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- PDB-9r8k: Structure of human NHE9 (core-TM domain) -

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Basic information

Entry
Database: PDB / ID: 9r8k
TitleStructure of human NHE9 (core-TM domain)
ComponentsSodium/hydrogen exchanger 9
KeywordsMEMBRANE PROTEIN / Na/H exchanger / sodium transport / proton transport / endosome
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
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Sodium/hydrogen exchanger 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 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 NHE9 (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: Sodium/hydrogen exchanger 9
B: Sodium/hydrogen exchanger 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,56014
Polymers160,2902
Non-polymers6,27012
Water25214
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 9 / Na(+)/H(+) exchanger 9 / NHE-9 / Solute carrier family 9 member 9


Mass: 80144.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A9, NHE9, Nbla00118 / Plasmid: CE02MG-X / Cell (production host): Jump In T-REx HEK 293 / Cell line (production host): HEK-SLC9A9-WTOE-p1 / Production host: Homo sapiens (human) / References: UniProt: Q8IVB4
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 790.145 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#4: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
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: NHE9 homodimer / Type: COMPLEX / Details: Homodimer / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.1601525 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.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: monodisperse
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
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 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: 2.93 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: 11504
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: EER movies were fractioned into 50 frames and motion-corrected in RELION using 5 x 5 patches
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1690899
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69556 / Algorithm: FOURIER SPACE
Details: Final non-uniform refinement of cryosieved particles for highest resolution map for core TM domain
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: Q8IVB4 / Source name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 63.03 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00267266
ELECTRON MICROSCOPYf_angle_d0.53539822
ELECTRON MICROSCOPYf_chiral_restr0.03661124
ELECTRON MICROSCOPYf_plane_restr0.0051176
ELECTRON MICROSCOPYf_dihedral_angle_d12.19772692

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