunit CobS
C: Cobaltochelatase subunit CobS
D: Cobaltochelatase subunit CobS
E: Cobaltochelatase subunit CobS
F: Cobaltochelatase subunit CobS
a: Cobaltochelatase subunit CobS
b: Cobaltochelatase subunit CobS
c: Cobaltochelatase subunit CobS
d: Cobaltochelatase subunit CobS
e: Cobaltochelatase subunit CobS
f: Cobaltochelatase subunit CobS


Theoretical massNumber of molelcules
Total (without water)441,22412
Polymers441,22412
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
Cobaltochelatase subunit CobS


Mass: 36768.629 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: BI318_03735 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AB36PZV1
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: CobS Dodecamer 2 / Type: COMPLEX / Entity ID: all / 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: 4.02 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135929 / Symmetry type: POINT
RefinementHighest resolution: 4.02 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00228329
ELECTRON MICROSCOPYf_angle_d0.56938517
ELECTRON MICROSCOPYf_dihedral_angle_d4.0323836
ELECTRON MICROSCOPYf_chiral_restr0.0414372
ELECTRON MICROSCOPYf_plane_restr0.0045018

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