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- EMDB-16656: Low-resolution structure of the NorQ chaperone from Paracoccus de... -

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Basic information

Entry
Database: EMDB / ID: EMD-16656
TitleLow-resolution structure of the NorQ chaperone from Paracoccus denitrificans
Map dataLow-resolution structure of the NorQ chaperone from Paracoccus denitrificans
Sample
  • Complex: NorQ hexamer
    • Protein or peptide: Pd. NorQ
KeywordsMoxR AAA+ and VWA domain proteins / CHAPERONE
Biological speciesParacoccus denitrificans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.82 Å
AuthorsAdelroth P / Carroni M / Kahle M / Appelgren S / Elofsson A
Funding support Sweden, 3 items
OrganizationGrant numberCountry
Swedish Research CouncilVR- 2015-04512 and 2019-04124 Sweden
Swedish Research CouncilVR-2016-06301 Sweden
Knut and Alice Wallenberg Foundation31001512 Sweden
CitationJournal: 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
DepositionFeb 6, 2023-
Header (metadata) releaseFeb 22, 2023-
Map releaseFeb 22, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16656.png

Downloads & links

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Map

FileDownload / File: emd_16656.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLow-resolution structure of the NorQ chaperone from Paracoccus denitrificans
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 300 pix.
= 297. Å		0.99 Å/pix.
x 300 pix.
= 297. Å		0.99 Å/pix.
x 300 pix.
= 297. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.0059480993 - 0.04447643
Average (Standard dev.)0.00012865195 (±0.0023566096)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 297.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16656_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Low-resolution structure of the NorQ chaperone from Paracoccus...

Fileemd_16656_half_map_1.map
AnnotationLow-resolution structure of the NorQ chaperone from Paracoccus denitrificans Half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Low-resolution structure of the NorQ chaperone from Paracoccus...

Fileemd_16656_half_map_2.map
AnnotationLow-resolution structure of the NorQ chaperone from Paracoccus denitrificans Half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NorQ hexamer

EntireName: NorQ hexamer
Components
  • Complex: NorQ hexamer
    • Protein or peptide: Pd. NorQ

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Supramolecule #1: NorQ hexamer

SupramoleculeName: NorQ hexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Paracoccus denitrificans (bacteria)

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Macromolecule #1: Pd. NorQ

MacromoleculeName: Pd. NorQ / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.6 / Details: 20 mM HEPES, 150 mM NaCl, 2 mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.82 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 41892
Initial angle assignmentType: OTHER / Details: SGD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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