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- EMDB-69357: Cryo-EM structure of human sodium/proton antiporter NHE1 in compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-69357
TitleCryo-EM structure of human sodium/proton antiporter NHE1 in complex with Zoniporide in an outward-open conformation
Map data
Sample
  • Complex: NHE1
    • Protein or peptide: Sodium/hydrogen exchanger 1
  • Ligand: Zoniporide
  • Ligand: 1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE]
  • Ligand: SODIUM ION
  • Ligand: water
Keywordssodium/proton antiporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of the force of heart contraction by cardiac conduction / positive regulation of mitochondrial membrane permeability / Sodium/Proton exchangers / cation-transporting ATPase complex / Hyaluronan degradation / cellular response to electrical stimulus / regulation of cardiac muscle cell membrane potential / regulation of pH / positive regulation of action potential / hyaluronan catabolic process ...regulation of the force of heart contraction by cardiac conduction / positive regulation of mitochondrial membrane permeability / Sodium/Proton exchangers / cation-transporting ATPase complex / Hyaluronan degradation / cellular response to electrical stimulus / regulation of cardiac muscle cell membrane potential / regulation of pH / positive regulation of action potential / hyaluronan catabolic process / maintenance of cell polarity / positive regulation of calcineurin-NFAT signaling cascade / sodium:proton antiporter activity / cellular response to cold / sodium ion export across plasma membrane / protein phosphatase 2B binding / regulation of stress fiber assembly / intracellular sodium ion homeostasis / response to acidic pH / sodium ion import across plasma membrane / regulation of focal adhesion assembly / regulation of cardiac muscle contraction by calcium ion signaling / positive regulation of cardiac muscle hypertrophy / cellular response to antibiotic / cardiac muscle cell contraction / positive regulation of the force of heart contraction / response to muscle stretch / protein complex oligomerization / intercalated disc / cellular response to acidic pH / proton transmembrane transport / phosphatidylinositol-4,5-bisphosphate binding / cellular response to epinephrine stimulus / T-tubule / regulation of intracellular pH / sodium ion transmembrane transport / cellular response to mechanical stimulus / phospholipid binding / calcium-dependent protein binding / cellular response to insulin stimulus / cell migration / positive regulation of cell growth / lamellipodium / cell differentiation / cellular response to hypoxia / basolateral plasma membrane / molecular adaptor activity / protein-macromolecule adaptor activity / 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 / extracellular exosome / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsCong Y / Kong F / Zhu A / Yan C
Funding support China, 1 items
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, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_69357.png

Downloads & links

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Map

FileDownload / File: emd_69357.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 256 pix.
= 281.062 Å		1.1 Å/pix.
x 256 pix.
= 281.062 Å		1.1 Å/pix.
x 256 pix.
= 281.062 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3
Minimum - Maximum-4.718516 - 7.201514
Average (Standard dev.)0.00216742 (±0.12407932)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 281.0624 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_69357_msk_1.map
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Half map: #1

Fileemd_69357_half_map_1.map
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Half map: #2

Fileemd_69357_half_map_2.map
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Sample components

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Entire : NHE1

EntireName: NHE1
Components
  • Complex: NHE1
    • Protein or peptide: Sodium/hydrogen exchanger 1
  • Ligand: Zoniporide
  • Ligand: 1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE]
  • Ligand: SODIUM ION
  • Ligand: water

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Supramolecule #1: NHE1

SupramoleculeName: NHE1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sodium/hydrogen exchanger 1

MacromoleculeName: Sodium/hydrogen exchanger 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 90.866766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVLRSGICGL SPHRIFPSLL VVVALVGLLP VLRSHGLQLS PTASTIRSSE PPRERSIGDV TTAPPEVTPE SRPVNHSVTD HGMKPRKAF PVLGIDYTHV RTPFEISLWI LLACLMKIGF HVIPTISSIV PESCLLIVVG LLVGGLIKGV GETPPFLQSD V FFLFLLPP ...String:
MVLRSGICGL SPHRIFPSLL VVVALVGLLP VLRSHGLQLS PTASTIRSSE PPRERSIGDV TTAPPEVTPE SRPVNHSVTD HGMKPRKAF PVLGIDYTHV RTPFEISLWI LLACLMKIGF HVIPTISSIV PESCLLIVVG LLVGGLIKGV GETPPFLQSD V FFLFLLPP IILDAGYFLP LRQFTENLGT ILIFAVVGTL WNAFFLGGLM YAVCLVGGEQ INNIGLLDNL LFGSIISAVD PV AVLAVFE EIHINELLHI LVFGESLLND AVTVVLYHLF EEFANYEHVG IVDIFLGFLS FFVVALGGVL VGVVYGVIAA FTS RFTSHI RVIEPLFVFL YSYMAYLSAE LFHLSGIMAL IASGVVMRPY VEANISHKSH TTIKYFLKMW SSVSETLIFI FLGV STVAG SHHWNWTFVI STLLFCLIAR VLGVLGLTWF INKFRIVKLT PKDQFIIAYG GLRGAIAFSL GYLLDKKHFP MCDLF LTAI ITVIFFTVFV QGMTIRPLVD LLAVKKKQET KRSINEEIHT QFLDHLLTGI EDICGHYGHH HWKDKLNRFN KKYVKK CLI AGERSKEPQL IAFYHKMEMK QAIELVESGG MGKIPSAVST VSMQNIHPKS LPSERILPAL SKDKEEEIRK ILRNNLQ KT RQRLRSYNRH TLVADPYEEA WNQMLLRRQK ARQLEQKINN YLTVPAHKLD SPTMSRARIG SDPLAYEPKE DLPVITID P ASPQSPESVD LVNEELKGKV LGLSRDPAKV AEEDEDDDGG IMMRSKETSS PGTDDVFTPA PSDSPSSQRI QRCLSDPGP HPEPGEGEPF FPKGQ

UniProtKB: Sodium/hydrogen exchanger 1

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Macromolecule #2: Zoniporide

MacromoleculeName: Zoniporide / type: ligand / ID: 2 / Number of copies: 2 / Formula: A1E6C
Molecular weightTheoretical: 320.349 Da

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Macromolecule #3: 1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE]

MacromoleculeName: 1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE] / type: ligand / ID: 3 / Number of copies: 3 / Formula: PS1
Molecular weightTheoretical: 566.642 Da
Chemical component information

ChemComp-PS1:
1,2-DIDECANOYL-SN-GLYCERO-3-[PHOSPHO-L-SERINE]

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 9 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 397056
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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