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- PDB-9s8g: Cryo-EM structure of Rat NHE6 K351A variant -

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Basic information

Entry
Database: PDB / ID: 9s8g
TitleCryo-EM structure of Rat NHE6 K351A variant
ComponentsSodium/hydrogen exchanger 6
KeywordsTRANSPORT PROTEIN / NHE6 / Na+/H+ exchanger
Function / homology: / DIUNDECYL PHOSPHATIDYL CHOLINE
Function and homology information
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsJung, S. / Kokane, S. / Reichenbach, T. / Yeo, H. / 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. / Li, H. / ManhHo, T. / 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)160,7108
Polymers157,6372
Non-polymers3,0746
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: 78818.336 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-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-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
#4: Chemical ChemComp-PLC / DIUNDECYL PHOSPHATIDYL CHOLINE


Mass: 622.834 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H65NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
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 K351A 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: 58.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cry3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 148933 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 101.63 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00237024
ELECTRON MICROSCOPYf_angle_d0.40039508
ELECTRON MICROSCOPYf_chiral_restr0.03171110
ELECTRON MICROSCOPYf_plane_restr0.00311142
ELECTRON MICROSCOPYf_dihedral_angle_d9.4431008

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