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- PDB-8pvr: Cryo-EM structure of horse Nhe9 bound to PI(3,5)P2 -

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Basic information

Entry
Database: PDB / ID: 8pvr
TitleCryo-EM structure of horse Nhe9 bound to PI(3,5)P2
ComponentsSodium/hydrogen exchanger 9
KeywordsTRANSPORT PROTEIN / Na+/H+ exchanger / membrane protein / SLC9A9 / ion transporter / PI(3 / 5)P2
Function / homology
Function and homology information


potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / sodium ion transmembrane transport / potassium ion transmembrane transport / proton transmembrane transport / regulation of intracellular pH / recycling endosome / recycling endosome membrane / phagocytic vesicle membrane ...potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / sodium ion transmembrane transport / potassium ion transmembrane transport / proton transmembrane transport / regulation of intracellular pH / recycling endosome / recycling endosome membrane / phagocytic vesicle membrane / late endosome membrane / early endosome membrane / protein homodimerization activity / 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 family
Similarity search - Domain/homology
Chem-EUJ / Sodium/hydrogen exchanger 9
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsKokane, S. / Meier, P. / Gulati, A. / Delemotte, L. / Drew, D.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)CoG-820187European Union
CitationJournal: To Be Published
Title: PIP2 mediated oligomerization of the endosomal sodium/proton exchanger NHE9
Authors: Kokane, S. / Meier, P. / Gulati, A. / Matsuoka, R. / Pipatpolkai, T. / Delemotte, L. / Drew, D.
History
DepositionJul 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Sodium/hydrogen exchanger 9
A: Sodium/hydrogen exchanger 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,2054
Polymers129,7122
Non-polymers1,4932
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 9 / Na(+)/H(+) exchanger 9 / NHE-9 / Sodium/hydrogen exchanger / Solute carrier family 9 member 9


Mass: 64856.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: SLC9A9, NHE9 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: F7B113
#2: Chemical ChemComp-EUJ / (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,4,6-trihydroxy-3,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dioctanoate


Mass: 746.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H49O19P3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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 Horse Nhe9 with PI(3,5)P2 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.064 MDa / Experimental value: NO
Source (natural)Organism: Equus caballus (horse)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 8
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: FEI TITAN 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: 68.5 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78370 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028424
ELECTRON MICROSCOPYf_angle_d0.49111438
ELECTRON MICROSCOPYf_dihedral_angle_d4.451112
ELECTRON MICROSCOPYf_chiral_restr0.0361286
ELECTRON MICROSCOPYf_plane_restr0.0031406

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