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- PDB-9s8e: Cryo-EM structure of Rat NHE6 in nanodisc -

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Basic information

Entry
Database: PDB / ID: 9s8e
TitleCryo-EM structure of Rat NHE6 in nanodisc
ComponentsSodium/hydrogen exchanger 6
KeywordsTRANSPORT PROTEIN / Na+/H+ exchanger / Nhe6
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsYeo, H. / Jung, S. / Reichenbach, T. / Kokane, S. / Gulati, A. / 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


Theoretical massNumber of molelcules
Total (without water)157,7532
Polymers157,7532
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 72 - 587 / Label seq-ID: 72 - 587

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.999997041986, 0.00237305480108, 0.00053350762761), (-0.00237299490633, -0.999997178074, 0.000112870949958), (0.00053377397104, 0.000111604605202, 0.999999851315) ...NCS oper: (Code: given
Matrix: (-0.999997041986, 0.00237305480108, 0.00053350762761), (-0.00237299490633, -0.999997178074, 0.000112870949958), (0.00053377397104, 0.000111604605202, 0.999999851315)
Vector: 254.858710363, 255.464586253, -0.0737130593908)

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Components

#1: Protein Sodium/hydrogen exchanger 6


Mass: 78876.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slc9a6 / Production host: Homo sapiens (human)
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 Rat NHE6 in nanodisc / Type: COMPLEX / Entity ID: all / 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: 2300 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 63 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: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 127174 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 132.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027282
ELECTRON MICROSCOPYf_angle_d0.4249878
ELECTRON MICROSCOPYf_chiral_restr0.03141148
ELECTRON MICROSCOPYf_plane_restr0.00231206
ELECTRON MICROSCOPYf_dihedral_angle_d3.6383958
Refine LS restraints NCSType: NCS constraints / Rms dev position: 6.42929322494E-13 Å

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