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- PDB-23xm: Cryo-EM structure of human sodium/proton antiporter NHE1 in compl... -

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Basic information

Entry
Database: PDB / ID: 23xm
TitleCryo-EM structure of human sodium/proton antiporter NHE1 in complex with Eniporide in an outward-open conformation
ComponentsSodium/hydrogen exchanger 1
KeywordsMEMBRANE PROTEIN / sodium/proton antiporter
Function / homology
Function and homology information


Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / cation-transporting ATPase complex / Hyaluronan degradation / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / potassium:proton antiporter activity / positive regulation of action potential / sodium:proton antiporter activity / hyaluronan catabolic process ...Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / cation-transporting ATPase complex / Hyaluronan degradation / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / potassium:proton antiporter activity / positive regulation of action potential / sodium:proton antiporter activity / hyaluronan catabolic process / maintenance of cell polarity / regulation of pH / positive regulation of calcineurin-NFAT signaling cascade / sodium ion export across plasma membrane / protein phosphatase 2B binding / intracellular sodium ion homeostasis / regulation of stress fiber assembly / cardiac muscle cell differentiation / sodium ion import across plasma membrane / positive regulation of mitochondrial membrane permeability / regulation of cardiac muscle contraction by calcium ion signaling / regulation of focal adhesion assembly / cardiac muscle cell contraction / response to acidic pH / cellular response to cold / positive regulation of cardiac muscle hypertrophy / positive regulation of the force of heart contraction / cellular response to antibiotic / protein complex oligomerization / intercalated disc / cellular response to acidic pH / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / monoatomic ion transport / cellular response to epinephrine stimulus / potassium ion transmembrane transport / T-tubule / proton transmembrane transport / stem cell differentiation / regulation of intracellular pH / cellular response to mechanical stimulus / phospholipid binding / cellular response to insulin stimulus / calcium-dependent protein binding / cell migration / lamellipodium / positive regulation of cell growth / cellular response to hypoxia / molecular adaptor activity / basolateral plasma membrane / protein-macromolecule adaptor activity / calmodulin binding / apical plasma membrane / positive regulation of apoptotic process / membrane raft / focal adhesion / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / nucleoplasm / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Sodium/hydrogen exchanger 1-like / Sodium/hydrogen exchanger, regulatory region / Regulatory region of Na+/H+ exchanger NHE binds to calmodulin / Na+/H+ exchanger / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane
Similarity search - Domain/homology
: / Sodium/hydrogen exchanger 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsCong, Y. / Kong, F. / Zhu, A. / Yan, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171204 China
CitationJournal: To Be Published
Title: Structure and transport mechanism of the human sodium/proton antiporter NHE1
Authors: Cong, Y. / Kong, F. / Zhu, A. / Yan, C.
History
DepositionFeb 24, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 8, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 8, 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
A: Sodium/hydrogen exchanger 1
B: Sodium/hydrogen exchanger 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,3744
Polymers181,7342
Non-polymers6412
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sodium/hydrogen exchanger 1 / APNH / Na(+)/H(+) antiporter / amiloride-sensitive / Na(+)/H(+) exchanger 1 / NHE-1 / Solute ...APNH / Na(+)/H(+) antiporter / amiloride-sensitive / Na(+)/H(+) exchanger 1 / NHE-1 / Solute carrier family 9 member 1


Mass: 90866.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A1, APNH1, NHE1 / Production host: Homo sapiens (human) / References: UniProt: P19634
#2: Chemical ChemComp-A1E6D / Eniporide


Mass: 320.367 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16N4O3S / 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: NHE1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
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: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
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: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.18_3855model refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179809 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0076824
ELECTRON MICROSCOPYf_angle_d0.729316
ELECTRON MICROSCOPYf_dihedral_angle_d10.01914
ELECTRON MICROSCOPYf_chiral_restr0.0731122
ELECTRON MICROSCOPYf_plane_restr0.0041124

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