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- PDB-25vk: Bacteroides thetaiotaomicron CcsBA mutant W703C -

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Basic information

Entry
Database: PDB / ID: 25vk
TitleBacteroides thetaiotaomicron CcsBA mutant W703C
ComponentsCytochrome c biogenesis protein (CcsA)
KeywordsMEMBRANE PROTEIN / cytochrome c maturation / heme lyase
Function / homology
Function and homology information


cytochrome complex assembly / heme binding / plasma membrane
Similarity search - Function
ResB-like domain / ResB-like family / Cytochrome c-type biogenesis protein CcsA/CcmC / Cytochrome c assembly protein / Cytochrome C assembly protein
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATIDYLETHANOLAMINE / Cytochrome c biogenesis protein (CcsA)
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsSeifermann, J. / Ilcu, L. / Moog, C. / Zhang, L. / Einsle, O.
Funding support Germany, European Union, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)403222702 Germany
German Research Foundation (DFG)536145634 Germany
European Research Council (ERC)101141673European Union
German Research Foundation (DFG)INST 35/1597-1 FUGG Germany
German Research Foundation (DFG)506518771 Germany
CitationJournal: J Biol Inorg Chem / Year: 2026
Title: Heme handling in the system II heme lyase CcsBA from Bacteroides thetaiotaomicron.
Authors: Julia Seifermann / Lorena Ilcu / Céline Moog / Lin Zhang / Oliver Einsle /
Abstract: Cytochrome c biogenesis in bacteria relies on complex membrane-bound machineries that facilitate the covalent attachment of heme to apocytochrome c. System II, mediated by the bifunctional protein ...Cytochrome c biogenesis in bacteria relies on complex membrane-bound machineries that facilitate the covalent attachment of heme to apocytochrome c. System II, mediated by the bifunctional protein CcsBA, is prevalent in Gram-positive and some Gram-negative bacteria, as well as chloroplasts. Here, we report a 2.9 Å resolution cryo-EM structure of a W703C mutant of CcsBA from Bacteroides thetaiotaomicron, revealing its conformation in the heme-loaded, closed state. Comparative analysis with the previously published Helicobacter hepaticus CcsBA structure shows a conserved membrane architecture and WxWD domain organization, but notable differences in the arrangement of the periplasmic domain and the active site configuration. The W703C mutation allowed heme occupancy in the active site without inducing the open conformation, implicating the native W703 in regulating structural transitions critical for heme attachment. Our findings suggest that while the open conformation facilitates heme ligation, it is not essential for heme translocation. This work expands the understanding of structure-function relationships in System II cytochrome c maturation and highlights the potential regulatory role of the periplasmic domain conformational dynamics.
History
DepositionApr 19, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome c biogenesis protein (CcsA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7964
Polymers93,8291
Non-polymers1,9673
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 Cytochrome c biogenesis protein (CcsA)


Mass: 93829.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_4430 / Production host: Escherichia coli (E. coli) / References: UniProt: Q89ZE7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PTY / PHOSPHATIDYLETHANOLAMINE


Mass: 734.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H80NO8P / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationY

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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: System II Heme Lyase CcsBA / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
2PHENIX2.0_5885model refinement
13cryoSPARC4.73D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143981 / Symmetry type: POINT
RefinementHighest resolution: 2.91 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036596
ELECTRON MICROSCOPYf_angle_d0.5848959
ELECTRON MICROSCOPYf_dihedral_angle_d9.15919
ELECTRON MICROSCOPYf_chiral_restr0.038973
ELECTRON MICROSCOPYf_plane_restr0.0041099

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