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- EMDB-53157: NorQ in complex with NorD VWA domain steep staircase subset 1 fro... -

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Basic information

Entry
Database: EMDB / ID: EMD-53157
TitleNorQ in complex with NorD VWA domain steep staircase subset 1 from Paracoccus denitrificans
Map datamain map
Sample
  • Complex: NorQ-NorD VWA domain complex in presence of ATP
    • Protein or peptide: Protein NorQ
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsAAA+ Protein / MoxR / VWA domain / Nitric Oxide Reductase / CHAPERONE
Function / homologyCbbQ/NirQ/NorQ, C-terminal / CbbQ/NirQ/NorQ C-terminal / : / ATPase, dynein-related, AAA domain / AAA domain (dynein-related subfamily) / ATP hydrolysis activity / P-loop containing nucleoside triphosphate hydrolase / ATP binding / Protein NorQ
Function and homology information
Biological speciesParacoccus denitrificans (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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_53157.png

Downloads & links

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Map

FileDownload / File: emd_53157.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 280 pix.
= 238.56 Å		0.85 Å/pix.
x 280 pix.
= 238.56 Å		0.85 Å/pix.
x 280 pix.
= 238.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.852 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.19031653 - 0.5314548
Average (Standard dev.)-0.00019928474 (±0.013265254)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 238.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53157_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_53157_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_53157_half_map_1.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_53157_half_map_2.map
Annotationhalf map 1
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-NorD VWA domain complex in presence of ATP

EntireName: NorQ-NorD VWA domain complex in presence of ATP
Components
  • Complex: NorQ-NorD VWA domain complex in presence of ATP
    • Protein or peptide: Protein NorQ
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: NorQ-NorD VWA domain complex in presence of ATP

SupramoleculeName: NorQ-NorD VWA domain complex in presence of ATP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 5 / 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 #3: MAGNESIUM ION

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

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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, 4mM ATP, 10mM MgCl2, 1mM DTT
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 300 / 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: 40.0 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: 130000
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: cryoSPARC / 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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 264861
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
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-9qh7:
NorQ in complex with NorD VWA domain steep staircase subset 1 from Paracoccus denitrificans

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