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- EMDB-13162: Cryo EM structure of bison NHA2 in nano disc structure -

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Basic information

Entry
Database: EMDB / ID: EMD-13162
TitleCryo EM structure of bison NHA2 in nano disc structure
Map data
Sample
  • Complex: detergent structure
    • Protein or peptide: mitochondrial sodium/hydrogen exchanger 9B2
KeywordsMembrane protein Sodium proton transporter / TRANSPORT PROTEIN
Function / homology
Function and homology information


lithium:proton antiporter activity / lithium ion transport / positive regulation of osteoclast development / sperm principal piece / sodium ion homeostasis / sodium:proton antiporter activity / regulation of insulin secretion involved in cellular response to glucose stimulus / clathrin-dependent endocytosis / flagellated sperm motility / sodium ion transport ...lithium:proton antiporter activity / lithium ion transport / positive regulation of osteoclast development / sperm principal piece / sodium ion homeostasis / sodium:proton antiporter activity / regulation of insulin secretion involved in cellular response to glucose stimulus / clathrin-dependent endocytosis / flagellated sperm motility / sodium ion transport / recycling endosome / mitochondrial membrane / recycling endosome membrane / synaptic vesicle membrane / basolateral plasma membrane / endosome membrane / apical plasma membrane / lysosomal membrane / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
: / Sodium/solute symporter superfamily / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane
Similarity search - Domain/homology
Sodium/hydrogen exchanger 9B2
Similarity search - Component
Biological speciesBison bison (American bison)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsMatsuoka R / Fudim R
Citation
Journal: Nat Struct Mol Biol / Year: 2022
Title: Structure, mechanism and lipid-mediated remodeling of the mammalian Na/H exchanger NHA2.
Authors: Rei Matsuoka / Roman Fudim / Sukkyeong Jung / Chenou Zhang / Andre Bazzone / Yurie Chatzikyriakidou / Carol V Robinson / Norimichi Nomura / So Iwata / Michael Landreh / Laura Orellana / ...Authors: Rei Matsuoka / Roman Fudim / Sukkyeong Jung / Chenou Zhang / Andre Bazzone / Yurie Chatzikyriakidou / Carol V Robinson / Norimichi Nomura / So Iwata / Michael Landreh / Laura Orellana / Oliver Beckstein / David Drew /
Abstract: The Na/H exchanger SLC9B2, also known as NHA2, correlates with the long-sought-after Na/Li exchanger linked to the pathogenesis of diabetes mellitus and essential hypertension in humans. Despite the ...The Na/H exchanger SLC9B2, also known as NHA2, correlates with the long-sought-after Na/Li exchanger linked to the pathogenesis of diabetes mellitus and essential hypertension in humans. Despite the functional importance of NHA2, structural information and the molecular basis for its ion-exchange mechanism have been lacking. Here we report the cryo-EM structures of bison NHA2 in detergent and in nanodiscs, at 3.0 and 3.5 Å resolution, respectively. The bison NHA2 structure, together with solid-state membrane-based electrophysiology, establishes the molecular basis for electroneutral ion exchange. NHA2 consists of 14 transmembrane (TM) segments, rather than the 13 TMs previously observed in mammalian Na/H exchangers (NHEs) and related bacterial antiporters. The additional N-terminal helix in NHA2 forms a unique homodimer interface with a large intracellular gap between the protomers, which closes in the presence of phosphoinositol lipids. We propose that the additional N-terminal helix has evolved as a lipid-mediated remodeling switch for the regulation of NHA2 activity.
#1: Journal: Nat.Struct.Mol.Biol. / Year: 2022
Title: Structure, mechanism and lipid-mediated remodeling of the mammalian Na+/H+ exchanger NHA2
Authors: Matsuoka R / Fudim F / Jung S / Drew F
History
DepositionJul 1, 2021-
Header (metadata) releaseJan 26, 2022-
Map releaseJan 26, 2022-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7p1j
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13162.png

Downloads & links

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Map

FileDownload / File: emd_13162.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 240 pix.
= 249. Å		1.04 Å/pix.
x 240 pix.
= 249. Å		1.04 Å/pix.
x 240 pix.
= 249. Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.014
Minimum - Maximum-0.03309723 - 0.060427576
Average (Standard dev.)0.000047691283 (±0.00173487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.03751.03751.0375
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z249.000249.000249.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ512512512
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0330.0600.000

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Supplemental data

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Mask #1

Fileemd_13162_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_13162_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_13162_half_map_2.map
Projections & Slices
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Sample components

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Entire : detergent structure

EntireName: detergent structure
Components
  • Complex: detergent structure
    • Protein or peptide: mitochondrial sodium/hydrogen exchanger 9B2

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Supramolecule #1: detergent structure

SupramoleculeName: detergent structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Bison bison (American bison)
Molecular weightTheoretical: 57373 kDa/nm

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Macromolecule #1: mitochondrial sodium/hydrogen exchanger 9B2

MacromoleculeName: mitochondrial sodium/hydrogen exchanger 9B2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bison bison (American bison)
Molecular weightTheoretical: 57.419203 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MRNQDKRAAH KDSEPSTEVN HTASSYQGRQ QETGMNLRGI DGNEPTEGSN LLNNNEKMQG TPAEPNHLQR RRQIHACPPR GLLARVITN VTMVILLWAV VWSVTGSECL PGGNLFGIIM LFYCAIIGGK LFGLIKLPTL PPLPPLLGML LAGFLIRNVP V ISDNIQIK ...String:
MRNQDKRAAH KDSEPSTEVN HTASSYQGRQ QETGMNLRGI DGNEPTEGSN LLNNNEKMQG TPAEPNHLQR RRQIHACPPR GLLARVITN VTMVILLWAV VWSVTGSECL PGGNLFGIIM LFYCAIIGGK LFGLIKLPTL PPLPPLLGML LAGFLIRNVP V ISDNIQIK HKWSSALRSI ALSVILVRAG LGLDSNALKK LKGVCVRLSL GPCLIEACTS AVLAYFLMGL PWQWGFMLGF VL GAVSPAV VVPSMLLLQE GGYGVEKGIP TLLMAAGSFD DILAITGFNT CLGMAFSTGS TVFNVLKGVL EVIIGVVTGL VLG FFIQYF PSSDQDNLVW KRAFLVLGLS VLAVFSSTYF GFPGSGGLCT LVTAFLAGRG WASTKTDVEK VIAVAWDIFQ PLLF GLIGA EVLITALRPE TIGLCVATLG IAVLIRILVT YLMVCFAGFN IKEKIFISFA WLPKATVQAA IGSVALDTAR SHGEK QLEG YGMDVLTVAF LSIIITAPVG SLLIGLLGPR LLQKAEQNKD EEDQGETSIQ V

UniProtKB: Sodium/hydrogen exchanger 9B2

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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

Concentration5 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
100.0 mMNaClsodium chloride
50.0 mMTris-HClTris hydroxy chloride
0.001 %LMNGLauryl Maltose Neopentyl Glycol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.13) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4cz9

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 255710
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)

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