[English] 日本語
Yorodumi
- EMDB-51913: [FeS] cluster-loaded SMS complex from M. jannaschii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-51913
Title[FeS] cluster-loaded SMS complex from M. jannaschii
Map data
Sample
  • Complex: [FeS] cluster-loaded SMS complex
    • Protein or peptide: Uncharacterized ABC transporter ATP-binding protein MJ0035
    • Protein or peptide: Iron-sulfur cluster assembly SufBD family protein MJ0034
  • Ligand: IRON/SULFUR CLUSTER
KeywordsIron-sulfur cluster / biogenesis / SMS / Archaea / METAL BINDING PROTEIN
Function / homology
Function and homology information


iron-sulfur cluster assembly / ATP hydrolysis activity / ATP binding
Similarity search - Function
SUF system FeS cluster assembly, SufBD / SUF system FeS cluster assembly, SufBD superfamily / : / SUF system FeS cluster assembly, SufBD core domain / FeS cluster assembly SUF system, ATPase SufC / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...SUF system FeS cluster assembly, SufBD / SUF system FeS cluster assembly, SufBD superfamily / : / SUF system FeS cluster assembly, SufBD core domain / FeS cluster assembly SUF system, ATPase SufC / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Iron-sulfur cluster assembly SufBD family protein MJ0034 / Uncharacterized ABC transporter ATP-binding protein MJ0035
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsMartinez-Carranza M / Sauguet L
Funding support France, 3 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-22-CE44-0043-First-FeS France
Agence Nationale de la Recherche (ANR)ANR-11-LABX-0003-01 France
Agence Nationale de la Recherche (ANR)ANR-10-LABX-62-IBEID France
CitationJournal: PLoS Biol / Year: 2025
Title: Ancestral [Fe-S] biogenesis system SMS has a unique mechanism of cluster assembly and sulfur utilization.
Authors: Macha Dussouchaud / Markel Martinez-Carranza / Pierre-Simon Garcia / Martin Clémancey / Geneviève Blondin / Jean Michel Betton / Ahmed Haouz / Simonetta Gribaldo / Sandrine Ollagnier de ...Authors: Macha Dussouchaud / Markel Martinez-Carranza / Pierre-Simon Garcia / Martin Clémancey / Geneviève Blondin / Jean Michel Betton / Ahmed Haouz / Simonetta Gribaldo / Sandrine Ollagnier de Choudens / Ludovic Sauguet / Ariel Mechaly / Frédéric Barras /
Abstract: [Fe-S] clusters are ancient and ubiquitous protein co-factors, which contributed to the emergence of life in an anoxic planet. We have recently identified two minimal [Fe-S] biogenesis systems, MIS ...[Fe-S] clusters are ancient and ubiquitous protein co-factors, which contributed to the emergence of life in an anoxic planet. We have recently identified two minimal [Fe-S] biogenesis systems, MIS and SMS, inferred to be ancestral systems dating back to the Last Universal Common Ancestor and which gave rise to the well-studied modern Iron-Sulfur Cluster (ISC), Nitrogen Fixation (NIF), and Sulfur Mobilization (SUF) machineries. The present study focuses on the ancestor SMS from the hyperthermophilic archaeon Methanocaldococcus jannaschii. Biochemical and structural studies showed that SMS is made of a SmsC2B2 heterotetratmer wherein the SmsC subunit hosts both ATP and [Fe-S] cluster binding sites. Binding of ATP and assembly of [Fe-S] were found to be mutually exclusive allowing for a regulatory coupling between binding of both substrates. Mutagenesis and in vitro transfer experiments revealed the key role of SmsC-contained Cys residues in cluster assembly. Strikingly, the SMS system rescued a non-viable Escherichia coli strain lacking endogenous ISC and SUF systems grown under anoxic conditions, in the presence of Na2S, indicating that sulfide is a source of sulfur for SMS. In addition, we predict that most archaea SmsC proteins hold a similar C-terminal [Fe-S] cluster assembly site. Taking into account those unique structural and functional features, we propose a mechanistic model describing how SmsC2B2 assembles and distributes [4Fe-4S] clusters. Altogether this study established SMS as a new bona fide [Fe-S] biogenesis system that operated in anaerobic prokaryotes prior to evolve to SUF after the Great Oxydation Event.
History
DepositionOct 27, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_51913.png

Downloads & links

-
Map

FileDownload / File: emd_51913.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.6 Å/pix.
x 400 pix.
= 240. Å		0.6 Å/pix.
x 400 pix.
= 240. Å		0.6 Å/pix.
x 400 pix.
= 240. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.002
Minimum - Maximum-0.006985298 - 0.012075916
Average (Standard dev.)0.0000070410547 (±0.0002063051)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 240.00002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_51913_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_51913_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_51913_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : [FeS] cluster-loaded SMS complex

EntireName: [FeS] cluster-loaded SMS complex
Components
  • Complex: [FeS] cluster-loaded SMS complex
    • Protein or peptide: Uncharacterized ABC transporter ATP-binding protein MJ0035
    • Protein or peptide: Iron-sulfur cluster assembly SufBD family protein MJ0034
  • Ligand: IRON/SULFUR CLUSTER

-
Supramolecule #1: [FeS] cluster-loaded SMS complex

SupramoleculeName: [FeS] cluster-loaded SMS complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)

-
Macromolecule #1: Uncharacterized ABC transporter ATP-binding protein MJ0035

MacromoleculeName: Uncharacterized ABC transporter ATP-binding protein MJ0035
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Molecular weightTheoretical: 28.636264 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GEFMVSIMLL KVEDLHVYRG NREILKGVNL TVEENEIHAI IGPNGAGKST LAYTIMGISG YKPTKGRIIF KGVDIIDKNI TERARMGMT LAWQEPARFE GIKVKNYLML GMNEKYKKDK EIAEEKIREA LKLVNLDPDK YLDRYVDETL SGGERKRIEL A SIICMEPD ...String:
GEFMVSIMLL KVEDLHVYRG NREILKGVNL TVEENEIHAI IGPNGAGKST LAYTIMGISG YKPTKGRIIF KGVDIIDKNI TERARMGMT LAWQEPARFE GIKVKNYLML GMNEKYKKDK EIAEEKIREA LKLVNLDPDK YLDRYVDETL SGGERKRIEL A SIICMEPD LAILDEPDSG IDIVSFDEIK RVFDYLKDKG CSLLVITHRE ELAEHADRVS LICAGEVIKS GDPKEVGEFY KK ECGKCYK KVPDGK

UniProtKB: Uncharacterized ABC transporter ATP-binding protein MJ0035

-
Macromolecule #2: Iron-sulfur cluster assembly SufBD family protein MJ0034

MacromoleculeName: Iron-sulfur cluster assembly SufBD family protein MJ0034
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Molecular weightTheoretical: 35.651328 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GEFELMSIKE ELMEIIEAIK YTSEKPEEIV HGKGPRIIVK ESRIIDVQGD EGIILEGKEE DGKIKAKIIV KKGYKFKYPI HMCFGITEE NISQIIDVEI ILEEDSSISL MSHCSFPKGK GIKHIMNGII KIGKNAKFSY NEFHYHGMDG DILVKPTVKV E IDEGGIYI ...String:
GEFELMSIKE ELMEIIEAIK YTSEKPEEIV HGKGPRIIVK ESRIIDVQGD EGIILEGKEE DGKIKAKIIV KKGYKFKYPI HMCFGITEE NISQIIDVEI ILEEDSSISL MSHCSFPKGK GIKHIMNGII KIGKNAKFSY NEFHYHGMDG DILVKPTVKV E IDEGGIYI SNFTLTKGRI GTLDIEQEII AKKDAIIDIT TRTYAIKEDV VKVNEVVKLN GENAKCIIKS RGAAMDNSKI SL KLKIEGN APYSKGHIDC AEIVKGNAEV ESIPIVVVRD DKARITHEAA IGSVDKKQLE TLMAKGLDED EATEIIVKGM IGD L

UniProtKB: Iron-sulfur cluster assembly SufBD family protein MJ0034

-
Macromolecule #3: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 3 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.8
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 277904
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-9h78:
[FeS] cluster-loaded SMS complex from M. jannaschii

+
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