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- PDB-9s0s: Cryo-EM structure of human NHE6 in C2 symmetry -

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Basic information

Entry
Database: PDB / ID: 9s0s
TitleCryo-EM structure of human NHE6 in C2 symmetry
ComponentsSodium/hydrogen exchanger 6
KeywordsTRANSPORT PROTEIN / NHE / C2 symmetry / homodimer / transporter
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 / sodium:proton antiporter activity / axon extension / 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 / sodium:proton antiporter activity / axon extension / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsFeilen, L.P. / Sach, L. / Tranchant, E.E. / Lalic, M.R. / Havelund, J.F. / Brauer, C.M. / Ginsthofer, M. / Ostendorf, J. / Ma, L. / Morrow, E.M. ...Feilen, L.P. / Sach, L. / Tranchant, E.E. / Lalic, M.R. / Havelund, J.F. / Brauer, C.M. / Ginsthofer, M. / Ostendorf, J. / Ma, L. / Morrow, E.M. / Faergeman, N.J. / Pedersen, S.F. / Kragelund, B.B. / Autzen, H.E.
Funding support Denmark, European Union, 5items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF20OC0060692 Denmark
The Carlsberg FoundationCF20-0533 Denmark
Independent Research Fund Denmark - Medical Sciences1131-00023B Denmark
European Research Council (ERC)101151923European Union
Danish Council for Independent Research3103-00217B Denmark
CitationJournal: To Be Published
Title: Integrative structural analysis of the human endosomal Na/H exchanger NHE6 reveals lipid-modulated gating of the ion-binding site
Authors: Feilen, L.P. / Sach, L. / Tranchant, E.E. / Lalic, M.R. / Havelund, J.F. / Brauer, C.M. / Ginsthofer, M. / Ostendorf, J. / Ma, L. / Morrow, E.M. / Faergeman, N.J. / Pedersen, S.F. / ...Authors: Feilen, L.P. / Sach, L. / Tranchant, E.E. / Lalic, M.R. / Havelund, J.F. / Brauer, C.M. / Ginsthofer, M. / Ostendorf, J. / Ma, L. / Morrow, E.M. / Faergeman, N.J. / Pedersen, S.F. / Kragelund, B.B. / Autzen, H.E.
History
DepositionJul 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 29, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium/hydrogen exchanger 6
B: Sodium/hydrogen exchanger 6


Theoretical massNumber of molelcules
Total (without water)155,9772
Polymers155,9772
Non-polymers00
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 Sodium/hydrogen exchanger 6 / Na(+)/H(+) exchanger 6 / NHE-6 / Solute carrier family 9 member 6


Mass: 77988.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A6, KIAA0267, NHE6 / Production host: Homo sapiens (human) / References: UniProt: Q92581
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: Homodimeric human NHE6 in C2 symmetry / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mM2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acidHEPES1
2150 mMsodium chlorideNaCl1
30.034 mMglyco-diosgeninGDN1
40.008 mMcholesteryl hemisuccinate Tris saltCHS1
SpecimenConc.: 2.63 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 49 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 4933
EM imaging opticsEnergyfilter name: TFS Selectris X

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Processing

EM software
IDNameVersionCategory
1RELION5.0-betaparticle selection
2EPUimage acquisition
4RELION5.0-betaCTF correction
9RELION5.0-betainitial Euler assignment
10RELION5.0-betafinal Euler assignment
12RELION5.0-beta3D reconstruction
19PHENIX1.21.1_5286model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 732718
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88691 / Num. of class averages: 1 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027248
ELECTRON MICROSCOPYf_angle_d0.4279832
ELECTRON MICROSCOPYf_dihedral_angle_d3.128952
ELECTRON MICROSCOPYf_chiral_restr0.0341142
ELECTRON MICROSCOPYf_plane_restr0.0031200

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