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Yorodumi- EMDB-16655: Low-resolution cryo-EM structure of the NorQD chaperone complex f... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16655 | ||||||||||||
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Title | Low-resolution cryo-EM structure of the NorQD chaperone complex from Paracoccus denitrificans | ||||||||||||
Map data | Structure of the NorQD complex from Paracoccus denitrificans | ||||||||||||
Sample |
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Keywords | MoxR AAA+ and VWA domain proteins / CHAPERONE | ||||||||||||
Biological species | Paracoccus denitrificans (bacteria) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.09 Å | ||||||||||||
Authors | Adelroth P / Carroni M / Kahle M / Appelgren S / Elofsson A | ||||||||||||
Funding support | Sweden, 3 items
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Citation | Journal: BMC Biol / Year: 2023 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 | emd_16655.map.gz | 59.2 MB | EMDB map data format | |
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Header (meta data) | emd-16655-v30.xml emd-16655.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
Images | emd_16655.png | 67.5 KB | ||
Others | emd_16655_half_map_1.map.gz emd_16655_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16655 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16655 | HTTPS FTP |
-Validation report
Summary document | emd_16655_validation.pdf.gz | 659.8 KB | Display | EMDB validaton report |
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Full document | emd_16655_full_validation.pdf.gz | 659.4 KB | Display | |
Data in XML | emd_16655_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | emd_16655_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16655 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16655 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16655.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Structure of the NorQD complex from Paracoccus denitrificans | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8464 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Structure of the NorQD complex from Paracoccus denitrificans halfA
File | emd_16655_half_map_1.map | ||||||||||||
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Annotation | Structure of the NorQD complex from Paracoccus denitrificans halfA | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Structure of the NorQD complex from Paracoccus denitrificans halfB
File | emd_16655_half_map_2.map | ||||||||||||
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Annotation | Structure of the NorQD complex from Paracoccus denitrificans halfB | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NorQD complex
Entire | Name: NorQD complex |
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Components |
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-Supramolecule #1: NorQD complex
Supramolecule | Name: NorQD complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Paracoccus denitrificans (bacteria) |
-Macromolecule #1: Pd. NorQ
Macromolecule | Name: Pd. NorQ / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Paracoccus denitrificans (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MASNAHVKTQ GNGAVDAPFY LPQGDEVAVF EAAAANDLPV LLKGPTGCGK TRFVAHMAAR LG RPLYTVA CHDDLSAADL IGRYLLKGGE TVWTDGPLTR AVREGAICYL DEVVEARKDV TVV LHPLTD DRRILPIDRT GEEIEAAPGF MLVASYNPGY QNILKTLKPS ...String: MASNAHVKTQ GNGAVDAPFY LPQGDEVAVF EAAAANDLPV LLKGPTGCGK TRFVAHMAAR LG RPLYTVA CHDDLSAADL IGRYLLKGGE TVWTDGPLTR AVREGAICYL DEVVEARKDV TVV LHPLTD DRRILPIDRT GEEIEAAPGF MLVASYNPGY QNILKTLKPS TRQRFVAMEF DFPE PAREV EIVARESGLD RDRTLGLVRL AGKIRGLKGQ DLEEGVSTRL VVYAASLTRR GMNLD RAIE AAMIEPLTDD AEVKRGLRDL AAAIFG |
-Macromolecule #2: Pd. NorD
Macromolecule | Name: Pd. NorD / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Paracoccus denitrificans (bacteria) |
Recombinant expression | Organism: Escherichia coli BL21(DE3) (bacteria) |
Sequence | String: MHHHHHHSRG LDLEPWEPEE TVGKIWHVW ASSFGAPQAF E DQAVALSE VSGRLAVLFR AL GGGAAVE IRPAAVQASH HRI GWLRRL GTPAETVPHA SFDG EILRL PERLSVLPSR QANGA LFLW LAACAAHGSL APAQGD PLC RDLVRLGAAQ RAVEATL QD ...String: MHHHHHHSRG LDLEPWEPEE TVGKIWHVW ASSFGAPQAF E DQAVALSE VSGRLAVLFR AL GGGAAVE IRPAAVQASH HRI GWLRRL GTPAETVPHA SFDG EILRL PERLSVLPSR QANGA LFLW LAACAAHGSL APAQGD PLC RDLVRLGAAQ RAVEATL QD APGLTGLYDD LAELVLSL R PVAPLPPAEA VVEALARHL LGDPAPLPPL ARDWLAMLDD PQVKAPRDY RPMRPVPLWP D LALPETTL AAAPGDAPDG IA ADPANAR MFRARRRQSD QPQ RRDSLI LHKFEALLSW ADLM NLNRH VDDDDQDDAK KAAED QEEL GLGQVSKAPA TRLRLH LDL APEDADLEAV AGIRTYP EW DARRGRYLAH HVRVLENR A PEHDEALTPD PRAQTRIRA VRRQFEALRP GRLITTGHRD GDELDAELT VRAAADLRAT G QGSDRIWR QSRPLARNLA VS ILLDVSR STESAVTGRA VIE IEREAL AALAWGLDAC GDRF AINAF SSLKRDRVFL SACKD FDEP MGAAIERRIA GLRPRF YTR LGAGIRHASA GLSAQAS SR RLLLVITDGK PNDLDHYE G RHGIEDSAMA VREARRAGH AVHGITVDRD AKSWFPRIFG QGGFSLIPH PDRLLAALPV I YRQLVA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 / Details: 50mM TRIS/HCl, 150 mM NaCl, 10% glycerol |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 25.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
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: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
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: 5.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 507400 |
Initial angle assignment | Type: OTHER / Details: SGD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |