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- EMDB-16656: Low-resolution structure of the NorQ chaperone from Paracoccus de... -
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Open data
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Basic information
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Title | Low-resolution structure of the NorQ chaperone from Paracoccus denitrificans | ||||||||||||
![]() | Low-resolution structure of the NorQ chaperone from Paracoccus denitrificans | ||||||||||||
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![]() | MoxR AAA+ and VWA domain proteins / CHAPERONE | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.82 Å | ||||||||||||
![]() | Adelroth P / Carroni M / Kahle M / Appelgren S / Elofsson A | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Insights into the structure-function relationship of the NorQ/NorD chaperones from Paracoccus denitrificans reveal shared principles of interacting MoxR AAA+/VWA domain proteins. Authors: Maximilian Kahle / Sofia Appelgren / Arne Elofsson / Marta Carroni / Pia Ädelroth / ![]() ![]() Abstract: BACKGROUND: NorQ, a member of the MoxR-class of AAA+ ATPases, and NorD, a protein containing a Von Willebrand Factor Type A (VWA) domain, are essential for non-heme iron (Fe) cofactor insertion into ...BACKGROUND: NorQ, a member of the MoxR-class of AAA+ ATPases, and NorD, a protein containing a Von Willebrand Factor Type A (VWA) domain, are essential for non-heme iron (Fe) cofactor insertion into cytochrome c-dependent nitric oxide reductase (cNOR). cNOR catalyzes NO reduction, a key step of bacterial denitrification. This work aimed at elucidating the specific mechanism of NorQD-catalyzed Fe insertion, and the general mechanism of the MoxR/VWA interacting protein families. RESULTS: We show that NorQ-catalyzed ATP hydrolysis, an intact VWA domain in NorD, and specific surface carboxylates on cNOR are all features required for cNOR activation. Supported by BN-PAGE, low- ...RESULTS: We show that NorQ-catalyzed ATP hydrolysis, an intact VWA domain in NorD, and specific surface carboxylates on cNOR are all features required for cNOR activation. Supported by BN-PAGE, low-resolution cryo-EM structures of NorQ and the NorQD complex show that NorQ forms a circular hexamer with a monomer of NorD binding both to the side and to the central pore of the NorQ ring. Guided by AlphaFold predictions, we assign the density that "plugs" the NorQ ring pore to the VWA domain of NorD with a protruding "finger" inserting through the pore and suggest this binding mode to be general for MoxR/VWA couples. CONCLUSIONS: Based on our results, we present a tentative model for the mechanism of NorQD-catalyzed cNOR remodeling and suggest many of its features to be applicable to the whole MoxR/VWA family. | ||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 78.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.5 KB 14.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.8 KB | Display | ![]() |
Images | ![]() | 78 KB | ||
Masks | ![]() | 103 MB | ![]() | |
Others | ![]() ![]() | 79.4 MB 79.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 665.9 KB | Display | ![]() |
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Full document | ![]() | 665.5 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Low-resolution structure of the NorQ chaperone from Paracoccus denitrificans | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.99 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: Low-resolution structure of the NorQ chaperone from Paracoccus...
File | emd_16656_half_map_1.map | ||||||||||||
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Annotation | Low-resolution structure of the NorQ chaperone from Paracoccus denitrificans Half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Low-resolution structure of the NorQ chaperone from Paracoccus...
File | emd_16656_half_map_2.map | ||||||||||||
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Annotation | Low-resolution structure of the NorQ chaperone from Paracoccus denitrificans Half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : NorQ hexamer
Entire | Name: NorQ hexamer |
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Components |
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-Supramolecule #1: NorQ hexamer
Supramolecule | Name: NorQ hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Pd. NorQ
Macromolecule | Name: Pd. NorQ / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MHHHHHHASN AHVKTQGNGA VDAPFYLPQG DEVAVFEAAA ANDLPVLLKG PTGCGKTRFV AHMAARLG R PLYTVACHDD LSAADLIGRY LLKGGETVWT DGPLTRAVRE GAICYLDQVV EARKDVTVV LHPLTDDRRI LPIDRTGEEI EAAPGFMLVA SYNPGYQNIL ...String: MHHHHHHASN AHVKTQGNGA VDAPFYLPQG DEVAVFEAAA ANDLPVLLKG PTGCGKTRFV AHMAARLG R PLYTVACHDD LSAADLIGRY LLKGGETVWT DGPLTRAVRE GAICYLDQVV EARKDVTVV LHPLTDDRRI LPIDRTGEEI EAAPGFMLVA SYNPGYQNIL KTLKPSTRQR FVAMEFDFPE PAREVEIVA RESGLDRDRT LGLVRLAGKI RGLKGQDLEE GVSTRLVVYA ASLTRRGMNL D RAIEAAMI EPLTDDAEVK RGLRDLAAAI FG |
-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 mg/mL |
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Buffer | pH: 7.6 / Details: 20 mM HEPES, 150 mM NaCl, 2 mM DTT |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K |
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Electron microscopy
Microscope | TFS TALOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |