+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30848 | |||||||||
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Title | Structure of a human NHE1-CHP1 complex under pH 7.5 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Transporter / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information cation-transporting ATPase complex / positive regulation of calcium:sodium antiporter activity / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / Hyaluronan uptake and degradation / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / potassium:proton antiporter activity / sodium:proton antiporter activity / positive regulation of action potential ...cation-transporting ATPase complex / positive regulation of calcium:sodium antiporter activity / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / Hyaluronan uptake and degradation / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / potassium:proton antiporter activity / sodium:proton antiporter activity / positive regulation of action potential / maintenance of cell polarity / regulation of pH / positive regulation of calcineurin-NFAT signaling cascade / sodium ion export across plasma membrane / cardiac muscle cell differentiation / cellular response to acidic pH / sodium ion import across plasma membrane / protein phosphatase 2B binding / intracellular sodium ion homeostasis / response to acidic pH / regulation of stress fiber assembly / cardiac muscle cell contraction / regulation of cardiac muscle contraction by calcium ion signaling / positive regulation of mitochondrial membrane permeability / cellular response to cold / cellular response to antibiotic / regulation of focal adhesion assembly / positive regulation of cardiac muscle hypertrophy / positive regulation of the force of heart contraction / cellular response to organic cyclic compound / protein complex oligomerization / intercalated disc / monoatomic ion transport / phosphatidylinositol-4,5-bisphosphate binding / T-tubule / potassium ion transmembrane transport / cellular response to epinephrine stimulus / response to muscle stretch / proton transmembrane transport / stem cell differentiation / regulation of intracellular pH / phospholipid binding / cellular response to insulin stimulus / cellular response to mechanical stimulus / calcium-dependent protein binding / cell migration / lamellipodium / protein-macromolecule adaptor activity / cellular response to hypoxia / positive regulation of cell growth / basolateral plasma membrane / molecular adaptor activity / calmodulin binding / positive regulation of apoptotic process / membrane raft / apical plasma membrane / focal adhesion / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Dong Y / Gao Y / Li B / Zhang XC / Zhao Y | |||||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Structure and mechanism of the human NHE1-CHP1 complex. Authors: Yanli Dong / Yiwei Gao / Alina Ilie / DuSik Kim / Annie Boucher / Bin Li / Xuejun C Zhang / John Orlowski / Yan Zhao / Abstract: Sodium/proton exchanger 1 (NHE1) is an electroneutral secondary active transporter present on the plasma membrane of most mammalian cells and plays critical roles in regulating intracellular pH and ...Sodium/proton exchanger 1 (NHE1) is an electroneutral secondary active transporter present on the plasma membrane of most mammalian cells and plays critical roles in regulating intracellular pH and volume homeostasis. Calcineurin B-homologous protein 1 (CHP1) is an obligate binding partner that promotes NHE1 biosynthetic maturation, cell surface expression and pH-sensitivity. Dysfunctions of either protein are associated with neurological disorders. Here, we elucidate structures of the human NHE1-CHP1 complex in both inward- and inhibitor (cariporide)-bound outward-facing conformations. We find that NHE1 assembles as a symmetrical homodimer, with each subunit undergoing an elevator-like conformational change during cation exchange. The cryo-EM map reveals the binding site for the NHE1 inhibitor cariporide, illustrating how inhibitors block transport activity. The CHP1 molecule differentially associates with these two conformational states of each NHE1 monomer, and this association difference probably underlies the regulation of NHE1 pH-sensitivity by CHP1. | |||||||||
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_30848.map.gz | 4.4 MB | EMDB map data format | |
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Header (meta data) | emd-30848-v30.xml emd-30848.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30848_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_30848.png | 198.3 KB | ||
Filedesc metadata | emd-30848.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30848 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30848 | HTTPS FTP |
-Validation report
Summary document | emd_30848_validation.pdf.gz | 378.2 KB | Display | EMDB validaton report |
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Full document | emd_30848_full_validation.pdf.gz | 377.8 KB | Display | |
Data in XML | emd_30848_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | emd_30848_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30848 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30848 | HTTPS FTP |
-Related structure data
Related structure data | 7dswMC 7dsvC 7dsxC 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_30848.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Human NHE1-CHP1 complex under pH 7.5
Entire | Name: Human NHE1-CHP1 complex under pH 7.5 |
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Components |
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-Supramolecule #1: Human NHE1-CHP1 complex under pH 7.5
Supramolecule | Name: Human NHE1-CHP1 complex under pH 7.5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Calcineurin B homologous protein 1 (CHP1) was not successfully resolved in this map because of conformational heterogeneity. |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 230 KDa |
-Macromolecule #1: Sodium/hydrogen exchanger 1
Macromolecule | Name: Sodium/hydrogen exchanger 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 46.610219 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: KAFPVLGIDY THVRTPFEIS LWILLACLMK IGFHVIPTIS SIVPESCLLI VVGLLVGGLI KGVGETPPFL QSDVFFLFLL PPIILDAGY FLPLRQFTEN LGTILIFAVV GTLWNAFFLG GLMYAVCLVG GEQINNIGLL DNLLFGSIIS AVDPVAVLAV F EEIHINEL ...String: KAFPVLGIDY THVRTPFEIS LWILLACLMK IGFHVIPTIS SIVPESCLLI VVGLLVGGLI KGVGETPPFL QSDVFFLFLL PPIILDAGY FLPLRQFTEN LGTILIFAVV GTLWNAFFLG GLMYAVCLVG GEQINNIGLL DNLLFGSIIS AVDPVAVLAV F EEIHINEL LHILVFGESL LNDAVTVVLY HLFEEFANYE HVGIVDIFLG FLSFFVVALG GVLVGVVYGV IAAFTSRFTS HI RVIEPLF VFLYSYMAYL SAELFHLSGI MALIASGVVM RPYVEANISH KSHTTIKYFL KMWSSVSETL IFIFLGVSTV AGS HHWNWT FVISTLLFCL IARVLGVLGL TWFINKFRIV KLTPKDQFII AYGGLRGAIA FSLGYLLDKK HFPMCDLFLT AIIT VIFFT VFVQGMTIRP LVDLL UniProtKB: Sodium/hydrogen exchanger 1 |
-Macromolecule #2: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
Macromolecule | Name: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 2 / Number of copies: 12 / Formula: LBN |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ChemComp-LBN: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 6 mg/mL |
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Buffer | pH: 6.5 |
Grid | Model: Quantifoil / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III |
Details | The NHE1-CHP1 complex was reconstituted into lipid nanodiscs. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-32 / Number grids imaged: 1 / Number real images: 2462 / Average electron dose: 60.0 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: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 13000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7dsw: |