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- EMDB-14674: Occ(apo/return) conformation of CydDC mutant (E500Q.C) in ATP(Cyd... -
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Open data
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Basic information
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Title | Occ(apo/return) conformation of CydDC mutant (E500Q.C) in ATP(CydC) bound state (Dataset-21) | |||||||||
![]() | RELION local-resolution filtered map | |||||||||
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![]() | ABC transporter / CydDC / Heme transporter / MEMBRANE PROTEIN | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 3.17 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°. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 57.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.2 KB 20.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.3 KB | Display | ![]() |
Images | ![]() | 69.5 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Others | ![]() ![]() ![]() ![]() | 8.7 MB 70.8 MB 71.1 MB 71.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zd5C ![]() 7zdaC ![]() 7zdbC ![]() 7zdcC ![]() 7zdeC ![]() 7zdfC ![]() 7zdgC ![]() 7zdkC ![]() 7zdlC ![]() 7zdrC ![]() 7zdsC ![]() 7zdtC ![]() 7zduC ![]() 7zdvC ![]() 7zdwC ![]() 7ze5C ![]() 7zecC 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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Annotation | RELION local-resolution filtered map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: RELION masked postprocessing map
File | emd_14674_additional_1.map | ||||||||||||
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Annotation | RELION masked postprocessing map | ||||||||||||
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Density Histograms |
-Additional map: RELION masked 3D refinement map
File | emd_14674_additional_2.map | ||||||||||||
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Annotation | RELION masked 3D refinement map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RELION 3D refinement half map 1
File | emd_14674_half_map_1.map | ||||||||||||
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Annotation | RELION 3D refinement half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: RELION 3D refinement half map 2
File | emd_14674_half_map_2.map | ||||||||||||
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Annotation | RELION 3D refinement half map 2 | ||||||||||||
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Density Histograms |
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Sample components
-Entire : CydDC heterodimer
Entire | Name: CydDC heterodimer |
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Components |
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-Supramolecule #1: CydDC heterodimer
Supramolecule | Name: CydDC heterodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 130 KDa |
-Macromolecule #1: CydC
Macromolecule | Name: CydC / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MRALLPYLAL YKRHKWMLSL GIVLAIVTLL ASIGLLTLSG WFLSASAVAG VAGLYSFNYM LPAAGVRGAA ITRTAGRYFE RLVSHDATF RVLQHLRIYT FSKLLPLSPA GLARYRQGEL LNRVVADVDT LDHLYLRVIS PLVGAFVVIM VVTIGLSFLD F TLAFTLGG ...String: MRALLPYLAL YKRHKWMLSL GIVLAIVTLL ASIGLLTLSG WFLSASAVAG VAGLYSFNYM LPAAGVRGAA ITRTAGRYFE RLVSHDATF RVLQHLRIYT FSKLLPLSPA GLARYRQGEL LNRVVADVDT LDHLYLRVIS PLVGAFVVIM VVTIGLSFLD F TLAFTLGG IMLLTLFLMP PLFYRAGKST GQNLTHLRGQ YRQQLTAWLQ GQAELTIFGA SDRYRTQLEN TEIQWLEAQR RQ SELTALS QAIMLLIGAL AVILMLWMAS GGVGGNAQPG ALIALFVFCA LAAFEALAPV TGAFQHLGQV IASAVRISDL TDQ KPEVTF PDTQTRVADR VSLTLRDVQF TYPEQSQQAL KGISLQVNAG EHIAILGRTG CGKSTLLQQL TRAWDPQQGE ILLN DSPIA SLNEAALRQT ISVVPQRVHL FSATLRDNLL LASPGSSDEA LSEILRRVGL EKLLEDAGLN SWLGEGGRQL SGGEL RRLA IARALLHDAP LVLLDQPTEG LDATTESQIL ELLAEMMREK TVLMVTHRLR GLSRFQQIIV MDNGQIIEQG THAELL ARQ GRYYQFKQGL UniProtKB: Glutathione/L-cysteine transport system ATP-binding/permease protein CydC |
-Macromolecule #2: CydD
Macromolecule | Name: CydD / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MNKSRQKELT RWLKQQSVIS QRWLNISRLL GFVSGILIIA QAWFMARILQ HMIMENIPRE ALLLPFTLL VLTFVLRAWV VWLRERVGYH AGQHIRFAIR RQVLDRLQQA GPAWIQGKPA G SWATLVLE QIDDMHDYYA RYLPQMALAV SVPLLIVVAI FPSNWAAALI ...String: MNKSRQKELT RWLKQQSVIS QRWLNISRLL GFVSGILIIA QAWFMARILQ HMIMENIPRE ALLLPFTLL VLTFVLRAWV VWLRERVGYH AGQHIRFAIR RQVLDRLQQA GPAWIQGKPA G SWATLVLE QIDDMHDYYA RYLPQMALAV SVPLLIVVAI FPSNWAAALI LLGTAPLIPL FM ALVGMGA ADANRRNFLA LARLSGHFLD RLRGMETLRI FGRGEAEIES IRSASEDFRQ RTM EVLRLA FLSSGILEFF TSLSIALVAV YFGFSYLGEL DFGHYDTGVT LAAGFLALIL APEF FQPLR DLGTFYHAKA QAVGAADSLK TFMETPLAHP QRGEAELAST DPVTIEAEEL FITSP EGKT LAGPLNFTLP AGQRAVLVGR SGSGKSSLLN ALSGFLSYQG SLRINGIELR DLSPES WRK HLSWVGQNPQ LPAATLRDNV LLARPDASEQ ELQAALDNAW VSEFLPLLPQ GVDTPVG DQ AARLSVGQAQ RVAVARALLN PCSLLLLDEP AASLDAHSEQ RVMEALNAAS LRQTTLMV T HQLEDLADWD VIWVMQDGRI IEQGRYAELS VAGGPFATLL AHRQEEI UniProtKB: Glutathione/L-cysteine transport system ATP-binding/permease protein CydD |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 6 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 µm / Nominal defocus min: 1.1 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |