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Open data
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Basic information
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Title | Cytochrome c maturation complex CcmABCDE | |||||||||||||||
![]() | sharpened map | |||||||||||||||
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![]() | Cytochrome c maturation / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | ![]() 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 ...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 / metal ion binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.81 Å | |||||||||||||||
![]() | Ilcu L / Zhang L / Einsle O | |||||||||||||||
Funding support | European Union, ![]()
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 49.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.7 KB 20.7 KB | Display Display | ![]() |
Images | ![]() | 116.4 KB | ||
Others | ![]() ![]() ![]() | 47.2 MB 48.9 MB 48.9 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 852.7 KB | Display | ![]() |
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Full document | ![]() | 852.2 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8ce8MC ![]() 8ce1C ![]() 8ce5C ![]() 8ceaC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.87 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: unsharpened map
File | emd_16601_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
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Density Histograms |
-Half map: half map A
File | emd_16601_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
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Density Histograms |
-Half map: half map B
File | emd_16601_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Complex of cytochrome c maturation sysmtem I, Ccm(ABCD)2E
Entire | Name: Complex of cytochrome c maturation sysmtem I, Ccm(ABCD)2E |
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Components |
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-Supramolecule #1: Complex of cytochrome c maturation sysmtem I, Ccm(ABCD)2E
Supramolecule | Name: Complex of cytochrome c maturation sysmtem I, Ccm(ABCD)2E type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Cytochrome c biogenesis ATP-binding export protein CcmA
Macromolecule | Name: 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 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 24.411713 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: Heme exporter protein B
Macromolecule | Name: Heme exporter protein B / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 23.632676 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: Heme exporter protein C
Macromolecule | Name: Heme exporter protein C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 27.911264 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #4: Heme exporter protein D
Macromolecule | Name: Heme exporter protein D / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 7.753103 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTPAFASWNE FFAMGGYAFF VWLAVVMTVI PLVVLVVHSV MQHRAILRGV AQQRAREARL RAAQQQEAA UniProtKB: Heme exporter protein D |
-Macromolecule #5: Cytochrome c-type biogenesis protein CcmE
Macromolecule | Name: Cytochrome c-type biogenesis protein CcmE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 17.720303 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNIRRKNRLW IACAVLAGLA LTIGLVLYAL RSNIDLFYTP GEILYGKRET QQMPEVGQRL RVGGMVMPGS VQRDPNSLKV TFTIYDAEG SVDVSYEGIL PDLFREGQGV VVQGELEKGN HILAKEVLAK HDENYTPPEV EKAMEANHRR PASVYKDPAS UniProtKB: Cytochrome c-type biogenesis protein CcmE |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination 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
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 135175 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |