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- PDB-7ze5: Occ(apo/return) conformation of CydDC mutant (E500Q.C) in ATP(Cyd... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ze5 | ||||||
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Title | Occ(apo/return) conformation of CydDC mutant (E500Q.C) in ATP(CydC)/AMP-PNP(CydD) bound state (Dataset-23) | ||||||
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![]() | MEMBRANE PROTEIN / ABC transporter / CydDC / Heme transporter | ||||||
Function / homology | ![]() cysteine export across plasma membrane / ATP-binding cassette (ABC) transporter complex, integrated substrate binding / cytochrome biosynthetic process / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / glutathione transmembrane transport / heme transmembrane transport / ABC-type heme transporter activity / ATPase-coupled lipid transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex ...cysteine export across plasma membrane / ATP-binding cassette (ABC) transporter complex, integrated substrate binding / cytochrome biosynthetic process / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / glutathione transmembrane transport / heme transmembrane transport / ABC-type heme transporter activity / ATPase-coupled lipid transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / cell redox homeostasis / transmembrane transport / ATP hydrolysis activity / ATP binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å | ||||||
![]() | Wu, D. / Safarian, S. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Dissecting the conformational complexity and mechanism of a bacterial heme transporter. Authors: Di Wu / Ahmad R Mehdipour / Franziska Finke / Hojjat G Goojani / Roan R Groh / Tamara N Grund / Thomas M B Reichhart / Rita Zimmermann / Sonja Welsch / Dirk Bald / Mark Shepherd / Gerhard ...Authors: Di Wu / Ahmad R Mehdipour / Franziska Finke / Hojjat G Goojani / Roan R Groh / Tamara N Grund / Thomas M B Reichhart / Rita Zimmermann / Sonja Welsch / Dirk Bald / Mark Shepherd / Gerhard Hummer / Schara Safarian / ![]() ![]() ![]() ![]() ![]() Abstract: Iron-bound cyclic tetrapyrroles (hemes) are redox-active cofactors in bioenergetic enzymes. However, the mechanisms of heme transport and insertion into respiratory chain complexes remain unclear. ...Iron-bound cyclic tetrapyrroles (hemes) are redox-active cofactors in bioenergetic enzymes. However, the mechanisms of heme transport and insertion into respiratory chain complexes remain unclear. Here, we used cellular, biochemical, structural and computational methods to characterize the structure and function of the heterodimeric bacterial ABC transporter CydDC. We provide multi-level evidence that CydDC is a heme transporter required for functional maturation of cytochrome bd, a pharmaceutically relevant drug target. Our systematic single-particle cryogenic-electron microscopy approach combined with atomistic molecular dynamics simulations provides detailed insight into the conformational landscape of CydDC during substrate binding and occlusion. Our simulations reveal that heme binds laterally from the membrane space to the transmembrane region of CydDC, enabled by a highly asymmetrical inward-facing CydDC conformation. During the binding process, heme propionates interact with positively charged residues on the surface and later in the substrate-binding pocket of the transporter, causing the heme orientation to rotate 180°. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 210.8 KB | Display | ![]() |
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PDB format | ![]() | 165.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 14684MC ![]() 7zd5C ![]() 7zdaC ![]() 7zdbC ![]() 7zdcC ![]() 7zdeC ![]() 7zdfC ![]() 7zdgC ![]() 7zdkC ![]() 7zdlC ![]() 7zdrC ![]() 7zdsC ![]() 7zdtC ![]() 7zduC ![]() 7zdvC ![]() 7zdwC ![]() 7zecC C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 62979.867 Da / Num. of mol.: 1 / Mutation: E500Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Protein | Mass: 65118.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
#3: Chemical | #4: Chemical | ChemComp-ATP / | #5: Chemical | ChemComp-ANP / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: CydDC heterodimer / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.130 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 6 |
Specimen | Conc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 1100 nm |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74444 / Symmetry type: POINT |