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Yorodumi- EMDB-11066: CryoEM structure of horse sodium/proton exchanger NHE9 in an inwa... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11066 | |||||||||
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Title | CryoEM structure of horse sodium/proton exchanger NHE9 in an inward-facing conformation | |||||||||
Map data | ||||||||||
Sample |
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Keywords | TRANSPORT PROTEIN / MEMBRANE 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 / late endosome membrane / early endosome membrane / protein homodimerization activity / plasma membrane Similarity search - Function | |||||||||
Biological species | Equus caballus (horse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.51 Å | |||||||||
Authors | Winkelmannm I / Matsuoka R | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11066.map.gz | 49 MB | EMDB map data format | |
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Header (meta data) | emd-11066-v30.xml emd-11066.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11066_fsc.xml | 8.6 KB | Display | FSC data file |
Images | emd_11066.png | 208.6 KB | ||
Masks | emd_11066_msk_1.map | 52.7 MB | Mask map | |
Filedesc metadata | emd-11066.cif.gz | 5.7 KB | ||
Others | emd_11066_half_map_1.map.gz emd_11066_half_map_2.map.gz | 40.8 MB 40.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11066 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11066 | HTTPS FTP |
-Validation report
Summary document | emd_11066_validation.pdf.gz | 444.8 KB | Display | EMDB validaton report |
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Full document | emd_11066_full_validation.pdf.gz | 443.9 KB | Display | |
Data in XML | emd_11066_validation.xml.gz | 14.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11066 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11066 | HTTPS FTP |
-Related structure data
Related structure data | 6z3yMC 6z3zC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_11066.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0375 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11066_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_11066_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_11066_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Sodium proton antiporter
Entire | Name: Sodium proton antiporter |
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Components |
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-Supramolecule #1: Sodium proton antiporter
Supramolecule | Name: Sodium proton antiporter / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Equus caballus (horse) |
-Macromolecule #1: Sodium/hydrogen exchanger
Macromolecule | Name: Sodium/hydrogen exchanger / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Equus caballus (horse) |
Molecular weight | Theoretical: 52.703551 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Sequence | String: GAVELLVFNF LLILTILTIW LFKNHRFRFL HETGGAMVYG LIMGLILRYA TAPTDIESGT VYDCGKLAFS PSTLLINITD QVYEYKYKR EISQHNINPH LGNAILEKMT FDPEIFFNVL LPPIIFHAGY SLKKRHFFQN LGSILTYAFL GTAISCIVIG L IMYGFVKA ...String: GAVELLVFNF LLILTILTIW LFKNHRFRFL HETGGAMVYG LIMGLILRYA TAPTDIESGT VYDCGKLAFS PSTLLINITD QVYEYKYKR EISQHNINPH LGNAILEKMT FDPEIFFNVL LPPIIFHAGY SLKKRHFFQN LGSILTYAFL GTAISCIVIG L IMYGFVKA MVYAGQLKNG DFHFTDCLFF GSLMSATDPV TVLAIFHELH VDPDLYTLLF GESVLNDAVA IVLTYSISIY SP KENPNAF DAAAFFQSVG NFLGIFAGSF AMGSAYAVVT ALLTKFTKLC EFPMLETGLF FLLSWSAFLS AEAAGLTGIV AVL FCGVTQ AHYTYNNLSL DSKMRTKQLF EFMNFLAENV IFCYMGLALF TFQNHIFNAL FILGAFLAIF VARACNIYPL SFLL NLGRK HKIPWNFQHM MMFSGLRGAI AFALAIRDTE SQPKQMMFST TLLLVFFTVW VFGGGTTPML TWLQI UniProtKB: Sodium/hydrogen exchanger 9 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Component:
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Vitrification | Cryogen name: HELIUM |
-Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Phase plate: ZERNIKE PHASE PLATE / Spherical aberration corrector: Nothing / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-40 / Average exposure time: 10.0 sec. / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 165000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |