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- PDB-6z3z: CryoEM structure of horse sodium/proton exchanger NHE9 without C-... -

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Basic information

Entry
Database: PDB / ID: 6z3z
TitleCryoEM structure of horse sodium/proton exchanger NHE9 without C-terminal regulatory domain in an inward-facing conformation
ComponentsSodium/hydrogen exchanger
KeywordsMEMBRANE PROTEIN / TRANSPORT PROTEIN
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
Sodium/hydrogen exchanger 9
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsWinkelmann, I. / Matsuoka, R. / Meier, P. / Drew, D.
CitationJournal: EMBO J / Year: 2020
Title: Structure and elevator mechanism of the mammalian sodium/proton exchanger NHE9.
Authors: Iven Winklemann / Rei Matsuoka / Pascal F Meier / Denis Shutin / Chenou Zhang / Laura Orellana / Ricky Sexton / Michael Landreh / Carol V Robinson / Oliver Beckstein / David Drew /
Abstract: Na /H exchangers (NHEs) are ancient membrane-bound nanomachines that work to regulate intracellular pH, sodium levels and cell volume. NHE activities contribute to the control of the cell cycle, cell ...Na /H exchangers (NHEs) are ancient membrane-bound nanomachines that work to regulate intracellular pH, sodium levels and cell volume. NHE activities contribute to the control of the cell cycle, cell proliferation, cell migration and vesicle trafficking. NHE dysfunction has been linked to many diseases, and they are targets of pharmaceutical drugs. Despite their fundamental importance to cell homeostasis and human physiology, structural information for the mammalian NHE was lacking. Here, we report the cryogenic electron microscopy structure of NHE isoform 9 (SLC9A9) from Equus caballus at 3.2 Å resolution, an endosomal isoform highly expressed in the brain and associated with autism spectrum (ASD) and attention deficit hyperactivity (ADHD) disorders. Despite low sequence identity, the NHE9 architecture and ion-binding site are remarkably similar to distantly related bacterial Na /H  antiporters with 13 transmembrane segments. Collectively, we reveal the conserved architecture of the NHE ion-binding site, their elevator-like structural transitions, the functional implications of autism disease mutations and the role of phosphoinositide lipids to promote homodimerization that, together, have important physiological ramifications.
History
DepositionMay 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 13, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Mar 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.5May 22, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
B: Sodium/hydrogen exchanger
A: Sodium/hydrogen exchanger


Theoretical massNumber of molelcules
Total (without water)105,1442
Polymers105,1442
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3820 Å2
ΔGint-44 kcal/mol
Surface area37880 Å2
MethodPISA

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Components

#1: Protein Sodium/hydrogen exchanger


Mass: 52572.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 'GENLYFQ' in C terminal comes from Tag / Source: (gene. exp.) Equus caballus (horse) / Gene: SLC9A9 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: F7B113

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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: Sodium proton antiporter / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Equus caballus (horse)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Buffer component
IDConc.FormulaBuffer-ID
1150 mMNaCl1
220 mMTri-HCl1
30.003 %LMNG1
40.0006 %CHS1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1
VitrificationCryogen name: HELIUM

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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 magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 80 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV / Phase plate: ZERNIKE PHASE PLATE / Spherical aberration corrector: Nothing
Image scansWidth: 3710 / Height: 3838 / Movie frames/image: 40 / Used frames/image: 1-40

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3particle selection
2EPUimage acquisition
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 595024 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0026246
ELECTRON MICROSCOPYf_angle_d0.5838454
ELECTRON MICROSCOPYf_dihedral_angle_d13.322796
ELECTRON MICROSCOPYf_chiral_restr0.036976
ELECTRON MICROSCOPYf_plane_restr0.0041024

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