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- PDB-12bj: Moorella thermoacetica LarC (conformation 2) -

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Basic information

Entry
Database: PDB / ID: 12bj
TitleMoorella thermoacetica LarC (conformation 2)
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: 3.85 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: Robert Wolfe / Aiko Turmo / Samantha Velasquez-Rivertte / Dexin Sui / Diego Granados-Villanueva / Benoit Desguin / Jian Hu / Robert P Hausinger / Kelly H Kim /
Abstract: Biosynthesis of the nickel-pincer mononucleotide metallocofactor requires a CTP-dependent nickel insertion reaction catalyzed by LarC, whose mechanism of C-Ni bond formation is not fully understood. ...Biosynthesis of the nickel-pincer mononucleotide metallocofactor requires a CTP-dependent nickel insertion reaction catalyzed by LarC, whose mechanism of C-Ni bond formation is not fully understood. Here, we report the first cryo-electron microscopy structures of full-length LarC from with and without a mimic of the CMPylated reaction intermediate. LarC assembles as a hexamer comprising a central LarC2 domain core and peripheral LarC1 domain trimers connected by long, flexible interdomain linkers. The LarC1 domains contain a conserved histidine-rich region for nickel binding and an adjacent conserved acidic pocket, both essential for activity. Structural modeling suggests that the intermediate binds within the acidic pocket adjacent to the putative nickel-binding site, while cryo-EM density for an intermediate analog identifies an interdomain cleft near the LarC2 CTP-binding site as a likely transfer site. Based on these findings, we propose that the intermediate is transferred through the interdomain cleft from LarC2, where it is CMPylated, to LarC1 for nickel insertion.
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
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
A: 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
F: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
D: 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&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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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: all / 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
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: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142648 / Symmetry type: POINT
RefinementHighest resolution: 3.85 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00318183
ELECTRON MICROSCOPYf_angle_d0.64724719
ELECTRON MICROSCOPYf_dihedral_angle_d3.4392537
ELECTRON MICROSCOPYf_chiral_restr0.0412877
ELECTRON MICROSCOPYf_plane_restr0.0053221

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