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- EMDB-16597: Cytochrome c maturation complex CcmABCD -

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Basic information

Entry
Database: EMDB / ID: EMD-16597
TitleCytochrome c maturation complex CcmABCD
Map datasharpened map
Sample
  • Complex: Heterooctameric complex of cytochrome c maturation sysmtem I, Ccm(ABCD)2
    • Protein or peptide: Cytochrome c biogenesis ATP-binding export protein CcmA
    • Protein or peptide: Heme exporter protein B
    • Protein or peptide: Heme exporter protein C
    • Protein or peptide: Heme exporter protein D
KeywordsCytochrome c maturation / MEMBRANE PROTEIN
Function / homology
Function and homology information


cytochrome c biosynthetic process / heme import across plasma membrane / ABC-type heme transporter / ABC-type heme transporter activity / heme transmembrane transporter activity / cytochrome complex assembly / ATP-binding cassette (ABC) transporter complex / heme binding / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
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-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 / 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
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Escherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.47 Å
AuthorsIlcu L / Zhang L / Einsle O
Funding supportEuropean Union, Germany, 4 items
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, 2023-
Header (metadata) releaseSep 6, 2023-
Map releaseSep 6, 2023-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16597.png

Downloads & links

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Map

FileDownload / File: emd_16597.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 240 pix.
= 208.8 Å		0.87 Å/pix.
x 240 pix.
= 208.8 Å		0.87 Å/pix.
x 240 pix.
= 208.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.7762923 - 2.869568
Average (Standard dev.)0.008552652 (±0.110426374)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 208.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_16597_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_16597_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_16597_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Heterooctameric complex of cytochrome c maturation sysmtem I, Ccm...

EntireName: Heterooctameric complex of cytochrome c maturation sysmtem I, Ccm(ABCD)2
Components
  • Complex: Heterooctameric complex of cytochrome c maturation sysmtem I, Ccm(ABCD)2
    • Protein or peptide: Cytochrome c biogenesis ATP-binding export protein CcmA
    • Protein or peptide: Heme exporter protein B
    • Protein or peptide: Heme exporter protein C
    • Protein or peptide: Heme exporter protein D

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Supramolecule #1: Heterooctameric complex of cytochrome c maturation sysmtem I, Ccm...

SupramoleculeName: Heterooctameric complex of cytochrome c maturation sysmtem I, Ccm(ABCD)2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Cytochrome c biogenesis ATP-binding export protein CcmA

MacromoleculeName: Cytochrome c biogenesis ATP-binding export protein CcmA
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: ABC-type heme transporter
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 24.411713 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASWSHPQFE KMGMLEAREL LCERDERTLF SGLSFTLNAG EWVQITGSNG AGKTTLLRLL TGLSRPDAGE VLWQGQPLHQ VRDSYHQNL LWIGHQPGIK TRLTALENLH FYHRDGDTAQ CLEALAQAGL AGFEDIPVNQ LSAGQQRRVA LARLWLTRAT L WILDEPFT ...String:
MASWSHPQFE KMGMLEAREL LCERDERTLF SGLSFTLNAG EWVQITGSNG AGKTTLLRLL TGLSRPDAGE VLWQGQPLHQ VRDSYHQNL LWIGHQPGIK TRLTALENLH FYHRDGDTAQ CLEALAQAGL AGFEDIPVNQ LSAGQQRRVA LARLWLTRAT L WILDEPFT AIDVNGVDRL TQRMAQHTEQ GGIVILTTHQ PLNVAESKIR RISLTQTRAA

UniProtKB: Cytochrome c biogenesis ATP-binding export protein CcmA

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Macromolecule #2: Heme exporter protein B

MacromoleculeName: Heme exporter protein B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 23.632676 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MMFWRIFRLE LRVAFRHSAE IANPLWFFLI VITLFPLSIG PEPQLLARIA PGIIWVAALL SSLLALERLF RDDLQDGSLE QLMLLPLPL PAVVLAKVMA HWMVTGLPLL ILSPLVAMLL GMDVYGWQVM ALTLLLGTPT LGFLGAPGVA LTVGLKRGGV L LSILVLPL ...String:
MMFWRIFRLE LRVAFRHSAE IANPLWFFLI VITLFPLSIG PEPQLLARIA PGIIWVAALL SSLLALERLF RDDLQDGSLE QLMLLPLPL PAVVLAKVMA HWMVTGLPLL ILSPLVAMLL GMDVYGWQVM ALTLLLGTPT LGFLGAPGVA LTVGLKRGGV L LSILVLPL TIPLLIFATA AMDAASMHLP VDGYLAILGA LLAGTATLSP FATAAALRIS IQ

UniProtKB: Heme exporter protein B

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Macromolecule #3: Heme exporter protein C

MacromoleculeName: Heme exporter protein C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 27.911264 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MWKTLHQLAI PPRLYQICGW FIPWLAIASV VVLTVGWIWG FGFAPADYQQ GNSYRIIYLH VPAAIWSMGI YASMAVAAFI GLVWQMKMA NLAVAAMAPI GAVFTFIALV TGSAWGKPMW GTWWVWDARL TSELVLLFLY VGVIALWHAF DDRRLAGRAA G ILVLIGVV ...String:
MWKTLHQLAI PPRLYQICGW FIPWLAIASV VVLTVGWIWG FGFAPADYQQ GNSYRIIYLH VPAAIWSMGI YASMAVAAFI GLVWQMKMA NLAVAAMAPI GAVFTFIALV TGSAWGKPMW GTWWVWDARL TSELVLLFLY VGVIALWHAF DDRRLAGRAA G ILVLIGVV NLPIIHYSVE WWNTLHQGST RMQQSIDPAM RSPLRWSIFG FLLLSATLTL MRMRNLILLM EKRRPWVSEL IL KRGRK

UniProtKB: Heme exporter protein C

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Macromolecule #4: Heme exporter protein D

MacromoleculeName: Heme exporter protein D / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Molecular weightTheoretical: 7.753103 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString:
MTPAFASWNE FFAMGGYAFF VWLAVVMTVI PLVVLVVHSV MQHRAILRGV AQQRAREARL RAAQQQEAA

UniProtKB: Heme exporter protein D

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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 GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 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

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.47 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 323473
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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