+Open data
-Basic information
Entry | Database: PDB / ID: 8ce5 | |||||||||||||||
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Title | Cytochrome c maturation complex CcmABCD, E154Q, ATP-bound | |||||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Cytochrome c maturation | |||||||||||||||
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 K-12 (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.62 Å | |||||||||||||||
Authors | Ilcu, L. / Zhang, L. / Einsle, O. | |||||||||||||||
Funding support | European Union, Germany, 4items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ce5.cif.gz | 206.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ce5.ent.gz | 163 KB | Display | PDB format |
PDBx/mmJSON format | 8ce5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ce5_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8ce5_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ce5_validation.xml.gz | 39.2 KB | Display | |
Data in CIF | 8ce5_validation.cif.gz | 58.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/8ce5 ftp://data.pdbj.org/pub/pdb/validation_reports/ce/8ce5 | HTTPS FTP |
-Related structure data
Related structure data | 16599MC 8ce1C 8ce8C 8ceaC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 2 molecules Aa
#1: Protein | Mass: 24410.729 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ccmA, yejW, b2201, JW5366 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): C43 / References: UniProt: P33931, ABC-type heme transporter |
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-Heme exporter protein ... , 3 types, 4 molecules BbCD
#2: Protein | Mass: 23632.676 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ccmB, yejV, b2200, JW2188 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ABL8 #3: Protein | | Mass: 27911.264 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ccmC, yejT, yejU, b2199, JW2187 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ABM1 #4: Protein | | Mass: 7753.103 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: ccmD, yojM, b2198, JW2186 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0ABM5 |
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-Non-polymers , 2 types, 4 molecules
#5: Chemical | #6: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of cytochrome c maturation sysmtem I, Ccm(AB)2CD Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli K-12 (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 355914 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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