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- EMDB-16932: NAPE-PLD bound to a nanodisc -

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Basic information

Entry
Database: EMDB / ID: EMD-16932
TitleNAPE-PLD bound to a nanodisc
Map data
Sample
  • Complex: NAPE-PLD bound to a nanodisc
KeywordsNAPE-PLD / Lipid / Membrane / nanodisc / LIPID BINDING PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 Å
AuthorsChaves-Sanjuan A / Garau G / Bolognesi M
Funding support Italy, 1 items
OrganizationGrant numberCountry
Italian Ministry of HealthSB2D-CNI-BGU Italy
CitationJournal: Cell Chem Biol / Year: 2025
Title: NAPE-PLD is target of thiazide diuretics.
Authors: Sara Chiarugi / Francesco Margheriti / Valentina De Lorenzi / Elisa Martino / Eleonora Germana Margheritis / Aldo Moscardini / Roberto Marotta / Antonio Chaves-Sanjuan / Cristina Del Seppia ...Authors: Sara Chiarugi / Francesco Margheriti / Valentina De Lorenzi / Elisa Martino / Eleonora Germana Margheritis / Aldo Moscardini / Roberto Marotta / Antonio Chaves-Sanjuan / Cristina Del Seppia / Giuseppe Federighi / Dominga Lapi / Tiziano Bandiera / Simona Rapposelli / Rossana Scuri / Martino Bolognesi / Gianpiero Garau /
Abstract: Thiazide and thiazide-like diuretics are among the most efficacious and used drugs for the treatment of hypertension, edema, and major cardiovascular outcomes. Despite more then than six decades of ...Thiazide and thiazide-like diuretics are among the most efficacious and used drugs for the treatment of hypertension, edema, and major cardiovascular outcomes. Despite more then than six decades of clinical use, the molecular target and mechanism of action by which these drugs cure hypertension after long-term use have remained mysterious. Here we report the discovery and validation of a previously unknown renal and extrarenal target of these antihypertensives, the membrane-associated phospholipase N-acylphosphatidylethanolamine-specific phospholipase D (NAPE-PLD) of the endocannabinoid system. Structural and functional insights, together with preclinical studies in hypertensive rats, disclose the molecular and physiological basis by which thiazides cause acute diuresis and, at the same time, the distinctive chronic reduction of vascular resistance. Our results shed light on the mechanism of treatment of hypertension and will be useful for developing more efficacious medications for the management of vascular risk factors, as well as associated leukoencephalopathies and myelin disorders.
History
DepositionMar 29, 2023-
Header (metadata) releaseJul 10, 2024-
Map releaseJul 10, 2024-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16932.png

Downloads & links

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Map

FileDownload / File: emd_16932.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 360 pix.
= 320.04 Å		0.89 Å/pix.
x 360 pix.
= 320.04 Å		0.89 Å/pix.
x 360 pix.
= 320.04 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.16202272 - 0.86983687
Average (Standard dev.)0.0012777091 (±0.050240632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 320.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16932_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_16932_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_16932_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NAPE-PLD bound to a nanodisc

EntireName: NAPE-PLD bound to a nanodisc
Components
  • Complex: NAPE-PLD bound to a nanodisc

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Supramolecule #1: NAPE-PLD bound to a nanodisc

SupramoleculeName: NAPE-PLD bound to a nanodisc / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 42 KDa

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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

Concentration0.6 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMTrisTris
100.0 mMNaClNaCl
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Details: 30 mA instrument> GloQube (Quorum Technologies)
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Details: incubated on grid for 60 s.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Number real images: 2500 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 214527
CTF correctionSoftware - Name: Warp (ver. 1.0.9) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.3) / Software - details: homogeneus refinement / Number images used: 11992
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.0.3) / Software - details: homogeneus refinement
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.0.3)
FSC plot (resolution estimation)

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