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- EMDB-80405: Bacteroides thetaiotaomicron CcsBA mutant W703C -

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Basic information

Entry
Database: EMDB / ID: EMD-80405
TitleBacteroides thetaiotaomicron CcsBA mutant W703C
Map dataunsharpened
Sample
  • Complex: System II Heme Lyase CcsBA
    • Protein or peptide: Cytochrome c biogenesis protein (CcsA)
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: PHOSPHATIDYLETHANOLAMINE
Keywordscytochrome c maturation / heme lyase / MEMBRANE PROTEIN
Function / homologyResB-like domain / ResB-like family / Cytochrome c-type biogenesis protein CcsA/CcmC / Cytochrome c assembly protein / Cytochrome C assembly protein / cytochrome complex assembly / heme binding / plasma membrane / Cytochrome c biogenesis protein (CcsA)
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsSeifermann J / Ilcu L / Moog C / Zhang L / Einsle O
Funding support Germany, European Union, 5 items
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, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_80405.png

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Map

FileDownload / File: emd_80405.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.76 Å/pix.
x 200 pix.
= 152.54 Å		0.76 Å/pix.
x 200 pix.
= 152.54 Å		0.76 Å/pix.
x 200 pix.
= 152.54 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7627 Å
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Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.22140594 - 0.43157554
Average (Standard dev.)0.0027264964 (±0.019950276)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 152.54001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_80405_msk_1.map
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Additional map: sharpened

Fileemd_80405_additional_1.map
Annotationsharpened
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Half map: half map B

Fileemd_80405_half_map_1.map
Annotationhalf map B
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Half map: half map A

Fileemd_80405_half_map_2.map
Annotationhalf map A
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Sample components

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Entire : System II Heme Lyase CcsBA

EntireName: System II Heme Lyase CcsBA
Components
  • Complex: System II Heme Lyase CcsBA
    • Protein or peptide: Cytochrome c biogenesis protein (CcsA)
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: PHOSPHATIDYLETHANOLAMINE

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Supramolecule #1: System II Heme Lyase CcsBA

SupramoleculeName: System II Heme Lyase CcsBA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)

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Macromolecule #1: Cytochrome c biogenesis protein (CcsA)

MacromoleculeName: Cytochrome c biogenesis protein (CcsA) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Molecular weightTheoretical: 93.829352 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKLIRLIASP ILMYVLAGVY ALVLAIATFV ENSSGPAVAR EYFYYAPWFI LLQLLQAVNL LAMFLQGGYF KRISKGSLIF HGALVFIWL GAAVTHYAGV TGIMHIREGE TVDRMMRDEG AGMGNASLPF SVTLDDFRLK RYPGSHSPMS YESDLVIKKE N EAPLQATV ...String:
MKLIRLIASP ILMYVLAGVY ALVLAIATFV ENSSGPAVAR EYFYYAPWFI LLQLLQAVNL LAMFLQGGYF KRISKGSLIF HGALVFIWL GAAVTHYAGV TGIMHIREGE TVDRMMRDEG AGMGNASLPF SVTLDDFRLK RYPGSHSPMS YESDLVIKKE N EAPLQATV RMNKVIEVDG YRLFQSSFDP DEQGTVLSVS YDRPGMQITY IGYFLLFAGF VLTLFSKKSR FGRLRRELGE MK KNAPFCL LLFLGLSGAL GTQASYAQET LSSSQLPCIP APHARKFGSL VLLNPNGRLE PVNSYTSAIL RKLYGADKLN SIN SDQFFL NLLAFPDEWG GYPFIKVDNK DILQRFGRDG KYIAWQDVFD ADGNYVLTDE VNAIYAKSAS ERKRMDSDLL KLDE SVNIV YRIMQHQLLP LFPDENDVQG KWYSAGDEQT VFHDKDSLFV SKIMDWYIYE LGNGVRTNNW KEADKIVDMM HIFQQ AKSK TPAIDNQRVK AELLYNQLNL FFWCRLAYLI LGGILLFIAC GEIIADFKWG SRLSSILIVL LIAAFLAHTT GVLLRW YIS ERAPWANAYE SMICTSWLLV GGGLLFARRF RILPALAGLL GGIMLFVAGL NHLNPEITPL VPVLQSYWLM SHVAIIM IG YVFFALCALT GLFNLILMNL LSATNRVKLL FRIREFTLLN EMAMILGLFF MTAGTFLGAI CANVSWGRYW GWDPKETW A LISIVVYALV LHIRFIPLLK GKTTWCYNLL SVVSILSIIM TWFGVNYYLS GLHSYGKTEG GDLLLWIWGA GLCVVLALA LFARRRLKKY SEFENLYFQS WSHPQFEK

UniProtKB: Cytochrome c biogenesis protein (CcsA)

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Macromolecule #2: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 2 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #3: PHOSPHATIDYLETHANOLAMINE

MacromoleculeName: PHOSPHATIDYLETHANOLAMINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: PTY
Molecular weightTheoretical: 734.039 Da
Chemical component information

ChemComp-PTY:
PHOSPHATIDYLETHANOLAMINE / phospholipid*YM

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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: 7.5
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: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 143981
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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