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

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Basic information

Entry
Database: PDB / ID: 9h78
Title[FeS] cluster-loaded SMS complex from M. jannaschii
Components
  • Iron-sulfur cluster assembly SufBD family protein MJ0034
  • Uncharacterized ABC transporter ATP-binding protein MJ0035
KeywordsMETAL BINDING PROTEIN / Iron-sulfur cluster / biogenesis / SMS / Archaea
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 / Iron-sulfur cluster assembly SufBD family protein MJ0034 / Uncharacterized ABC transporter ATP-binding protein MJ0035
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsMartinez-Carranza, M. / Sauguet, L.
Funding support France, 3items
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: Dussouchaud, M. / Martinez-Carranza, M. / Garcia, P.S. / Clemancey, M. / Blondin, G. / Betton, J.M. / Haouz, A. / Gribaldo, S. / Ollagnier de Choudens, S. / Sauguet, L. / Mechaly, A. / Barras, F.
History
DepositionOct 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 4, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized ABC transporter ATP-binding protein MJ0035
B: Iron-sulfur cluster assembly SufBD family protein MJ0034
C: Uncharacterized ABC transporter ATP-binding protein MJ0035
D: Iron-sulfur cluster assembly SufBD family protein MJ0034
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,9275
Polymers128,5754
Non-polymers3521
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 Uncharacterized ABC transporter ATP-binding protein MJ0035 / SmsC


Mass: 28636.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0035 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q60350
#2: Protein Iron-sulfur cluster assembly SufBD family protein MJ0034


Mass: 35651.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0034 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q60349
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: [FeS] cluster-loaded SMS complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
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
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPU3image acquisition
7PHENIX1.2model fitting
13ISOLDE1.7model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 277904 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT

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