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- EMDB-67827: Human NHA1 in an inward-open conformation -

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Basic information

Entry
Database: EMDB / ID: EMD-67827
TitleHuman NHA1 in an inward-open conformation
Map data
Sample
  • Complex: Human NHA1 in outward open conformation
    • Protein or peptide: Sodium/hydrogen exchanger 9B1
Keywordstransporter / CPA / sodium / membrane protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


sodium:proton antiporter activity / sperm principal piece / flagellated sperm motility / regulation of intracellular pH / transmembrane transport / Stimuli-sensing channels / monoatomic ion transmembrane transport / plasma membrane / cytosol
Similarity search - Function
: / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane
Similarity search - Domain/homology
Sodium/hydrogen exchanger 9B1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.64 Å
AuthorsTang B / Dang S
Funding support Hong Kong, 5 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC)GRF16103321 Hong Kong
The University Grants Committee, Research Grants Council (RGC)GRF16102822 Hong Kong
The University Grants Committee, Research Grants Council (RGC)GRF16100223 Hong Kong
The University Grants Committee, Research Grants Council (RGC)C6001-21E Hong Kong
The University Grants Committee, Research Grants Council (RGC)C6012-22G Hong Kong
CitationJournal: To Be Published
Title: Cryo-EM Structure of Human Na+/H+ Exchanger NHA1 in an Inward-open Conformation
Authors: Tang B / Dang S
History
DepositionDec 19, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_67827.png

Downloads & links

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Map

FileDownload / File: emd_67827.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å		1.06 Å/pix.
x 256 pix.
= 271.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.54
Minimum - Maximum-2.2206707 - 2.6994767
Average (Standard dev.)0.003525902 (±0.062686585)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 271.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_67827_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_67827_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human NHA1 in outward open conformation

EntireName: Human NHA1 in outward open conformation
Components
  • Complex: Human NHA1 in outward open conformation
    • Protein or peptide: Sodium/hydrogen exchanger 9B1

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Supramolecule #1: Human NHA1 in outward open conformation

SupramoleculeName: Human NHA1 in outward open conformation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Sodium/hydrogen exchanger 9B1

MacromoleculeName: Sodium/hydrogen exchanger 9B1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.100184 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MHTTESKNEH LEDENFQTST TPQSLIDPNN TAQEETKTVL SDTEEIKPQT KKETYISCPL RGVLNVIITN GVILFVIWCM TWSILGSEA LPGGNLFGLF IIFYSAIIGG KILQLIRIPL VPPLPPLLGM LLAGFTIRNV PFINEHVHVP NTWSSILRSI A LTIILIRA ...String:
MHTTESKNEH LEDENFQTST TPQSLIDPNN TAQEETKTVL SDTEEIKPQT KKETYISCPL RGVLNVIITN GVILFVIWCM TWSILGSEA LPGGNLFGLF IIFYSAIIGG KILQLIRIPL VPPLPPLLGM LLAGFTIRNV PFINEHVHVP NTWSSILRSI A LTIILIRA GLGLDPQALR HLKVVCFRLA VGPCLMEASA AAVFSHFIMK FPWQWAFLLG FVLGAVSPAV VVPYMMVLQE NG YGVEEGI PTLLMAASSM DDILAITGFN TCLSIVFSSG GILNNAIASI RNVCISLLAG IVLGFFVRYF PSEDQKKLTL KRG FLVLTM CVSAVLGSQR IGLHGSGGLC TLVLSFIAGT KWSQEKMKVQ KIITTVWDIF QPLLFGLVGA EVSVSSLESN IVGI SVATL SLALCVRILT TYLLMCFAGF SFKEKIFIAL AWMPKATVQA VLGPLALETA RVSAPHLEPY AKDVMTVAFL AILIT APNG ALLMGILGPK MLTRHYDPSK IKLQLSTLEH H

UniProtKB: Sodium/hydrogen exchanger 9B1

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (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: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 270161
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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