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- PDB-11mp: E. coli SufE bound to SufBC2D -

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Basic information

Entry
Database: PDB / ID: 11mp
TitleE. coli SufE bound to SufBC2D
Components
  • Cysteine desulfuration protein SufE
  • Iron-sulfur cluster assembly protein SufB
  • Iron-sulfur cluster assembly protein SufD
  • Probable ATP-dependent transporter SufC
KeywordsMETAL BINDING PROTEIN / Fe-S / Suf pathway / persulfide / iron-sulfur / sulfur transfer
Function / homology
Function and homology information


metallo-sulfur cluster assembly / sulfurtransferase complex / sulfur compound metabolic process / sulfur carrier activity / iron-sulfur cluster assembly complex / iron-sulfur cluster assembly / response to radiation / 2 iron, 2 sulfur cluster binding / enzyme activator activity / 4 iron, 4 sulfur cluster binding ...metallo-sulfur cluster assembly / sulfurtransferase complex / sulfur compound metabolic process / sulfur carrier activity / iron-sulfur cluster assembly complex / iron-sulfur cluster assembly / response to radiation / 2 iron, 2 sulfur cluster binding / enzyme activator activity / 4 iron, 4 sulfur cluster binding / response to oxidative stress / ATP hydrolysis activity / ATP binding / cytosol
Similarity search - Function
SUF system FeS cluster assembly, SufB / SUF system FeS cluster assembly, SufBD, N-terminal / SufBD protein N-terminal region / Cysteine desulfuration protein SufE / SUF system FeS cluster assembly, SufD / SUF system FeS cluster assembly, SufBD / Fe-S metabolism associated domain, SufE-like / SUF system FeS cluster assembly, SufBD superfamily / : / SUF system FeS cluster assembly, SufBD core domain ...SUF system FeS cluster assembly, SufB / SUF system FeS cluster assembly, SufBD, N-terminal / SufBD protein N-terminal region / Cysteine desulfuration protein SufE / SUF system FeS cluster assembly, SufD / SUF system FeS cluster assembly, SufBD / Fe-S metabolism associated domain, SufE-like / SUF system FeS cluster assembly, SufBD superfamily / : / SUF system FeS cluster assembly, SufBD core domain / Fe-S metabolism associated 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
Cysteine desulfuration protein SufE / Probable ATP-dependent transporter SufC / Iron-sulfur cluster assembly protein SufB / Iron-sulfur cluster assembly protein SufD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.21 Å
AuthorsChhikara, N. / Dunkle, J.A. / Frantom, P.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM112919 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM142966 United States
Citation
Journal: bioRxiv / Year: 2026
Title: The structure of the SufBCD-SufE complex reveals the mechanism of sulfur transfer in bacterial Fe-S cluster assembly.
Authors: Nidhi Chhikara / Nadia Mireku / Jack A Dunkle / Patrick A Frantom /
Abstract: Iron-sulfur clusters are essential cofactors assembled in bacteria by the Suf pathway through a series of transient protein-protein interactions that transfer sulfur from L-cysteine to a scaffold ...Iron-sulfur clusters are essential cofactors assembled in bacteria by the Suf pathway through a series of transient protein-protein interactions that transfer sulfur from L-cysteine to a scaffold complex. While early steps in persulfide transfer are well characterized, the mechanism of sulfur delivery to the SufBCD scaffold has remained unresolved. Here, we report the first structure of the SufBCD-SufE complex, capturing the final step in persulfide transfer in the Suf pathway. The structure reveals coordinated conformational changes in both SufB and SufE that expose the otherwise buried C254 acceptor site and position the SufE C51 loop beneath the SufB-SufD axis. Biochemical analysis of SufB variants demonstrates that substitutions in the globally conserved 220s β-strand enhance SufE binding affinity and persulfide transfer rates, consistent with stabilization of a locally rearranged, transfer-competent conformation. Together, these results support a model in which conformational gating regulates persulfide transfer, providing a mechanism for controlling access to reactive sulfur intermediates.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 5, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Iron-sulfur cluster assembly protein SufB
E: Cysteine desulfuration protein SufE
A: Probable ATP-dependent transporter SufC
B: Probable ATP-dependent transporter SufC
D: Iron-sulfur cluster assembly protein SufD


Theoretical massNumber of molelcules
Total (without water)174,3255
Polymers174,3255
Non-polymers00
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 Iron-sulfur cluster assembly protein SufB


Mass: 56396.637 Da / Num. of mol.: 1 / Mutation: Y224A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sufB, ynhE, b1683, JW5273 / Production host: Escherichia coli (E. coli) / References: UniProt: P77522
#2: Protein Cysteine desulfuration protein SufE


Mass: 15817.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sufE, ynhA, b1679, JW1669 / Production host: Escherichia coli (E. coli) / References: UniProt: P76194
#3: Protein Probable ATP-dependent transporter SufC


Mass: 27613.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sufC, ynhD, b1682, JW1672 / Production host: Escherichia coli (E. coli) / References: UniProt: P77499
#4: Protein Iron-sulfur cluster assembly protein SufD


Mass: 46884.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: sufD, ynhC, b1681, JW1671 / Production host: Escherichia coli (E. coli) / References: UniProt: P77689
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: SufBC2D-SufE complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.174 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3341 nm / Nominal defocus min: 100 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.2particle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC4.63D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 76000 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 313.39 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002611661
ELECTRON MICROSCOPYf_angle_d0.576215776
ELECTRON MICROSCOPYf_chiral_restr0.04281756
ELECTRON MICROSCOPYf_plane_restr0.00342072
ELECTRON MICROSCOPYf_dihedral_angle_d4.41311577

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