+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16599 | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cytochrome c maturation complex CcmABCD, E154Q, ATP-bound | |||||||||||||||
Map data | sharpened map | |||||||||||||||
Sample |
| |||||||||||||||
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: 3.62 Å | |||||||||||||||
Authors | Ilcu L / Zhang L / Einsle O | |||||||||||||||
Funding support | European Union, Germany, 4 items
| |||||||||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_16599.map.gz | 48.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-16599-v30.xml emd-16599.xml | 20.2 KB 20.2 KB | Display Display | EMDB header |
Images | emd_16599.png | 124.2 KB | ||
Others | emd_16599_additional_1.map.gz emd_16599_half_map_1.map.gz emd_16599_half_map_2.map.gz | 47.1 MB 48.8 MB 48.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16599 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16599 | HTTPS FTP |
-Related structure data
Related structure data | 8ce5MC 8ce1C 8ce8C 8ceaC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_16599.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.878 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: unsharpened map
File | emd_16599_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | unsharpened map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map A
File | emd_16599_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: half map A
File | emd_16599_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | half map A | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Complex of cytochrome c maturation sysmtem I, Ccm(AB)2CD
Entire | Name: Complex of cytochrome c maturation sysmtem I, Ccm(AB)2CD |
---|---|
Components |
|
-Supramolecule #1: Complex of cytochrome c maturation sysmtem I, Ccm(AB)2CD
Supramolecule | Name: 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) |
-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 |
---|---|
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 |
---|---|
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 |
---|---|
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 |
---|---|
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 |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: ATP |
---|---|
Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
---|---|
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
-Image processing
Startup model | Type of model: INSILICO MODEL |
---|---|
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 355914 |