[English] 日本語
Yorodumi
- PDB-9h7y: SmsC2B2 complex from M. jannaschii (orthorhombic form) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9h7y
TitleSmsC2B2 complex from M. jannaschii (orthorhombic 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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 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: 3.198 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
DepositionOct 28, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,2424
Polymers63,7122
Non-polymers5312
Water30617
1
A: Uncharacterized ABC transporter ATP-binding protein MJ0035
B: Iron-sulfur cluster assembly SufBD family protein MJ0034
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)128,4858
Polymers127,4244
Non-polymers1,0614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area9540 Å2
ΔGint-37 kcal/mol
Surface area41230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.167, 125.038, 133.056
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Uncharacterized ABC transporter ATP-binding protein MJ0035 / SmsC


Mass: 28636.264 Da / Num. of mol.: 1
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 / SmsB


Mass: 35075.723 Da / Num. of mol.: 1
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 5% PEG3350, 10% tacsimate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 1.27819 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 31, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27819 Å / Relative weight: 1
ReflectionResolution: 3.198→70.39 Å / Num. obs: 8240 / % possible obs: 90.6 % / Redundancy: 18.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.307 / Rpim(I) all: 0.075 / Rrim(I) all: 0.317 / Net I/σ(I): 7.4
Reflection shellResolution: 3.198→3.532 Å / Redundancy: 16.4 % / Rmerge(I) obs: 4.205 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 412 / CC1/2: 0.45 / Rpim(I) all: 1.075 / Rrim(I) all: 4.344 / % possible all: 57.8

-
Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.198→70.39 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.74
RfactorNum. reflection% reflectionSelection details
Rfree0.2904 428 -RANDOM
Rwork0.272 ---
obs0.273 8240 68.2 %-
Displacement parametersBiso mean: 150.03 Å2
Baniso -1Baniso -2Baniso -3
1-40.8205 Å20 Å20 Å2
2---21.8322 Å20 Å2
3----18.9883 Å2
Refine analyzeLuzzati coordinate error obs: 0.58 Å
Refinement stepCycle: LAST / Resolution: 3.198→70.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 32 17 4201
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0064253HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.935712HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1606SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes715HARMONIC5
X-RAY DIFFRACTIONt_it4253HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion582SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3104SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.4
X-RAY DIFFRACTIONt_other_torsion19.87
LS refinement shellResolution: 3.2→3.52 Å
RfactorNum. reflection% reflection
Rfree0.3243 17 -
Rwork0.3135 --
obs0.314 393 13.04 %
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)
18.69133.35770.23747.15932.439212.6789-1.06280.15211.25750.15210.21880.89091.25750.89090.84410.6411-0.18540.3577-0.94340.0881-0.3509-13.1257-60.7732-23.4474
24.95472.15962.21266.0964-1.21073.65610.56531.4684-0.38781.4684-0.67460.0303-0.38780.03030.10930.9116-0.4033-0.1374-0.4316-0.1181-0.39017.8189-24.925-15.1876
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

+
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