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Yorodumi- PDB-6z3y: CryoEM structure of horse sodium/proton exchanger NHE9 in an inwa... -
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-Basic information
Entry | Database: PDB / ID: 6z3y | ||||||
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Title | CryoEM structure of horse sodium/proton exchanger NHE9 in an inward-facing conformation | ||||||
Components | Sodium/hydrogen exchanger | ||||||
Keywords | MEMBRANE PROTEIN / TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / sodium ion transmembrane transport / potassium ion transmembrane transport / proton transmembrane transport / regulation of intracellular pH / recycling endosome / recycling endosome membrane / phagocytic vesicle membrane ...potassium:proton antiporter activity / sodium:proton antiporter activity / sodium ion import across plasma membrane / sodium ion transmembrane transport / potassium ion transmembrane transport / proton transmembrane transport / regulation of intracellular pH / recycling endosome / recycling endosome membrane / phagocytic vesicle membrane / early endosome membrane / late endosome membrane / protein homodimerization activity / plasma membrane Similarity search - Function | ||||||
Biological species | Equus caballus (horse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.51 Å | ||||||
Authors | Winkelmannm, I. / Matsuoka, R. / Meier, P. / Drew, D. | ||||||
Citation | Journal: EMBO J / Year: 2020 Title: Structure and elevator mechanism of the mammalian sodium/proton exchanger NHE9. Authors: Iven Winklemann / Rei Matsuoka / Pascal F Meier / Denis Shutin / Chenou Zhang / Laura Orellana / Ricky Sexton / Michael Landreh / Carol V Robinson / Oliver Beckstein / David Drew / Abstract: Na /H exchangers (NHEs) are ancient membrane-bound nanomachines that work to regulate intracellular pH, sodium levels and cell volume. NHE activities contribute to the control of the cell cycle, cell ...Na /H exchangers (NHEs) are ancient membrane-bound nanomachines that work to regulate intracellular pH, sodium levels and cell volume. NHE activities contribute to the control of the cell cycle, cell proliferation, cell migration and vesicle trafficking. NHE dysfunction has been linked to many diseases, and they are targets of pharmaceutical drugs. Despite their fundamental importance to cell homeostasis and human physiology, structural information for the mammalian NHE was lacking. Here, we report the cryogenic electron microscopy structure of NHE isoform 9 (SLC9A9) from Equus caballus at 3.2 Å resolution, an endosomal isoform highly expressed in the brain and associated with autism spectrum (ASD) and attention deficit hyperactivity (ADHD) disorders. Despite low sequence identity, the NHE9 architecture and ion-binding site are remarkably similar to distantly related bacterial Na /H antiporters with 13 transmembrane segments. Collectively, we reveal the conserved architecture of the NHE ion-binding site, their elevator-like structural transitions, the functional implications of autism disease mutations and the role of phosphoinositide lipids to promote homodimerization that, together, have important physiological ramifications. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6z3y.cif.gz | 144.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z3y.ent.gz | 112.4 KB | Display | PDB format |
PDBx/mmJSON format | 6z3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z3y_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6z3y_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6z3y_validation.xml.gz | 34.3 KB | Display | |
Data in CIF | 6z3y_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z3/6z3y ftp://data.pdbj.org/pub/pdb/validation_reports/z3/6z3y | HTTPS FTP |
-Related structure data
Related structure data | 11066MC 6z3zC 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: 52703.551 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Equus caballus (horse) / Gene: SLC9A9 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: F7B113 |
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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: Sodium proton antiporter / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT | ||||||||||||||||||||
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Source (natural) | Organism: Equus caballus (horse) | ||||||||||||||||||||
Source (recombinant) | Organism: Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||||||||||
Buffer solution | pH: 7.5 | ||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Vitrification | Cryogen name: HELIUM |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 10 sec. / Electron dose: 80 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV / Phase plate: ZERNIKE PHASE PLATE / Spherical aberration corrector: Nothing |
Image scans | Width: 3710 / Height: 3838 / Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
Software | Name: PHENIX / Version: 1.18.2_3874: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.51 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 139511 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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