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- PDB-9hbl: SmsC2B2 complex from M. jannaschii (monoclinic form) -

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Basic information

Entry
Database: PDB / ID: 9hbl
TitleSmsC2B2 complex from M. jannaschii (monoclinic form)
Components
  • Iron-sulfur cluster assembly SufBD family protein MJ0034
  • Uncharacterized ABC transporter ATP-binding protein MJ0035
KeywordsMETAL TRANSPORT / Iron-sulfur cluster / biogenesis / SMS / Archaea
Function / homology
Function and homology information


iron-sulfur cluster assembly complex / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.191 Å
AuthorsMechaly, A.E. / Dussouchaud, M. / Haouz, A. / Betton, J.M. / Barras, F.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) 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
DepositionNov 7, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)129,54618
Polymers128,5754
Non-polymers97114
Water7,909439
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.291, 132.733, 75.34
Angle α, β, γ (deg.)90, 111.66, 90
Int Tables number4
Space group name H-MP1211

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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 (E. coli) / 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 (E. coli) / References: UniProt: Q60349
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.1M Ammonium sulfate 0.3M Sodium formate 0.1M Sodium acetate 3% w/v PGA (Na+ form, LM) 3% w/v PEG20000 pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.191→61.931 Å / Num. obs: 42393 / % possible obs: 93.8 % / Redundancy: 7.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.044 / Rrim(I) all: 0.121 / Net I/σ(I): 8.9
Reflection shellResolution: 2.191→2.46 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2120 / CC1/2: 0.77 / Rpim(I) all: 0.35 / Rrim(I) all: 0.928 / % possible all: 70.7

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.191→42.3 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU R Cruickshank DPI: 0.601 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.603 / SU Rfree Blow DPI: 0.296 / SU Rfree Cruickshank DPI: 0.301
RfactorNum. reflection% reflectionSelection details
Rfree0.2546 2104 -RANDOM
Rwork0.2082 ---
obs0.2105 42388 60.1 %-
Displacement parametersBiso mean: 63.15 Å2
Baniso -1Baniso -2Baniso -3
1--5.0214 Å20 Å25.2215 Å2
2--5.058 Å20 Å2
3----0.0366 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.191→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8304 0 59 439 8802
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0078481HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9911354HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3191SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1416HARMONIC5
X-RAY DIFFRACTIONt_it8481HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1155SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6718SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.71
X-RAY DIFFRACTIONt_other_torsion18.62
LS refinement shellResolution: 2.191→2.35 Å
RfactorNum. reflection% reflection
Rfree0.2779 27 -
Rwork0.2648 --
obs--6.19 %
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.24520.6058-0.74910.8939-1.30471.72690.08790.3439-0.20150.34390.3777-0.243-0.2015-0.243-0.4656-0.17460.08930.0208-0.03370.11990.0043-42.261742.5071-11.6082
21.3635-0.2694-0.383800.26120.83970.1047-0.0102-0.0045-0.01020.08270.118-0.00450.118-0.1874-0.1973-0.1050.02380.0004-0.04440.1952-1.026650.4018-14.5349
30.6786-0.5091-0.78281.5944-0.64972.111-0.12990.1909-0.25530.19090.2785-0.0602-0.2553-0.0602-0.14870.03210.11910.1051-0.05070.1118-0.1325-27.759322.66439.8628
41.14950.3613-0.73510-0.11320.9585-0.39590.00230.33010.00230.1153-0.03530.3301-0.03530.28060.0999-0.0540.14590.0399-0.1267-0.1037-9.917414.424-27.6232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-2 - 239
2X-RAY DIFFRACTION2{ B|* }B28 - 316
3X-RAY DIFFRACTION3{ C|* }C-2 - 239
4X-RAY DIFFRACTION4{ D|* }D28 - 316

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