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- EMDB-11067: CryoEM structure of horse sodium/proton exchanger NHE9 without C-... -

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Basic information

Entry
Database: EMDB / ID: EMD-11067
TitleCryoEM structure of horse sodium/proton exchanger NHE9 without C-terminal regulatory domain in an inward-facing conformation
Map data
Sample
  • Organelle or cellular component: Sodium proton antiporter
    • Protein or peptide: Sodium/hydrogen exchanger
KeywordsTRANSPORT PROTEIN / MEMBRANE PROTEIN
Function / homology
Function and homology information


phagosome maturation / potassium:proton antiporter activity / sodium:proton antiporter activity / early phagosome / sodium ion import across plasma membrane / potassium ion transmembrane transport / sodium ion transmembrane transport / proton transmembrane transport / regulation of intracellular pH / recycling endosome ...phagosome maturation / potassium:proton antiporter activity / sodium:proton antiporter activity / early phagosome / sodium ion import across plasma membrane / potassium ion transmembrane transport / sodium ion transmembrane transport / proton transmembrane transport / regulation of intracellular pH / recycling endosome / phagocytic vesicle membrane / recycling endosome membrane / late endosome membrane / early endosome membrane / defense response to bacterium / protein homodimerization activity / plasma membrane
Similarity search - Function
Sodium/hydrogen exchanger 6/7/9 / Na+/H+ exchanger / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane
Similarity search - Domain/homology
Sodium/hydrogen exchanger 9
Similarity search - Component
Biological speciesEquus caballus (horse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsWinkelmann I / Matsuoka R
CitationJournal: EMBO J / Year: 2020
Title: Structure and elevator mechanism of the mammalian sodium/proton exchanger NHE9.
Authors: Iven Winklemann / Rei Matsuoka / Pascal F Meier / Denis Shutin / Chenou Zhang / Laura Orellana / Ricky Sexton / Michael Landreh / Carol V Robinson / Oliver Beckstein / David Drew /
Abstract: Na /H exchangers (NHEs) are ancient membrane-bound nanomachines that work to regulate intracellular pH, sodium levels and cell volume. NHE activities contribute to the control of the cell cycle, cell ...Na /H exchangers (NHEs) are ancient membrane-bound nanomachines that work to regulate intracellular pH, sodium levels and cell volume. NHE activities contribute to the control of the cell cycle, cell proliferation, cell migration and vesicle trafficking. NHE dysfunction has been linked to many diseases, and they are targets of pharmaceutical drugs. Despite their fundamental importance to cell homeostasis and human physiology, structural information for the mammalian NHE was lacking. Here, we report the cryogenic electron microscopy structure of NHE isoform 9 (SLC9A9) from Equus caballus at 3.2 Å resolution, an endosomal isoform highly expressed in the brain and associated with autism spectrum (ASD) and attention deficit hyperactivity (ADHD) disorders. Despite low sequence identity, the NHE9 architecture and ion-binding site are remarkably similar to distantly related bacterial Na /H  antiporters with 13 transmembrane segments. Collectively, we reveal the conserved architecture of the NHE ion-binding site, their elevator-like structural transitions, the functional implications of autism disease mutations and the role of phosphoinositide lipids to promote homodimerization that, together, have important physiological ramifications.
History
DepositionMay 22, 2020-
Header (metadata) releaseNov 4, 2020-
Map releaseNov 4, 2020-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-6z3z
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11067.png

Downloads & links

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Map

FileDownload / File: emd_11067.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 240 pix.
= 249. Å		1.04 Å/pix.
x 240 pix.
= 249. Å		1.04 Å/pix.
x 240 pix.
= 249. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.030737817 - 0.06690605
Average (Standard dev.)-0.00001098096 (±0.0022964117)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.03751.03751.0375
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z249.000249.000249.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0310.067-0.000

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Supplemental data

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Mask #1

Fileemd_11067_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_11067_half_map_1.map
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Half map: #1

Fileemd_11067_half_map_2.map
Projections & Slices
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Sample components

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Entire : Sodium proton antiporter

EntireName: Sodium proton antiporter
Components
  • Organelle or cellular component: Sodium proton antiporter
    • Protein or peptide: Sodium/hydrogen exchanger

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Supramolecule #1: Sodium proton antiporter

SupramoleculeName: Sodium proton antiporter / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Equus caballus (horse)

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Macromolecule #1: Sodium/hydrogen exchanger

MacromoleculeName: Sodium/hydrogen exchanger / type: protein_or_peptide / ID: 1 / Details: 'GENLYFQ' in C terminal comes from Tag / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Equus caballus (horse)
Molecular weightTheoretical: 52.572227 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: GAVELLVFNF LLILTILTIW LFKNHRFRFL HETGGAMVYG LIMGLILRYA TAPTDIESGT VYDCGKLAFS PSTLLINITD QVYEYKYKR EISQHNINPH LGNAILEKMT FDPEIFFNVL LPPIIFHAGY SLKKRHFFQN LGSILTYAFL GTAISCIVIG L IMYGFVKA ...String:
GAVELLVFNF LLILTILTIW LFKNHRFRFL HETGGAMVYG LIMGLILRYA TAPTDIESGT VYDCGKLAFS PSTLLINITD QVYEYKYKR EISQHNINPH LGNAILEKMT FDPEIFFNVL LPPIIFHAGY SLKKRHFFQN LGSILTYAFL GTAISCIVIG L IMYGFVKA MVYAGQLKNG DFHFTDCLFF GSLMSATDPV TVLAIFHELH VDPDLYTLLF GESVLNDAVA IVLTYSISIY SP KENPNAF DAAAFFQSVG NFLGIFAGSF AMGSAYAVVT ALLTKFTKLC EFPMLETGLF FLLSWSAFLS AEAAGLTGIV AVL FCGVTQ AHYTYNNLSL DSKMRTKQLF EFMNFLAENV IFCYMGLALF TFQNHIFNAL FILGAFLAIF VARACNIYPL SFLL NLGRK HKIPWNFQHM MMFSGLRGAI AFALAIRDTE SQPKQMMFST TLLLVFFTVW VFGGGTTGEN LYFQ

UniProtKB: Sodium/hydrogen exchanger 9

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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
Component:
ConcentrationFormula
150.0 mMNaCl
20.0 mMTri-HCl
0.003 %LMNG
0.0006 %CHS
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 400
VitrificationCryogen name: HELIUM

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsPhase plate: ZERNIKE PHASE PLATE / Spherical aberration corrector: Nothing / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-40 / Average exposure time: 10.0 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 165000
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 correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 595024
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 3 / Avg.num./class: 140000
FSC plot (resolution estimation)

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