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Open data
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Basic information
Entry | Database: PDB / ID: 7p1j | ||||||
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Title | Cryo EM structure of bison NHA2 in detergent structure | ||||||
![]() | mitochondrial sodium/hydrogen exchanger 9B2 | ||||||
![]() | TRANSPORT PROTEIN / Membrane protein Sodium proton transporter | ||||||
Function / homology | ![]() lithium:proton antiporter activity / lithium ion transport / sperm principal piece / sodium ion homeostasis / sodium:proton antiporter activity / sodium ion transport / mitochondrial membrane / recycling endosome / synaptic vesicle membrane / recycling endosome membrane ...lithium:proton antiporter activity / lithium ion transport / sperm principal piece / sodium ion homeostasis / sodium:proton antiporter activity / sodium ion transport / mitochondrial membrane / recycling endosome / synaptic vesicle membrane / recycling endosome membrane / basolateral plasma membrane / endosome membrane / apical plasma membrane / lysosomal membrane / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å | ||||||
![]() | Matsuoka, R. / Fudim, R. / Jung, S. / Drew, D. | ||||||
![]() | ![]() 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: ![]() Title: Structure, mechanism and lipid-mediated remodeling of the mammalian Na+/H+ exchanger NHA2 Authors: Matsuoka, R. / Fudim, F. / Jung, S. / Drew, F. | ||||||
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 152.2 KB | Display | ![]() |
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PDB format | ![]() | 119 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 13162MC ![]() 7p1iC ![]() 7p1kC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 57419.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: detergent structure / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Value: 57373 kDa/nm / Experimental value: YES | ||||||||||||||||||||
Source (natural) | Organism: ![]() | ||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | ||||||||||||||||||||
Buffer solution | pH: 7 | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Instrument: 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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 80 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
Image scans | Width: 3838 / Height: 3710 |
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Processing
Software | Name: PHENIX / Version: 1.19_4092: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 255710 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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