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- PDB-9s8d: Cryo-EM structure of Rat NHE6 in detergent -

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Basic information

Entry
Database: PDB / ID: 9s8d
TitleCryo-EM structure of Rat NHE6 in detergent
ComponentsSodium/hydrogen exchanger 6
KeywordsTRANSPORT PROTEIN / Na+/H+ exchanger / Nhe6
Function / homology: / Chem-LPP
Function and homology information
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 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. / Reichenbach, T. / Kokane, S. / 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: Additional map / Part number: 1 / Data content type: Additional map / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)160,8798
Polymers157,7532
Non-polymers3,1266
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 "B"
d_2ens_1chain "A"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERTYRTYRBA72 - 61172 - 611
d_12LPPLPPLPPLPPBC801
d_13A1JMMA1JMMA1JMMA1JMMBD802
d_21SERSERTYRTYRAB72 - 61172 - 611
d_22LPPLPPLPPLPPAF801
d_23A1JMMA1JMMA1JMMA1JMMAG802

NCS oper: (Code: givenMatrix: (-0.999999998917, 3.96131759921E-5, 2.44432287057E-5), (-3.95902260687E-5, -0.999999559112, 0.000938194440607), (2.44803827904E-5, 0.000938193471878, 0.999999559597) ...NCS oper: (Code: given
Matrix: (-0.999999998917, 3.96131759921E-5, 2.44432287057E-5), (-3.95902260687E-5, -0.999999559112, 0.000938194440607), (2.44803827904E-5, 0.000938193471878, 0.999999559597)
Vector: 248.829553616, 248.720849597, -0.0961261584393)

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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)
#2: Chemical ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H69O8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / 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 Rat NHE6 / 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: 2300 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 56.87 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: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 256599 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 96.6 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00277832
ELECTRON MICROSCOPYf_angle_d0.481910616
ELECTRON MICROSCOPYf_chiral_restr0.03151230
ELECTRON MICROSCOPYf_plane_restr0.00461282
ELECTRON MICROSCOPYf_dihedral_angle_d12.05941128
Refine LS restraints NCSType: NCS constraints / Rms dev position: 1.56844412604E-12 Å

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