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- EMDB-53827: Structure of human NHE9 -

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Basic information

Entry
Database: EMDB / ID: EMD-53827
TitleStructure of human NHE9
Map dataFinal cryoSPARC non-uniform refinement map sharpened with a Bfactor of -25
Sample
  • Complex: NHE9 homodimer
    • Protein or peptide: Sodium/hydrogen exchanger 9
  • Ligand: SODIUM ION
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: water
KeywordsNa/H exchanger / sodium transport / proton transport / endosome / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective SLC9A9 causes autism 16 (AUTS16) / Sodium/Proton exchangers / potassium:proton antiporter activity / phagosome maturation / sodium:proton antiporter activity / early phagosome / sodium ion import across plasma membrane / potassium ion transmembrane transport / regulation of intracellular pH / sodium ion transmembrane transport ...Defective SLC9A9 causes autism 16 (AUTS16) / Sodium/Proton exchangers / potassium:proton antiporter activity / phagosome maturation / sodium:proton antiporter activity / early phagosome / sodium ion import across plasma membrane / potassium ion transmembrane transport / regulation of intracellular pH / sodium ion transmembrane transport / recycling endosome / phagocytic vesicle membrane / recycling endosome membrane / late endosome membrane / early endosome membrane / early endosome / defense response to bacterium / 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsHansen JS / Pike ACW / Chi G / Wolf G / Ingles-Prieto A / Tranberg-Jensen J / Ye M / Speedman D / Goericke F / Sauer DB ...Hansen JS / Pike ACW / Chi G / Wolf G / Ingles-Prieto A / Tranberg-Jensen J / Ye M / Speedman D / Goericke F / Sauer DB / Beck H / Superti-Furga G / Huber KVM
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Innovative Medicines Initiative777372 Switzerland
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Structure of human NHE9
Authors: Hansen JS / Pike ACW / Chi G / Wolf G / Ingles-Prieto A / Tranberg-Jensen J / Ye M / Speedman D / Goericke F / Sauer DB / Beck H / Superti-Furga G / Huber KVM
History
DepositionMay 16, 2025-
Header (metadata) releaseSep 16, 2026-
Map releaseSep 16, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53827.png

Downloads & links

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Map

FileDownload / File: emd_53827.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal cryoSPARC non-uniform refinement map sharpened with a Bfactor of -25
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 280.435 Å		1.1 Å/pix.
x 256 pix.
= 280.435 Å		1.1 Å/pix.
x 256 pix.
= 280.435 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09545 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.7160907 - 2.7815285
Average (Standard dev.)0.0028846217 (±0.061391667)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 280.4352 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53827_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_53827_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Final unsharpened cryoSPARC non-uniform refinement map

Fileemd_53827_additional_1.map
AnnotationFinal unsharpened cryoSPARC non-uniform refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Final autosharpened cryoSPARC non-uniform refinement map

Fileemd_53827_additional_2.map
AnnotationFinal autosharpened cryoSPARC non-uniform refinement map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Final cryoSPARC non-uniform refinement map halfmap1

Fileemd_53827_half_map_1.map
AnnotationFinal cryoSPARC non-uniform refinement map halfmap1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Final cryoSPARC non-uniform refinement map halfmap2

Fileemd_53827_half_map_2.map
AnnotationFinal cryoSPARC non-uniform refinement map halfmap2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NHE9 homodimer

EntireName: NHE9 homodimer
Components
  • Complex: NHE9 homodimer
    • Protein or peptide: Sodium/hydrogen exchanger 9
  • Ligand: SODIUM ION
  • Ligand: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: water

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Supramolecule #1: NHE9 homodimer

SupramoleculeName: NHE9 homodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Homodimer
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 160.1525 KDa

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Macromolecule #1: Sodium/hydrogen exchanger 9

MacromoleculeName: Sodium/hydrogen exchanger 9 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 80.144867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MERQSRVMSE KDEYQFQHQG AVELLVFNFL LILTILTIWL FKNHRFRFLH ETGGAMVYGL IMGLILRYAT APTDIESGTV YDCVKLTFS PSTLLVNITD QVYEYKYKRE ISQHNINPHQ GNAILEKMTF DPEIFFNVLL PPIIFHAGYS LKKRHFFQNL G SILTYAFL ...String:
MERQSRVMSE KDEYQFQHQG AVELLVFNFL LILTILTIWL FKNHRFRFLH ETGGAMVYGL IMGLILRYAT APTDIESGTV YDCVKLTFS PSTLLVNITD QVYEYKYKRE ISQHNINPHQ GNAILEKMTF DPEIFFNVLL PPIIFHAGYS LKKRHFFQNL G SILTYAFL GTAISCIVIG LIMYGFVKAM IHAGQLKNGD FHFTDCLFFG SLMSATDPVT VLAIFHELHV DPDLYTLLFG ES VLNDAVA IVLTYSISIY SPKENPNAFD AAAFFQSVGN FLGIFAGSFA MGSAYAIITA LLTKFTKLCE FPMLETGLFF LLS WSAFLS AEAAGLTGIV AVLFCGVTQA HYTYNNLSSD SKIRTKQLFE FMNFLAENVI FCYMGLALFT FQNHIFNALF ILGA FLAIF VARACNIYPL SFLLNLGRKQ KIPWNFQHMM MFSGLRGAIA FALAIRNTES QPKQMMFTTT LLLVFFTVWV FGGGT TPML TWLQIRVGVD LDENLKEDPS SQHQEANNLD KNMTKAESAR LFRMWYSFDH KYLKPILTHS GPPLTTTLPE WCGPIS RLL TSPQAYGEQL KEDDVECIVN QDELAINYQE QASSPCSPPA RLGLDQKASP QTPGKENIYE GDLGLGGYEL KLEQTLG QS QLNDPAFLYK VVDIKAADIT SLYKKVGWSH PQFEKGGGSG GGSGGGSWSH PQFEKGTELG STMASYPYDV PDYA

UniProtKB: Sodium/hydrogen exchanger 9

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #3: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

MacromoleculeName: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 3 / Number of copies: 4 / Formula: PC1
Molecular weightTheoretical: 790.145 Da
Chemical component information

ChemComp-PC1:
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / phospholipid*YM

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Macromolecule #4: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 4 / Number of copies: 6 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 14 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
200.0 mMNaClSodium chloride
0.015 w/vC24H46O11Dodecylmaltoside
0.0015 w/vC31H50O4Cholesteryl hemisuccinate

Details: 20 mM HEPES pH 7.5; 200 mM NaCl; 0.015% DDM/ 0.0015% CHS;
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Sample vol 3ul; blot force -5; Blot time 7s; Wait time 30sec.
Detailsmonodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 11504 / Average exposure time: 2.93 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 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

DetailsEER movies were fractioned into 50 frames and motion-corrected in RELION using 5 x 5 patches
Particle selectionNumber selected: 1690899
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab-initio model from cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Details: Final refinement using non-uniform refinement / Number images used: 212666
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final 3D classificationNumber classes: 10 / Avg.num./class: 306503 / Software - Name: cryoSPARC (ver. 3.3.1)
Details: Final 3D classification in RELION without alignment using a protein-only mask.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

ivb4


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
DetailsInitial model fitted and manually rebuilt/refined in COOT and final refinement in ISOLDE and PHENIX
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9r8j:
Structure of human NHE9

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