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- PDB-9s8c: Cryo-EM structure of Rat NHE6 D293A variant -

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Basic information

Entry
Database: PDB / ID: 9s8c
TitleCryo-EM structure of Rat NHE6 D293A variant
ComponentsSodium/hydrogen exchanger 6
KeywordsTRANSPORT PROTEIN / Na+/H+ exchanger / NHE6
Function / homology: / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / Chem-PIO / Chem-POV
Function and homology information
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.28 Å
AuthorsJung, S. / Gulati, A. / Reichenbach, T. / Kokane, S. / Yeo, H. / Drew, D.
Funding supportEuropean Union, Sweden, 2items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: To Be Published
Title: Structure of NHE6 and its lipid-mediated interactions regulating endosomal pH
Authors: Jung, S. / Yeo, H. / Kokane, S. / Reichenbach, T. / Gulati, A. / Albano, G. / Kirschbaum, C. / Manh Ho, T. / Li, H. / Landreh, M. / Abramsson, M. / Robinson, C. / Fuster, D. / Drew, D.
History
DepositionAug 5, 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: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)163,94810
Polymers157,6652
Non-polymers6,2838
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


Mass: 78832.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slc9a6, Slc9a6_predicted, rCG_39230 / Production host: Homo sapiens (human)
#2: Chemical ChemComp-A1JMM / [(2~{S})-2-hexadecanoyloxy-3-[oxidanyl-[(1~{S},2~{R},3~{S},4~{S},5~{R},6~{R})-2,3,4,6-tetrakis(oxidanyl)-5-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate


Mass: 891.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H80O16P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-POV / (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#4: Chemical ChemComp-PEE / 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine / DOPE


Mass: 744.034 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: DOPE, phospholipid*YM
#5: Chemical ChemComp-PIO / [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate / dioctanoyl l-alpha-phosphatidyl-d-myo-inositol 4,5-diphosphate


Mass: 746.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49O19P3 / Feature type: SUBJECT OF INVESTIGATION
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: Dimeric structure of Rat NHE6 D293A variant / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Rattus norvegicus (Norway rat)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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: 2000 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 53 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 767151 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 115.49 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048076
ELECTRON MICROSCOPYf_angle_d0.594710930
ELECTRON MICROSCOPYf_chiral_restr0.0361258
ELECTRON MICROSCOPYf_plane_restr0.00311298
ELECTRON MICROSCOPYf_dihedral_angle_d16.61011346

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