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- PDB-9r8n: Structure of human NHE6.1 bound to PIP2 (core-TM domain) -

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Basic information

Entry
Database: PDB / ID: 9r8n
TitleStructure of human NHE6.1 bound to PIP2 (core-TM domain)
ComponentsIsoform 2 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-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE / Sodium/hydrogen exchanger 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.33 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 NHE6.1 bound to PIP2 (core-TM domain)
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 2 of Sodium/hydrogen exchanger 6
B: Isoform 2 of Sodium/hydrogen exchanger 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,09414
Polymers171,0162
Non-polymers7,07912
Water75742
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

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Protein / Sugars , 2 types, 6 molecules AB

#1: Protein Isoform 2 of Sodium/hydrogen exchanger 6 / Na(+)/H(+) exchanger 6 / NHE-6 / Solute carrier family 9 member 6


Mass: 85507.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A6, KIAA0267, NHE6 / Cell (production host): Jump In T-REx HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q92581
#3: 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

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Non-polymers , 5 types, 50 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#5: Chemical ChemComp-PCF / 1,2-DIACYL-SN-GLYCERO-3-PHOSHOCHOLINE


Mass: 734.039 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C40H80NO8P
#6: Chemical ChemComp-A1JDN / Dipalmitoyl Phosphatidylinositol 3,5-bisphosphate / [(2~{R})-2-hexadecanoyloxy-3-[oxidanyl-[(2~{R},3~{S},5~{R},6~{R})-2,4,6-tris(oxidanyl)-3,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate


Mass: 970.992 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H81O19P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: NHE6.1 homodimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.170856 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; 200mM NaCl; 0.015% DDM / 0.0015% CHS; 0.64mM PI(3,5)P2 (16:0)
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESC8H18N2O4S1
2200 mMSodium chlorideNaCl1
30.015 w/vDodecylmaltosideC24H46O111
40.0015 w/vCholesteryl hemisuccinateC31H50O41
50.64 mMPI(3,5)P2 diC16C41H76Na5O19P31
SpecimenConc.: 5 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
Details: Sample vol 3ul; blot force -5; Blot time 9s; Wait time 20sec

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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 magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.7 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: 9002
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
11PHENIX1.21.1_5286model refinement
12cryoSPARC3.3.1initial Euler assignment
13cryoSPARC3.3.1final Euler assignment
14cryoSPARC3.3.1classification
15cryoSPARC3.3.13D reconstruction
Image processingDetails: Movies were patch motioncorrected in cryoSPARC
CTF correctionDetails: Patch CTF in cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1090375
Details: Blob picked particles from a subset of micrographs were used to train a TOPAZ model for picking
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153800 / Algorithm: FOURIER SPACE
Details: cryoSPARC non-uniform refinement of CROSIEVED particles
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: 52.36 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00378288
ELECTRON MICROSCOPYf_angle_d0.639311218
ELECTRON MICROSCOPYf_chiral_restr0.03971310
ELECTRON MICROSCOPYf_plane_restr0.00541330
ELECTRON MICROSCOPYf_dihedral_angle_d13.13443130

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