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- EMDB-69359: Cryo-EM structure of human sodium/proton antiporter NHE1 in compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-69359
TitleCryo-EM structure of human sodium/proton antiporter NHE1 in complex with Eniporide in an outward-open conformation
Map data
Sample
  • Complex: NHE1
    • Protein or peptide: Sodium/hydrogen exchanger 1
  • Ligand: Eniporide
Keywordssodium/proton antiporter / MEMBRANE PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 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) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_69359.png

Downloads & links

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Map

FileDownload / File: emd_69359.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-3.169948 - 5.4262857
Average (Standard dev.)0.004836615 (±0.10332199)
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_69359_msk_1.map
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Half map: #1

Fileemd_69359_half_map_1.map
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Half map: #2

Fileemd_69359_half_map_2.map
Projections & Slices
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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: Eniporide

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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: Eniporide

MacromoleculeName: Eniporide / type: ligand / ID: 2 / Number of copies: 2 / Formula: A1E6D
Molecular weightTheoretical: 320.367 Da

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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: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 179809
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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