[English] 日本語
Yorodumi
- EMDB-76281: Moorella thermoacetica LarC (conformation 3) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-76281
TitleMoorella thermoacetica LarC (conformation 3)
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: 3.87 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: 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, 2026-
Header (metadata) releaseJul 29, 2026-
Map releaseJul 29, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_76281.png

Downloads & links

-
Map

FileDownload / File: emd_76281.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: 0.15
Minimum - Maximum-0.5923043 - 0.88993865
Average (Standard dev.)0.00021044308 (±0.01852678)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #2

Fileemd_76281_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_76281_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
Supramolecule #1: Homohexameric complex of LarC

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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

+
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: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 93068
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more