+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-30847 | |||||||||
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Title | Structure of a human NHE1-CHP1 complex under pH 6.5 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Transporter / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information positive regulation of sodium:proton antiporter activity / sodium:proton antiporter activity involved in regulation of cardiac muscle cell membrane potential / cation-transporting ATPase complex / Sodium/Proton exchangers / negative regulation of phosphatase activity / regulation of the force of heart contraction by cardiac conduction / transporter complex / positive regulation of calcium:sodium antiporter activity / positive regulation of protein glycosylation / Hyaluronan uptake and degradation ...positive regulation of sodium:proton antiporter activity / sodium:proton antiporter activity involved in regulation of cardiac muscle cell membrane potential / cation-transporting ATPase complex / Sodium/Proton exchangers / negative regulation of phosphatase activity / regulation of the force of heart contraction by cardiac conduction / transporter complex / positive regulation of calcium:sodium antiporter activity / positive regulation of protein glycosylation / Hyaluronan uptake and degradation / membrane docking / regulation of cardiac muscle cell membrane potential / cellular response to electrical stimulus / positive regulation of phospholipid biosynthetic process / negative regulation of protein autophosphorylation / potassium:proton antiporter activity / sodium:proton antiporter activity / positive regulation of action potential / positive regulation of protein transport / maintenance of cell polarity / positive regulation of calcineurin-NFAT signaling cascade / regulation of pH / sodium ion export across plasma membrane / cellular response to acidic pH / cardiac muscle cell differentiation / membrane organization / ion binding / sodium ion import across plasma membrane / protein phosphatase 2B binding / intracellular sodium ion homeostasis / microtubule bundle formation / cardiac muscle cell contraction / response to acidic pH / regulation of stress fiber assembly / regulation of cardiac muscle contraction by calcium ion signaling / positive regulation of mitochondrial membrane permeability / cellular response to cold / negative regulation of calcineurin-NFAT signaling cascade / cellular response to antibiotic / regulation of focal adhesion assembly / negative regulation of protein import into nucleus / small GTPase-mediated signal transduction / negative regulation of NF-kappaB transcription factor activity / positive regulation of cardiac muscle hypertrophy / protein kinase inhibitor activity / positive regulation of the force of heart contraction / cellular response to organic cyclic compound / endoplasmic reticulum-Golgi intermediate compartment / intercalated disc / potassium channel regulator activity / positive regulation of protein targeting to membrane / monoatomic ion transport / cytoplasmic microtubule organization / transport vesicle / potassium ion transmembrane transport / negative regulation of protein ubiquitination / proton transmembrane transport / T-tubule / cellular response to epinephrine stimulus / response to muscle stretch / phosphatidylinositol-4,5-bisphosphate binding / protein export from nucleus / negative regulation of protein phosphorylation / stem cell differentiation / regulation of intracellular pH / negative regulation of protein kinase activity / potassium ion transport / phospholipid binding / kinase binding / cellular response to mechanical stimulus / cellular response to insulin stimulus / calcium-dependent protein binding / microtubule cytoskeleton / cell migration / lamellipodium / protein complex oligomerization / protein-macromolecule adaptor activity / cellular response to hypoxia / positive regulation of cell growth / microtubule binding / basolateral plasma membrane / molecular adaptor activity / membrane fusion / protein stabilization / calmodulin binding / positive regulation of apoptotic process / membrane raft / apical plasma membrane / Golgi membrane / focal adhesion / calcium ion binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 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_30847.map.gz | 9.3 MB | EMDB map data format | |
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Header (meta data) | emd-30847-v30.xml emd-30847.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_30847_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_30847.png | 122.9 KB | ||
Filedesc metadata | emd-30847.cif.gz | 6.2 KB | ||
Others | emd_30847_additional_1.map.gz | 8.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-30847 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-30847 | HTTPS FTP |
-Validation report
Summary document | emd_30847_validation.pdf.gz | 420.7 KB | Display | EMDB validaton report |
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Full document | emd_30847_full_validation.pdf.gz | 420.2 KB | Display | |
Data in XML | emd_30847_validation.xml.gz | 10 KB | Display | |
Data in CIF | emd_30847_validation.cif.gz | 13.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30847 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-30847 | HTTPS FTP |
-Related structure data
Related structure data | 7dsvMC 7dswC 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_30847.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_30847_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human NHE1-CHP1 complex under pH 6.5
Entire | Name: Human NHE1-CHP1 complex under pH 6.5 |
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Components |
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-Supramolecule #1: Human NHE1-CHP1 complex under pH 6.5
Supramolecule | Name: Human NHE1-CHP1 complex under pH 6.5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 Details: CHP1 in this map was locally refined using symmetry expansion to improve resolution. |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 230 KDa |
-Supramolecule #2: Sodium/protein exchanger 1 (NHE1)
Supramolecule | Name: Sodium/protein exchanger 1 (NHE1) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 182 KDa |
-Supramolecule #3: Calcineurin B homologous protein 1 (CHP1)
Supramolecule | Name: Calcineurin B homologous protein 1 (CHP1) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-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: 52.893367 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 LVDLLAVKKK QETKRSINEE IHTQFLDHLL TGIEDICGHY GHHHWKDKLN RFNKKYV UniProtKB: Sodium/hydrogen exchanger 1 |
-Macromolecule #2: Calcineurin B homologous protein 1
Macromolecule | Name: Calcineurin B homologous protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 21.36983 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DEELEEIKKE TGFSHSQITR LYSRFTSLDK GENGTLSRED FQRIPELAIN PLGDRIINAF FPEGEDQVNF RGFMRTLAHF RPIEDNEKS KDVNGPEPLN SRSNKLHFAF RLYDLDKDEK ISRDELLQVL RMMVGVNISD EQLGSIADRT IQEADQDGDS A ASFTEFVK VLEKVDVEQK MSIRFLH UniProtKB: Calcineurin B homologous protein 1 |
-Macromolecule #3: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
Macromolecule | Name: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 3 / Number of copies: 16 / 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: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: OTHER |
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 TALOS ARCTICA |
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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: 2205 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 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: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-7dsv: |