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- EMDB-53156: NorQ in complex with NorD VWA domain from Paracoccus denitrificans -

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Basic information

Entry
Database: EMDB / ID: EMD-53156
TitleNorQ in complex with NorD VWA domain from Paracoccus denitrificans
Map dataraw map
Sample
  • Complex: NorQ in complex with NorD VWA domain
    • Protein or peptide: Protein NorQ
    • Protein or peptide: von Willebrand factor, type A
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsAAA+ Protein / MoxR / VWA domain / Nitric Oxide Reductase / CHAPERONE
Function / homology
Function and homology information


ATP hydrolysis activity / ATP binding
Similarity search - Function
: / CbbQ/NirQ/NorQ, C-terminal / CbbQ/NirQ/NorQ C-terminal / : / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
von Willebrand factor, type A / Protein NorQ
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKahle M / Appelgren S / Carroni M / Adelroth P / Wendler P
Funding support Germany, Sweden, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
Swedish Research Council Sweden
CitationJournal: To Be Published
Title: NorQD - a MoxR like AAA+ complex with a twist
Authors: Kahle M / Appelgren S / Carroni M / Adelroth P / Wendler P
History
DepositionMar 14, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53156.png

Downloads & links

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Map

FileDownload / File: emd_53156.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationraw map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 288 pix.
= 243.648 Å		0.85 Å/pix.
x 288 pix.
= 243.648 Å		0.85 Å/pix.
x 288 pix.
= 243.648 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.846 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.23008518 - 0.6447695
Average (Standard dev.)0.0012161772 (±0.022504145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 243.64801 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53156_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: sharpened map

Fileemd_53156_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_53156_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_53156_half_map_2.map
Annotationhalf 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 in complex with NorD VWA domain

EntireName: NorQ in complex with NorD VWA domain
Components
  • Complex: NorQ in complex with NorD VWA domain
    • Protein or peptide: Protein NorQ
    • Protein or peptide: von Willebrand factor, type A
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: NorQ in complex with NorD VWA domain

SupramoleculeName: NorQ in complex with NorD VWA domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: truncated NorD, leaving the only the C-terminal VWA domain, no reductants added
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Molecular weightTheoretical: 222 KDa

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Macromolecule #1: Protein NorQ

MacromoleculeName: Protein NorQ / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Molecular weightTheoretical: 29.450729 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MNAHVKTQGN GAVDAPFYLP QGDEVAVFEA AAANDLPVLL KGPTGCGKTR FVAHMAARLG RPLYTVACHD DLSAADLIGR YLLKGGETV WTDGPLTRAV REGAICYLDQ VVEARKDVTV VLHPLTDDRR ILPIDRTGEE IEAAPGFMLV ASYNPGYQNI L KTLKPSTR ...String:
MNAHVKTQGN GAVDAPFYLP QGDEVAVFEA AAANDLPVLL KGPTGCGKTR FVAHMAARLG RPLYTVACHD DLSAADLIGR YLLKGGETV WTDGPLTRAV REGAICYLDQ VVEARKDVTV VLHPLTDDRR ILPIDRTGEE IEAAPGFMLV ASYNPGYQNI L KTLKPSTR QRFVAMEFDF PEPAREVEIV ARESGLDRDR TLGLVRLAGK IRGLKGQDLE EGVSTRLVVY AASLTRRGMN LD RAIEAAM IEPLTDDAEV KRGLRDLAAA IFG

UniProtKB: Protein NorQ

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Macromolecule #2: von Willebrand factor, type A

MacromoleculeName: von Willebrand factor, type A / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Molecular weightTheoretical: 69.927336 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGLDLEPWEP EETVGKIWHV WASSFGAPQA FEDQAVALSE VSGRLAVLFR ALGGGAAVEI RPAAVQASHH RIGWLRRLGT PAETVPHAS FDGEILRLPE RLSVLPSRQA NGALFLWLAA CAAHGSLAPA QGDPLCRDLV RLGAAQRAVE ATLQDAPGLT G LYDDLAEL ...String:
MGLDLEPWEP EETVGKIWHV WASSFGAPQA FEDQAVALSE VSGRLAVLFR ALGGGAAVEI RPAAVQASHH RIGWLRRLGT PAETVPHAS FDGEILRLPE RLSVLPSRQA NGALFLWLAA CAAHGSLAPA QGDPLCRDLV RLGAAQRAVE ATLQDAPGLT G LYDDLAEL VLSLRPVAPL PPAEAVVEAL ARHLLGDPAP LPPLARDWLA MLDDPQVKAP RDYRPMRPVP LWPDLALPET TL AAAPGDA PDGIAADPAN ARMFRARRRQ SDQPQRRDSL ILHKFEALLS WADLMNLNRH VDDDDQDDAK KAAEDQEELG LGQ VSKAPA TRLRLHLDLA PEDADLEAVA GIRTYPEWDA RRGRYLAHHV RVLENRAPEH DEALTPDPRA QTRIRAVRRQ FEAL RPGRL ITTGHRDGDE LDAELTVRAA ADLRATGQGS DRIWRQSRPL ARNLAVSILL DVSRSTESAV TGRAVIEIER EALAA LAWG LDACGDRFAI NAFSSLKRDR VFLSACKDFD EPMGAAIERR IAGLRPRFYT RLGAGIRHAS AGLSAQASSR RLLLVI TDG KPNDLDHYEG RHGIEDSAMA VREARRAGHA VHGITVDRDA KSWFPRIFGQ GGFSLIPHPD RLLAALPVIY RQLVA

UniProtKB: von Willebrand factor, type A

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 3 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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: 8 / Details: 50mM TRIS/HCl,150mM KCl
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.05 kPa / Details: PELCO easiGlow at 20mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: SGD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 50874
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
SoftwareName: UCSF ChimeraX
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9qh6:
NorQ in complex with NorD VWA domain from Paracoccus denitrificans

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