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Yorodumi- EMDB-31395: Cytochrome c-type biogenesis protein CcmABCD from E. coli in comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31395 | |||||||||
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Title | Cytochrome c-type biogenesis protein CcmABCD from E. coli in complex with ANP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | ATP-binding exporter / Heme transmembrane transporter / Cytochrome c biogenesis protein. / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information cytochrome c biosynthetic process / heme import across plasma membrane / ABC-type heme transporter / heme transmembrane transporter activity / ABC-type heme 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 BL21(DE3) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.29 Å | |||||||||
Authors | Li J / Zheng W | |||||||||
Citation | Journal: Nat Commun / Year: 2022 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 | emd_31395.map.gz | 64.3 MB | EMDB map data format | |
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Header (meta data) | emd-31395-v30.xml emd-31395.xml | 14.3 KB 14.3 KB | Display Display | EMDB header |
Images | emd_31395.png | 47.8 KB | ||
Filedesc metadata | emd-31395.cif.gz | 5.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31395 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31395 | HTTPS FTP |
-Validation report
Summary document | emd_31395_validation.pdf.gz | 511.9 KB | Display | EMDB validaton report |
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Full document | emd_31395_full_validation.pdf.gz | 511.5 KB | Display | |
Data in XML | emd_31395_validation.xml.gz | 6.7 KB | Display | |
Data in CIF | emd_31395_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31395 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31395 | HTTPS FTP |
-Related structure data
Related structure data | 7f03MC 7f02C 7f04C 7vfjC 7vfpC 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_31395.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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
-Sample components
-Entire : Cytochrome c-type biogenesis protein CcmABCD
Entire | Name: Cytochrome c-type biogenesis protein CcmABCD |
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Components |
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-Supramolecule #1: Cytochrome c-type biogenesis protein CcmABCD
Supramolecule | Name: Cytochrome c-type biogenesis protein CcmABCD / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Escherichia coli BL21(DE3) (bacteria) |
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: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 23.080213 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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: Escherichia coli BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 23.632676 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 27.911264 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 BL21(DE3) (bacteria) |
Molecular weight | Theoretical: 7.753103 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 6 / Number of copies: 2 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Macromolecule #7: 1,2-Distearoyl-sn-glycerophosphoethanolamine
Macromolecule | Name: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 7 / Number of copies: 1 / Formula: 3PE |
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Molecular weight | Theoretical: 748.065 Da |
Chemical component information | ChemComp-3PE: |
-Macromolecule #8: water
Macromolecule | Name: water / type: ligand / ID: 8 / Number of copies: 4 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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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 K3 (6k x 4k) / Average electron dose: 1.5255 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 142289 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |