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- PDB-9ukg: CryoEM structure of Brucella melitensis CobS-CobT complex with AM... -

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Basic information

Entry
Database: PDB / ID: 9ukg
TitleCryoEM structure of Brucella melitensis CobS-CobT complex with AMPPNP (conformation 5)
Components
  • Cobaltochelatase subunit CobS
  • Cobaltochelatase subunit CobT
KeywordsLIGASE / Cobalt chelatase / CobS-CobT complex / AMPPNP
Function / homology
Function and homology information


cobaltochelatase / cobaltochelatase activity / cobalamin biosynthetic process / ATP hydrolysis activity / ATP binding
Similarity search - Function
Cobalt chelatase, CobT subunit / Cobalamin biosynthesis protein CobT VWA domain / Cobalamin biosynthesis protein CobT / Cobalamin biosynthesis protein CobT VWA domain / Cobaltochelatase subunit CobS / Cobaltochelatase subunit CobS N-terminal domain / Cobaltochelatase CobS subunit N terminal / : / : / ATPase, dynein-related, AAA domain ...Cobalt chelatase, CobT subunit / Cobalamin biosynthesis protein CobT VWA domain / Cobalamin biosynthesis protein CobT / Cobalamin biosynthesis protein CobT VWA domain / Cobaltochelatase subunit CobS / Cobaltochelatase subunit CobS N-terminal domain / Cobaltochelatase CobS subunit N terminal / : / : / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Cobaltochelatase subunit CobT / Cobaltochelatase subunit CobS
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 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
G: Cobaltochelatase subunit CobT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,39511
Polymers291,3347
Non-polymers1,0614
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.: 6
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
#2: Protein Cobaltochelatase subunit CobT


Mass: 70722.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Gene: BI318_03740 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AB36PXH5
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / 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: CobST-AMPPNP complex 5 / Type: COMPLEX / Entity ID: #1-#2 / 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
CTF correctionType: NONE
3D reconstructionResolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65726 / Symmetry type: POINT
RefinementHighest resolution: 3.54 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00417264
ELECTRON MICROSCOPYf_angle_d0.5523476
ELECTRON MICROSCOPYf_dihedral_angle_d5.4152365
ELECTRON MICROSCOPYf_chiral_restr0.0432661
ELECTRON MICROSCOPYf_plane_restr0.0043058

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