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Yorodumi- PDB-7p1i: Cryo EM structure of bison NHA2 in detergent and N-terminal exten... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p1i | ||||||
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Title | Cryo EM structure of bison NHA2 in detergent and N-terminal extension helix | ||||||
Components | mitochondrial sodium/hydrogen exchanger 9B2 | ||||||
Keywords | TRANSPORT PROTEIN / Membrane protein Sodium proton transporter | ||||||
Function / homology | Function and homology information 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 | Bison bison (American bison) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.15 Å | ||||||
Authors | Matsuoka, R. / Fudim, R. / Jung, S. / Drew, D. | ||||||
Funding support | 1items
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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 |
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-Structure visualization
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Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7p1i.cif.gz | 154.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p1i.ent.gz | 121.7 KB | Display | PDB format |
PDBx/mmJSON format | 7p1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p1i_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 7p1i_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 7p1i_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 7p1i_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p1/7p1i ftp://data.pdbj.org/pub/pdb/validation_reports/p1/7p1i | HTTPS FTP |
-Related structure data
Related structure data | 13161MC 7p1jC 7p1kC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Bison bison (American bison) / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6P3HVI0 |
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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 |
-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: Bison bison (American bison) | ||||||||||||||||||||
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||
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 | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 | ||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
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 |
-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: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 255710 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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