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

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Basic information

Entry
Database: PDB / ID: 9qh6
TitleNorQ in complex with NorD VWA domain from Paracoccus denitrificans
Components
  • Protein NorQ
  • von Willebrand factor, type A
KeywordsCHAPERONE / AAA+ Protein / MoxR / VWA domain / Nitric Oxide Reductase
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
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / von Willebrand factor, type A / Protein NorQ
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKahle, M. / Appelgren, S. / Carroni, M. / Adelroth, P. / Wendler, P.
Funding support Germany, Sweden, 2items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein NorQ
B: Protein NorQ
C: Protein NorQ
D: Protein NorQ
E: Protein NorQ
F: Protein NorQ
G: von Willebrand factor, type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,08115
Polymers246,6327
Non-polymers2,4498
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Protein NorQ


Mass: 29450.729 Da / Num. of mol.: 6 / Mutation: E109Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: norQ, Pden_2482 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q51664
#2: Protein von Willebrand factor, type A


Mass: 69927.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paracoccus denitrificans (bacteria) / Gene: Pden_2481 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A1B4X4
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NorQ in complex with NorD VWA domain / Type: COMPLEX
Details: truncated NorD, leaving the only the C-terminal VWA domain, no reductants added
Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.222 MDa / Experimental value: NO
Source (natural)Organism: Paracoccus denitrificans (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8 / Details: 50mM TRIS/HCl,150mM KCl
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: PELCO easiGlow at 20mA / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2EPUimage acquisition
4RELIONCTF correction
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
10PHENIXmodel refinement
11Cootmodel refinement
12RELIONinitial Euler assignment
13RELIONfinal Euler assignment
15cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 50874 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementHighest resolution: 3.2 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00313731
ELECTRON MICROSCOPYf_angle_d0.46418708
ELECTRON MICROSCOPYf_dihedral_angle_d10.4655005
ELECTRON MICROSCOPYf_chiral_restr0.0382195
ELECTRON MICROSCOPYf_plane_restr0.0042429

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