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- EMDB-16599: Cytochrome c maturation complex CcmABCD, E154Q, ATP-bound -

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Basic information

Entry
Database: EMDB / ID: EMD-16599
TitleCytochrome c maturation complex CcmABCD, E154Q, ATP-bound
Map datasharpened map
Sample
  • Complex: Complex of cytochrome c maturation sysmtem I, Ccm(AB)2CD
    • 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
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
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 assembly protein ...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: 3.62 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-
UpdateSep 6, 2023-
Current statusSep 6, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16599.png

Downloads & links

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Map

FileDownload / File: emd_16599.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Voxel sizeX=Y=Z: 0.878 Å
Density
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-1.0041591 - 1.5439371
Average (Standard dev.)0.0014692176 (±0.042900197)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 210.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map

Fileemd_16599_additional_1.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_16599_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 A

Fileemd_16599_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of cytochrome c maturation sysmtem I, Ccm(AB)2CD

EntireName: Complex of cytochrome c maturation sysmtem I, Ccm(AB)2CD
Components
  • Complex: Complex of cytochrome c maturation sysmtem I, Ccm(AB)2CD
    • 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
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Complex of cytochrome c maturation sysmtem I, Ccm(AB)2CD

SupramoleculeName: Complex of cytochrome c maturation sysmtem I, Ccm(AB)2CD
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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 K-12 (bacteria)
Molecular weightTheoretical: 24.410729 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (bacteria)
SequenceString: MASWSHPQFE KMGMLEAREL LCERDERTLF SGLSFTLNAG EWVQITGSNG AGKTTLLRLL TGLSRPDAGE VLWQGQPLHQ VRDSYHQNL LWIGHQPGIK TRLTALENLH FYHRDGDTAQ CLEALAQAGL AGFEDIPVNQ LSAGQQRRVA LARLWLTRAT L WILDQPFT ...String:
MASWSHPQFE KMGMLEAREL LCERDERTLF SGLSFTLNAG EWVQITGSNG AGKTTLLRLL TGLSRPDAGE VLWQGQPLHQ VRDSYHQNL LWIGHQPGIK TRLTALENLH FYHRDGDTAQ CLEALAQAGL AGFEDIPVNQ LSAGQQRRVA LARLWLTRAT L WILDQPFT 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 K-12 (bacteria)
Molecular weightTheoretical: 23.632676 KDa
Recombinant expressionOrganism: Escherichia coli K-12 (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: 1 / 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: 1 / 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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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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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
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 355914

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