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- PDB-9r8l: Structure of human NHE6.0 -

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Basic information

Entry
Database: PDB / ID: 9r8l
TitleStructure of human NHE6.0
ComponentsIsoform 1 of Sodium/hydrogen exchanger 6
KeywordsMEMBRANE PROTEIN / Na/H exchanger / sodium transport / proton transport / endosome
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 / regulation of intracellular pH ...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 / regulation of intracellular pH / sodium ion transmembrane transport / recycling endosome / recycling endosome membrane / late endosome membrane / early endosome membrane / 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
1,2-Distearoyl-sn-glycerophosphoethanolamine / Sodium/hydrogen exchanger 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHansen, J.S. / Pike, A.C.W. / Chi, G. / Wolf, G. / Ingles-Prieto, A. / Tranberg-Jensen, J. / Ye, M. / Speedman, D. / Goericke, F. / Sauer, D.B. ...Hansen, J.S. / Pike, A.C.W. / Chi, G. / Wolf, G. / Ingles-Prieto, A. / Tranberg-Jensen, J. / Ye, M. / Speedman, D. / Goericke, F. / Sauer, D.B. / Beck, H. / Superti-Furga, G. / Huber, K.V.M.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Innovative Medicines Initiative777372 Switzerland
Innovative Medicines Initiative875510 Switzerland
CitationJournal: To Be Published
Title: Structure of human NHE6.0
Authors: Hansen, J.S. / Pike, A.C.W. / Chi, G. / Wolf, G. / Ingles-Prieto, A. / Tranberg-Jensen, J. / Ye, M. / Speedman, D. / Goericke, F. / Sauer, D.B. / Beck, H. / Superti-Furga, G. / Huber, K.V.M.
History
DepositionMay 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 1 of Sodium/hydrogen exchanger 6
B: Isoform 1 of Sodium/hydrogen exchanger 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,53010
Polymers163,4952
Non-polymers5,0358
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Isoform 1 of Sodium/hydrogen exchanger 6 / Na(+)/H(+) exchanger 6 / NHE-6 / Solute carrier family 9 member 6


Mass: 81747.586 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A6, KIAA0267, NHE6 / Plasmid: CE02KN-S / Cell (production host): Jump In T-REx HEK 293 / Cell line (production host): HEK-SLC9A6-WTOE-p1 / Production host: Homo sapiens (human) / References: UniProt: Q92581
#2: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#3: Chemical
ChemComp-3PE / 1,2-Distearoyl-sn-glycerophosphoethanolamine / 3-SN-PHOSPHATIDYLETHANOLAMINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 748.065 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C41H82NO8P / Comment: phospholipid*YM
Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: NHE6.0 dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.16334582 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.5
Details: 20 mM HEPES pH 7.5; 200 mM NaCl; 0.015% DDM / 0.0015% CHS
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2200 mMSodium chlorideNaCl1
30.015 w/vDodecylmaltosideC24H46O111
40.0015 w/vcholesteryl hemisuccinateC31H50O41
SpecimenConc.: 4.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: Sample vol 3ul; blot force -5; Blot time 7s; Wait time 30sec

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS / Details: eBIC KriosIII
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 5.27 sec. / Electron dose: 50 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6700
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1Topaz0.2.4particle selection
2cryoSPARC3.3.1particle selection
3EPUimage acquisition
5cryoSPARC3.3.1CTF correction
8Coot0.9.8.93model fitting
9ISOLDE1.3model fitting
11cryoSPARC3.3.1initial Euler assignment
12cryoSPARC3.3.1final Euler assignment
13RELION4classification
14cryoSPARC3.3.13D reconstruction
15PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1001670
Details: TOPAZ trained using classified CRYOLO-picked particles
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52384 / Algorithm: FOURIER SPACE / Details: Final non-uniform refinement in cryoSPARC / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: Initial model fitted and manually rebuilt/refined in COOT and final refinement in ISOLDE and PHENIX
Atomic model buildingAccession code: Q92581 / Source name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 64.56 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00438005
ELECTRON MICROSCOPYf_angle_d0.566110850
ELECTRON MICROSCOPYf_chiral_restr0.04041275
ELECTRON MICROSCOPYf_plane_restr0.00541310
ELECTRON MICROSCOPYf_dihedral_angle_d11.19862948

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