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- EMDB-76279: Moorella thermoacetica LarC (conformation 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-76279
TitleMoorella thermoacetica LarC (conformation 1)
Map data
Sample
  • Complex: Homohexameric complex of LarC
    • Protein or peptide: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
KeywordsEnzyme / Nickel insertase / Cyclometalliase / METAL BINDING PROTEIN
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 speciesNeomoorella thermoacetica (bacteria) / Moorella thermoacetica (strain ATCC 39073 / JCM 9320) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.97 Å
AuthorsKim KH / Wolfe R
Funding support United States, 2 items
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 RP / Kim KH
History
DepositionMar 25, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76279.png

Downloads & links

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Map

FileDownload / File: emd_76279.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 384 pix.
= 325.901 Å		0.85 Å/pix.
x 384 pix.
= 325.901 Å		0.85 Å/pix.
x 384 pix.
= 325.901 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8487 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.5529481 - 0.828835
Average (Standard dev.)0.00021513735 (±0.01787096)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 325.9008 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_76279_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_76279_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Homohexameric complex of LarC

EntireName: Homohexameric complex of LarC
Components
  • Complex: Homohexameric complex of LarC
    • Protein or peptide: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

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Supramolecule #1: Homohexameric complex of LarC

SupramoleculeName: Homohexameric complex of LarC / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Neomoorella thermoacetica (bacteria)

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Macromolecule #1: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel inser...

MacromoleculeName: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
EC number: pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel chelatase
Source (natural)Organism: Moorella thermoacetica (strain ATCC 39073 / JCM 9320) (bacteria)
Strain: ATCC 39073 / JCM 9320
Molecular weightTheoretical: 44.255699 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MHHHHHHSGT ENLYFQGHMK IAYFDCFSGI SGDMCLGALI ACGLSQDELT SGLKGLGLEG WELRVREVKQ HSIAATDVAV QVTGSQPHR HLADILGLIN NSSLPAPVKE KSAAVFKNLA RAEGQVHGID ASQVHFHEVG AVDAIIDIVG SILGLHLLGI E KVISSPLP ...String:
MHHHHHHSGT ENLYFQGHMK IAYFDCFSGI SGDMCLGALI ACGLSQDELT SGLKGLGLEG WELRVREVKQ HSIAATDVAV QVTGSQPHR HLADILGLIN NSSLPAPVKE KSAAVFKNLA RAEGQVHGID ASQVHFHEVG AVDAIIDIVG SILGLHLLGI E KVISSPLP AGSGWVDCRH GKLPVPAPAT LYLLQGYPVY GTEDKAELVT PTGAALITTL ADSFGPFPAM NLTRVGFGAG KT ELPHPNL LRLALGEINS GQLEGEESSL VIETTIDDMN PEFFPALLEE TMAAGAVDAF FTPVQMKKGR PGILFTALCP ENK LAAVAA AIFTHSSTLG LRFRRDQRLV CQRRMAEVVT PYGTVPVKLG LYRDPTGQVI TNIAPEYESC RQIAKSAGAP LKEV YAAAL AAARALKAF

UniProtKB: Pyridinium-3,5-bisthiocarboxylic acid mononucleotide nickel insertion protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 5572 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 535683
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.97 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 82129
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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