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- EMDB-17841: Cryo-EM structure of Sodium proton exchanger NhaA with bound card... -

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Basic information

Entry
Database: EMDB / ID: EMD-17841
TitleCryo-EM structure of Sodium proton exchanger NhaA with bound cardiolipin
Map data
Sample
  • Complex: NhaA dimer
    • Protein or peptide: Na(+)/H(+) antiporter NhaA
  • Ligand: CARDIOLIPIN
KeywordsSodium proton exchanger / Cardiolipin / NhaA / TRANSPORT PROTEIN
Function / homologyNa+/H+ antiporter NhaA / Na+/H+ antiporter domain superfamily / Na+/H+ antiporter 1 / sodium:proton antiporter activity / regulation of pH / plasma membrane / Na(+)/H(+) antiporter NhaA
Function and homology information
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsGulati A / Meier P / Kokane S / Drew D
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)CoG-820187European Union
CitationJournal: Nat Commun / Year: 2025
Title: PIP-mediated oligomerization of the endosomal sodium/proton exchanger NHE9.
Authors: Surabhi Kokane / Ashutosh Gulati / Pascal F Meier / Rei Matsuoka / Tanadet Pipatpolkai / Giuseppe Albano / Tin Manh Ho / Lucie Delemotte / Daniel Fuster / David Drew /
Abstract: The strict exchange of Na for H ions across cell membranes is a reaction carried out in almost every cell. Na/H exchangers that perform this task are physiological homodimers, and whilst the ion ...The strict exchange of Na for H ions across cell membranes is a reaction carried out in almost every cell. Na/H exchangers that perform this task are physiological homodimers, and whilst the ion transporting domain is highly conserved, their dimerization differs. The Na/H exchanger NhaA from Escherichia coli has a weak dimerization interface mediated by a β-hairpin domain and with dimer retention dependent on cardiolipin. Similarly, organellar Na/H exchangers NHE6, NHE7 and NHE9 also contain β-hairpin domains and recent analysis of Equus caballus NHE9 indicated PIP lipids could bind at the dimer interface. However, structural validation of the predicted lipid-mediated oligomerization has been lacking. Here, we report cryo-EM structures of E. coli NhaA and E. caballus NHE9 in complex with cardiolipin and phosphatidylinositol-3,5-bisphosphate PI(3,5)P lipids binding at their respective dimer interfaces. We further show how the endosomal specific PI(3,5)P lipid stabilizes the NHE9 homodimer and enhances transport activity. Indeed, we show that NHE9 is active in endosomes, but not at the plasma membrane where the PI(3,5)P lipid is absent. Thus, specific lipids can regulate Na/H exchange activity by stabilizing dimerization in response to either cell specific cues or upon trafficking to their correct membrane location.
History
DepositionJul 13, 2023-
Header (metadata) releaseFeb 21, 2024-
Map releaseFeb 21, 2024-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17841.png

Downloads & links

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Map

FileDownload / File: emd_17841.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesX (Sec.)Y (Row.)Z (Col.)
0.91 Å/pix.
x 320 pix.
= 292.384 Å		0.91 Å/pix.
x 320 pix.
= 292.384 Å		0.91 Å/pix.
x 320 pix.
= 292.384 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9137 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-41.509846000000003 - 79.94014
Average (Standard dev.)0.000000000000374 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 292.384 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17841_msk_1.map
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Half map: #2

Fileemd_17841_half_map_1.map
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Half map: #1

Fileemd_17841_half_map_2.map
Projections & Slices
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Sample components

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Entire : NhaA dimer

EntireName: NhaA dimer
Components
  • Complex: NhaA dimer
    • Protein or peptide: Na(+)/H(+) antiporter NhaA
  • Ligand: CARDIOLIPIN

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Supramolecule #1: NhaA dimer

SupramoleculeName: NhaA dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Na(+)/H(+) antiporter NhaA

MacromoleculeName: Na(+)/H(+) antiporter NhaA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 42.304422 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKHLHRFFSS DASGGIILII AAILAMIMAN SGATSGWYHD FLETPVQLRV GSLEINKNML LWINDALMAV FFLLVGLEVK RELMQGSLA SLRQAAFPVI AAIGGMIVPT LLYLAFNYAD PITREGWAIP AATDIAFALG VLALLGSRVP LALKIFLMAL A IIDDLGAI ...String:
MKHLHRFFSS DASGGIILII AAILAMIMAN SGATSGWYHD FLETPVQLRV GSLEINKNML LWINDALMAV FFLLVGLEVK RELMQGSLA SLRQAAFPVI AAIGGMIVPT LLYLAFNYAD PITREGWAIP AATDIAFALG VLALLGSRVP LALKIFLMAL A IIDDLGAI IIIALFYTND LSMASLGVAA VAIAVLAVLN LCGARRTGVY ILVGVVLWTA VLKSGVHATL AGVIVGFFIP LK EKHGRSP AKRLEHVLHP WVAYLILPLF AFANAGVSLG GVTLDGLTSI LPLGIIAGML IGKPLGISLF CWLALRLKLA HLP EGTTYQ QIMVVGILCG IGFTMSIFIA SLAFGSVDPE LINWAKLGIL VGSISSAVIG YSWLRVRLRP SVGSENLYFQ

UniProtKB: Na(+)/H(+) antiporter NhaA

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Macromolecule #2: CARDIOLIPIN

MacromoleculeName: CARDIOLIPIN / type: ligand / ID: 2 / Number of copies: 3 / Formula: CDL
Molecular weightTheoretical: 1.464043 KDa
Chemical component information

ChemComp-CDL:
CARDIOLIPIN / phospholipid*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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 68.11 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 78917
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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