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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Cytochrome c-type biogenesis protein CcmABCD | |||||||||
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![]() | ATP-binding exporter / heme transmembrane transporter / Cytochrome c biogenesis protein. / 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 / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.98 Å | |||||||||
![]() | Zhu JP / Zhang K / Li J / Zheng W / Gu M | |||||||||
Funding support | 1 items
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![]() | ![]() Title: Structures of the CcmABCD heme release complex at multiple states. Authors: Jiao Li / Wan Zheng / Ming Gu / Long Han / Yanmei Luo / Koukou Yu / Mengxin Sun / Yuliang Zong / Xiuxiu Ma / Bing Liu / Ethan P Lowder / Deanna L Mendez / Robert G Kranz / Kai Zhang / Jiapeng Zhu / ![]() ![]() Abstract: Cytochromes c use heme as a cofactor to carry electrons in respiration and photosynthesis. The cytochrome c maturation system I, consisting of eight membrane proteins (CcmABCDEFGH), results in the ...Cytochromes c use heme as a cofactor to carry electrons in respiration and photosynthesis. The cytochrome c maturation system I, consisting of eight membrane proteins (CcmABCDEFGH), results in the attachment of heme to cysteine residues of cytochrome c proteins. Since all c-type cytochromes are periplasmic, heme is first transported to a periplasmic heme chaperone, CcmE. A large membrane complex, CcmABCD has been proposed to carry out this transport and linkage to CcmE, yet the structural basis and mechanisms underlying the process are unknown. We describe high resolution cryo-EM structures of CcmABCD in an unbound form, in complex with inhibitor AMP-PNP, and in complex with ATP and heme. We locate the ATP-binding site in CcmA and the heme-binding site in CcmC. Based on our structures combined with functional studies, we propose a hypothetic model of heme trafficking, heme transfer to CcmE, and ATP-dependent release of holoCcmE from CcmABCD. CcmABCD represents an ABC transporter complex using the energy of ATP hydrolysis for the transfer of heme from one binding partner (CcmC) to another (CcmE). | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 117.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 13.3 KB 13.3 KB | Display Display | ![]() |
Images | ![]() | 33.9 KB | ||
Filedesc metadata | ![]() | 5.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 491.1 KB | Display | ![]() |
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Full document | ![]() | 490.7 KB | Display | |
Data in XML | ![]() | 6.5 KB | Display | |
Data in CIF | ![]() | 7.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7vfjMC ![]() 7f02C ![]() 7f03C ![]() 7f04C ![]() 7vfpC 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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Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : The cytochrome c maturation complex CcmABCD.
Entire | Name: The cytochrome c maturation complex CcmABCD. |
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Components |
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-Supramolecule #1: The cytochrome c maturation complex CcmABCD.
Supramolecule | Name: The cytochrome c maturation complex CcmABCD. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 130 KDa |
-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: 23.080213 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGMLEARELL CERDERTLFS GLSFTLNAGE WVQITGSNGA GKTTLLRLLT GLSRPDAGEV LWQGQPLHQV RDSYHQNLLW IGHQPGIKT RLTALENLHF YHRDGDTAQC LEALAQAGLA GFEDIPVNQL SAGQQRRVAL ARLWLTRATL WILDEPFTAI D VNGVDRLT ...String: MGMLEARELL CERDERTLFS GLSFTLNAGE WVQITGSNGA GKTTLLRLLT GLSRPDAGEV LWQGQPLHQV RDSYHQNLLW IGHQPGIKT RLTALENLHF YHRDGDTAQC LEALAQAGLA GFEDIPVNQL SAGQQRRVAL ARLWLTRATL WILDEPFTAI D VNGVDRLT QRMAQHTEQG GIVILTTHQP LNVAESKIRR ISLTQTRAA 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: 1 / 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: 1 / 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 |
-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: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.4388 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 147351 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |