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- PDB-7p1j: Cryo EM structure of bison NHA2 in detergent structure -

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Basic information

Entry
Database: PDB / ID: 7p1j
TitleCryo EM structure of bison NHA2 in detergent structure
Componentsmitochondrial sodium/hydrogen exchanger 9B2
KeywordsTRANSPORT PROTEIN / Membrane protein Sodium proton transporter
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsMatsuoka, R. / Fudim, R. / Jung, S. / Drew, D.
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, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
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Revision 1.1Feb 2, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Mar 2, 2022Group: Database references / Structure summary / Category: citation / citation_author / struct / Item: _struct.title
Revision 1.3Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
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Assembly

Deposited unit
B: mitochondrial sodium/hydrogen exchanger 9B2
A: mitochondrial sodium/hydrogen exchanger 9B2


Theoretical massNumber of molelcules
Total (without water)114,8382
Polymers114,8382
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2240 Å2
ΔGint-24 kcal/mol
Surface area43270 Å2

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Components

#1: Protein mitochondrial sodium/hydrogen exchanger 9B2


Mass: 57419.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bison bison (American bison) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6P3HVI0
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: detergent structure / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 57373 kDa/nm / Experimental value: YES
Source (natural)Organism: Bison bison (American bison)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
250 mMTris hydroxy chlorideTris-HCl1
30.001 %Lauryl Maltose Neopentyl GlycolLMNG1
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 80 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k)
Image scansWidth: 3838 / Height: 3710

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Processing

SoftwareName: PHENIX / Version: 1.19_4092: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4.13CTF correction
8PHENIXmodel refinement
10RELION3initial Euler assignment
11RELION3final Euler assignment
13RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 255710 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0016646
ELECTRON MICROSCOPYf_angle_d0.4439052
ELECTRON MICROSCOPYf_dihedral_angle_d8.8942314
ELECTRON MICROSCOPYf_chiral_restr0.0341118
ELECTRON MICROSCOPYf_plane_restr0.0031094

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