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- PDB-8ce8: Cytochrome c maturation complex CcmABCDE -

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Basic information

Entry
Database: PDB / ID: 8ce8
TitleCytochrome c maturation complex CcmABCDE
Components
  • Cytochrome c biogenesis ATP-binding export protein CcmA
  • Cytochrome c-type biogenesis protein CcmE
  • Heme exporter protein B
  • Heme exporter protein C
  • Heme exporter protein D
KeywordsMEMBRANE PROTEIN / Cytochrome c maturation
Function / homology
Function and homology information


cytochrome c biosynthetic process / heme import across plasma membrane / ABC-type heme transporter / heme transmembrane transporter activity / ABC-type heme transporter activity / cytochrome complex assembly / ATP-binding cassette (ABC) transporter complex / heme binding / ATP hydrolysis activity / ATP binding ...cytochrome c biosynthetic process / heme import across plasma membrane / ABC-type heme transporter / heme transmembrane transporter activity / ABC-type heme transporter activity / cytochrome complex assembly / ATP-binding cassette (ABC) transporter complex / heme binding / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
CcmE/CycJ protein / CcmE-like superfamily / CcmE / Cytochrome c-type biogenesis protein CcmB / Cytochrome c-type biogenesis protein CcmC / ABC transporter, haem export, CcmA / Haem exporter protein D (CcmD) / Cytochrome c-type biogenesis protein CcmB, bacteria / : / CcmB protein ...CcmE/CycJ protein / CcmE-like superfamily / CcmE / Cytochrome c-type biogenesis protein CcmB / Cytochrome c-type biogenesis protein CcmC / ABC transporter, haem export, CcmA / Haem exporter protein D (CcmD) / Cytochrome c-type biogenesis protein CcmB, bacteria / : / CcmB protein / Heme exporter protein D (CcmD) / Cytochrome C biogenesis export ATP-binding protein ccmA family profile. / Cytochrome c-type biogenesis protein CcsA/CcmC / Cytochrome c assembly protein / Cytochrome C assembly protein / 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 / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Heme exporter protein B / Heme exporter protein C / Heme exporter protein D / Cytochrome c biogenesis ATP-binding export protein CcmA / Cytochrome c-type biogenesis protein CcmE
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsIlcu, L. / Zhang, L. / Einsle, O.
Funding supportEuropean Union, Germany, 4items
OrganizationGrant numberCountry
European Research Council (ERC)310656European Union
German Research Foundation (DFG)403222702 Germany
German Research Foundation (DFG)192904750 Germany
German Research Foundation (DFG)46710898 Germany
CitationJournal: Nat Commun / Year: 2023
Title: Architecture of the Heme-translocating CcmABCD/E complex required for Cytochrome c maturation.
Authors: Lorena Ilcu / Lukas Denkhaus / Anton Brausemann / Lin Zhang / Oliver Einsle /
Abstract: Mono- and multiheme cytochromes c are post-translationally matured by the covalent attachment of heme. For this, Escherichia coli employs the most complex type of maturation machineries, the Ccm- ...Mono- and multiheme cytochromes c are post-translationally matured by the covalent attachment of heme. For this, Escherichia coli employs the most complex type of maturation machineries, the Ccm-system (for cytochrome c maturation). It consists of two membrane protein complexes, one of which shuttles heme across the membrane to a mobile chaperone that then delivers the cofactor to the second complex, an apoprotein:heme lyase, for covalent attachment. Here we report cryo-electron microscopic structures of the heme translocation complex CcmABCD from E. coli, alone and bound to the heme chaperone CcmE. CcmABCD forms a heterooctameric complex centered around the ABC transporter CcmAB that does not by itself transport heme. Our data suggest that the complex flops a heme group from the inner to the outer leaflet at its CcmBC interfaces, driven by ATP hydrolysis at CcmA. A conserved heme-handling motif (WxWD) at the periplasmic side of CcmC rotates the heme by 90° for covalent attachment to the heme chaperone CcmE that we find interacting exclusively with the CcmB subunit.
History
DepositionFeb 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: 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 ATP-binding export protein CcmA
B: Heme exporter protein B
C: Heme exporter protein C
D: Heme exporter protein D
a: Cytochrome c biogenesis ATP-binding export protein CcmA
b: Heme exporter protein B
c: Heme exporter protein C
d: Heme exporter protein D
E: Cytochrome c-type biogenesis protein CcmE


Theoretical massNumber of molelcules
Total (without water)185,1389
Polymers185,1389
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area26050 Å2
ΔGint-199 kcal/mol
Surface area66680 Å2

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Components

#1: Protein Cytochrome c biogenesis ATP-binding export protein CcmA / Heme exporter protein A


Mass: 24411.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ccmA, yejW, b2201, JW5366 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P33931, ABC-type heme transporter
#2: Protein Heme exporter protein B / Cytochrome c-type biogenesis protein CcmB


Mass: 23632.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ccmB, yejV, b2200, JW2188 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ABL8
#3: Protein Heme exporter protein C / Cytochrome c-type biogenesis protein CcmC


Mass: 27911.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ccmC, yejT, yejU, b2199, JW2187 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ABM1
#4: Protein Heme exporter protein D / Cytochrome c-type biogenesis protein CcmD


Mass: 7753.103 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ccmD, yojM, b2198, JW2186 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ABM5
#5: Protein Cytochrome c-type biogenesis protein CcmE / Cytochrome c maturation protein E / Heme chaperone CcmE


Mass: 17720.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ccmE, yejS, b2197, JW2185 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P69490

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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: Complex of cytochrome c maturation sysmtem I, Ccm(ABCD)2E
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli K-12 (bacteria)
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

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 135175 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00612989
ELECTRON MICROSCOPYf_angle_d1.18617711
ELECTRON MICROSCOPYf_dihedral_angle_d6.2221748
ELECTRON MICROSCOPYf_chiral_restr0.0572059
ELECTRON MICROSCOPYf_plane_restr0.012203

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