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- EMDB-51913: [FeS] cluster-loaded SMS complex from M. jannaschii -

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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: To Be Published
Title: The ancestral iron-sulfur biogenesis SMS system of Methanocaldococcus jannaschii: a link between geochemistry and microbiology
Authors: Dussouchaud M / Martinez-Carranza M / Garcia PS / Clemancey M / Blondin G / Betton JM / Haouz A / Ollagnier de Choudens S / Sauguet L / Mechaly A / Barras F
History
DepositionOct 27, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51913.png

Downloads & links

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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 °

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Supplemental data

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Mask #1

Fileemd_51913_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51913_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51913_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 : [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

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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)

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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

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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

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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

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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

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

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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

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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)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

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

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