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- PDB-12bi: Moorella thermoacetica LarC (conformation 1) -

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Basic information

Entry
Database: PDB / ID: 12bi
TitleMoorella thermoacetica LarC (conformation 1)
ComponentsPyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
KeywordsMETAL BINDING PROTEIN / Enzyme / Nickel insertase / Cyclometalliase
Function / homologypyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel chelatase / Nickel insertion protein / Nickel insertion protein / nickel cation binding / protein maturation / lyase activity / Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
Function and homology information
Biological speciesMoorella thermoacetica (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsKim, K.H. / Wolfe, R.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM128959 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM140931 United States
CitationJournal: Sci Adv / Year: 2026
Title: Structural and Functional Analysis of LarC, a CTP-Dependent Cyclometallase Required for Nickel-Pincer Nucleotide Cofactor Biosynthesis
Authors: Wolfe, R. / Turmo, A. / Velasquez-Rivertte, S. / Sui, D. / Granados-Villanueva, D. / Desguin, B. / Hu, J. / Hausinger, R.P. / Kim, K.H.
History
DepositionMar 25, 2026Deposition site: RCSB / Processing site: RCSB
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
D: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
E: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
B: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
C: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
A: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
F: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein


Theoretical massNumber of molelcules
Total (without water)265,5346
Polymers265,5346
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein / P2TMN nickel insertion protein / Nickel-pincer cofactor biosynthesis protein LarC


Mass: 44255.699 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moorella thermoacetica (strain ATCC 39073 / JCM 9320) (bacteria)
Strain: ATCC 39073 / JCM 9320 / Gene: larC, Moth_2512 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2RFJ5, pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel chelatase
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: Homohexameric complex of LarC / Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Neomoorella thermoacetica (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)
Buffer solutionpH: 7.5
SpecimenConc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5572

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 535683
3D reconstructionResolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 82129 / Symmetry type: POINT
RefinementHighest resolution: 3.97 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00618219
ELECTRON MICROSCOPYf_angle_d0.84624768
ELECTRON MICROSCOPYf_dihedral_angle_d4.3922542
ELECTRON MICROSCOPYf_chiral_restr0.0442881
ELECTRON MICROSCOPYf_plane_restr0.0053227

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