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- EMDB-53829: Structure of human NHE6.0 -

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Basic information

Entry
Database: EMDB / ID: EMD-53829
TitleStructure of human NHE6.0
Map dataAutosharpened cryoSPARC map after final non-uniform refinement. This map was used for real space refinement of model
Sample
  • Complex: NHE6.0 dimer
    • Protein or peptide: Isoform 1 of Sodium/hydrogen exchanger 6
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine
KeywordsNa/H exchanger / sodium transport / proton transport / endosome / MEMBRANE PROTEIN
Function / homology
Function and homology information


Defective SLC9A6 causes X-linked, syndromic mental retardation,, Christianson type (MRXSCH) / Sodium/Proton exchangers / dendrite extension / potassium:proton antiporter activity / axon extension / sodium:proton antiporter activity / sodium ion import across plasma membrane / establishment of cell polarity / neuron projection morphogenesis / potassium ion transmembrane transport ...Defective SLC9A6 causes X-linked, syndromic mental retardation,, Christianson type (MRXSCH) / Sodium/Proton exchangers / dendrite extension / potassium:proton antiporter activity / axon extension / sodium:proton antiporter activity / sodium ion import across plasma membrane / establishment of cell polarity / neuron projection morphogenesis / potassium ion transmembrane transport / regulation of intracellular pH / sodium ion transmembrane transport / recycling endosome / recycling endosome membrane / late endosome membrane / early endosome membrane / endoplasmic reticulum membrane / identical protein binding / 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 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 NHE6.0
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_53829.png

Downloads & links

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Map

FileDownload / File: emd_53829.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAutosharpened cryoSPARC map after final non-uniform refinement. This map was used for real space refinement of model
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 256 pix.
= 353.664 Å		1.38 Å/pix.
x 256 pix.
= 353.664 Å		1.38 Å/pix.
x 256 pix.
= 353.664 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3815 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.38
Minimum - Maximum-2.1375914 - 3.6028852
Average (Standard dev.)-0.00061465707 (±0.059831314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 353.664 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53829_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_53829_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Final cryoSPARC non-uniform refinement map (unsharpened)

Fileemd_53829_additional_1.map
AnnotationFinal cryoSPARC non-uniform refinement map (unsharpened)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap1 for final non-uniform refinement in cryosPARC

Fileemd_53829_half_map_1.map
Annotationhalfmap1 for final non-uniform refinement in cryosPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: halfmap2 for final non-uniform refinement in cryosPARC

Fileemd_53829_half_map_2.map
Annotationhalfmap2 for final non-uniform refinement in cryosPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NHE6.0 dimer

EntireName: NHE6.0 dimer
Components
  • Complex: NHE6.0 dimer
    • Protein or peptide: Isoform 1 of Sodium/hydrogen exchanger 6
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-Distearoyl-sn-glycerophosphoethanolamine

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Supramolecule #1: NHE6.0 dimer

SupramoleculeName: NHE6.0 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 163.34582 KDa

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Macromolecule #1: Isoform 1 of Sodium/hydrogen exchanger 6

MacromoleculeName: Isoform 1 of Sodium/hydrogen exchanger 6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.747586 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MARRGWRRAP LRRGVGSSPR ARRLMRPLWL LLAVGVFDWA GASDGGGGEA RAMDEEIVSE KQAEESHRQD SANLLIFILL LTLTILTIW LFKHRRARFL HETGLAMIYG LLVGLVLRYG IHVPSDVNNV TLSCEVQSSP TTLLVTFDPE VFFNILLPPI I FYAGYSLK ...String:
MARRGWRRAP LRRGVGSSPR ARRLMRPLWL LLAVGVFDWA GASDGGGGEA RAMDEEIVSE KQAEESHRQD SANLLIFILL LTLTILTIW LFKHRRARFL HETGLAMIYG LLVGLVLRYG IHVPSDVNNV TLSCEVQSSP TTLLVTFDPE VFFNILLPPI I FYAGYSLK RRHFFRNLGS ILAYAFLGTA ISCFVIGSIM YGCVTLMKVT GQLAGDFYFT DCLLFGAIVS ATDPVTVLAI FH ELQVDVE LYALLFGESV LNDAVAIVLS SSIVAYQPAG DNSHTFDVTA MFKSIGIFLG IFSGSFAMGA ATGVVTALVT KFT KLREFQ LLETGLFFLM SWSTFLLAEA WGFTGVVAVL FCGITQAHYT YNNLSTESQH RTKQLFELLN FLAENFIFSY MGLT LFTFQ NHVFNPTFVV GAFVAIFLGR AANIYPLSLL LNLGRRSKIG SNFQHMMMFA GLRGAMAFAL AIRDTATYAR QMMFS TTLL IVFFTVWVFG GGTTAMLSCL HIRVGVDSDQ EHLGVPENER RTTKAESAWL FRMWYNFDHN YLKPLLTHSG PPLTTT LPA CCGPIARCLT SPQAYENQEQ LKDDDSDLIL NDGDISLTYG DSTVNTEPAT SSAPRRFMGN SSEDALDREL AFGDHEL VI RGTRLVLPMD DSEPPLNLLD NTRHGPADPA FLYKVVDIKA ADITSLYKKV GWSHPQFEKG GGSGGGSGGG SWSHPQFE K GTELGSTMAS YPYDVPDYA

UniProtKB: Sodium/hydrogen exchanger 6

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Macromolecule #2: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #3: 1,2-Distearoyl-sn-glycerophosphoethanolamine

MacromoleculeName: 1,2-Distearoyl-sn-glycerophosphoethanolamine / type: ligand / ID: 3 / Number of copies: 4 / Formula: 3PE
Molecular weightTheoretical: 748.065 Da
Chemical component information

ChemComp-3PE:
1,2-Distearoyl-sn-glycerophosphoethanolamine / 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

Concentration4.2 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.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
DetailseBIC KriosIII
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 6700 / Average exposure time: 5.27 sec. / Average electron dose: 50.0 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: 2.4 µm / Nominal defocus min: 1.0 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

Particle selectionNumber selected: 1001670
Details: TOPAZ trained using classified CRYOLO-picked particles
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.1) / Details: Final non-uniform refinement in cryoSPARC / Number images used: 52384
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1) / Details: Non-uniform refinement
Final 3D classificationNumber classes: 10 / Avg.num./class: 199829 / Software - Name: RELION (ver. 4.0)
Details: Particles with statically classified in 3D using a protein-only mask in RELION. Particles were further filtered using CRYOSIEVE.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2581


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-9r8l:
Structure of human NHE6.0

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