+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16602 | |||||||||||||||
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Title | Cytochrome c maturation complex CcmABCD, E154Q | |||||||||||||||
Map data | sharpened map | |||||||||||||||
Sample |
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Keywords | Cytochrome 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 | |||||||||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli K-12 (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.94 Å | |||||||||||||||
Authors | Ilcu L / Zhang L / Einsle O | |||||||||||||||
Funding support | European Union, Germany, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16602.map.gz | 49.4 MB | EMDB map data format | |
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Header (meta data) | emd-16602-v30.xml emd-16602.xml | 19.5 KB 19.5 KB | Display Display | EMDB header |
Images | emd_16602.png | 115.6 KB | ||
Others | emd_16602_additional_1.map.gz emd_16602_half_map_1.map.gz emd_16602_half_map_2.map.gz | 41.4 MB 49 MB 49 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16602 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16602 | HTTPS FTP |
-Validation report
Summary document | emd_16602_validation.pdf.gz | 921.3 KB | Display | EMDB validaton report |
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Full document | emd_16602_full_validation.pdf.gz | 920.9 KB | Display | |
Data in XML | emd_16602_validation.xml.gz | 11.8 KB | Display | |
Data in CIF | emd_16602_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16602 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16602 | HTTPS FTP |
-Related structure data
Related structure data | 8ceaMC 8ce1C 8ce5C 8ce8C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16602.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 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_16602_additional_1.map | ||||||||||||
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Annotation | unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_16602_half_map_1.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_16602_half_map_2.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of cytochrome c maturation system I, Ccm(AB)2CD
Entire | Name: Complex of cytochrome c maturation system I, Ccm(AB)2CD |
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Components |
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-Supramolecule #1: Complex of cytochrome c maturation system I, Ccm(AB)2CD
Supramolecule | Name: Complex of cytochrome c maturation system I, Ccm(AB)2CD type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-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: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 24.410729 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: 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 |
-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: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 23.632676 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
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: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 27.911264 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
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: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 7.753103 KDa |
Recombinant expression | Organism: Escherichia coli K-12 (bacteria) |
Sequence | String: MTPAFASWNE FFAMGGYAFF VWLAVVMTVI PLVVLVVHSV MQHRAILRGV AQQRAREARL RAAQQQEAA UniProtKB: Heme exporter protein D |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 204806 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |