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- PDB-7dsx: Structure of a human NHE1-CHP1 complex under pH 7.5, bound by car... -

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Basic information

Entry
Database: PDB / ID: 7dsx
TitleStructure of a human NHE1-CHP1 complex under pH 7.5, bound by cariporide
Components
  • Calcineurin B homologous protein 1
  • Sodium/hydrogen exchanger 1
KeywordsMEMBRANE PROTEIN / Transporter
Function / homology
Function and homology information


negative regulation of phosphatase activity / positive regulation of sodium:proton antiporter activity / cation-transporting ATPase complex / positive regulation of calcium:sodium antiporter activity / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / transporter complex / positive regulation of protein glycosylation / Hyaluronan uptake and degradation / membrane docking ...negative regulation of phosphatase activity / positive regulation of sodium:proton antiporter activity / cation-transporting ATPase complex / positive regulation of calcium:sodium antiporter activity / Sodium/Proton exchangers / regulation of the force of heart contraction by cardiac conduction / transporter complex / 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 / potassium:proton antiporter activity / negative regulation of protein autophosphorylation / sodium:proton antiporter activity / positive regulation of action potential / positive regulation of protein transport / maintenance of cell polarity / regulation of pH / positive regulation of calcineurin-NFAT signaling cascade / sodium ion export across plasma membrane / cardiac muscle cell differentiation / membrane organization / cellular response to acidic pH / sodium ion import across plasma membrane / microtubule bundle formation / 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 / negative regulation of calcineurin-NFAT signaling cascade / cellular response to antibiotic / regulation of focal adhesion assembly / negative regulation of protein import into nucleus / negative regulation of NF-kappaB transcription factor activity / small GTPase-mediated signal transduction / 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 / protein complex oligomerization / intercalated disc / positive regulation of protein targeting to membrane / potassium channel regulator activity / monoatomic ion transport / cytoplasmic microtubule organization / phosphatidylinositol-4,5-bisphosphate binding / transport vesicle / negative regulation of protein ubiquitination / T-tubule / potassium ion transmembrane transport / cellular response to epinephrine stimulus / response to muscle stretch / protein export from nucleus / proton transmembrane transport / negative regulation of protein phosphorylation / stem cell differentiation / regulation of intracellular pH / negative regulation of protein kinase activity / potassium ion transport / kinase binding / phospholipid binding / cellular response to insulin stimulus / cellular response to mechanical stimulus / calcium-dependent protein binding / microtubule cytoskeleton / cell migration / lamellipodium / protein-macromolecule adaptor activity / cellular response to hypoxia / microtubule binding / positive regulation of cell growth / basolateral plasma membrane / molecular adaptor activity / membrane fusion / calmodulin binding / protein stabilization / 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 / membrane / nucleus
Similarity search - Function
: / Sodium/hydrogen exchanger 1-like / Sodium/hydrogen exchanger, regulatory region / Regulatory region of Na+/H+ exchanger NHE binds to calmodulin / Na+/H+ exchanger / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger family / EF-hand domain pair / EF-hand, calcium binding motif ...: / Sodium/hydrogen exchanger 1-like / Sodium/hydrogen exchanger, regulatory region / Regulatory region of Na+/H+ exchanger NHE binds to calmodulin / Na+/H+ exchanger / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger family / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Chem-HG0 / Chem-PGT / Sodium/hydrogen exchanger 1 / Calcineurin B homologous protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsDong, Y. / Gao, Y. / Li, B. / Zhang, X.C. / Zhao, Y.
CitationJournal: 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
DepositionJan 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

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Assembly

Deposited unit
D: Calcineurin B homologous protein 1
B: Sodium/hydrogen exchanger 1
C: Calcineurin B homologous protein 1
A: Sodium/hydrogen exchanger 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,01312
Polymers156,9404
Non-polymers5,0738
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area20770 Å2
ΔGint-203 kcal/mol
Surface area59810 Å2

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Components

#1: Protein Calcineurin B homologous protein 1 / Calcineurin B-like protein / Calcium-binding protein CHP / Calcium-binding protein p22 / EF-hand ...Calcineurin B-like protein / Calcium-binding protein CHP / Calcium-binding protein p22 / EF-hand calcium-binding domain-containing protein p22


Mass: 21369.830 Da / Num. of mol.: 2 / Mutation: I171A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHP1, CHP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q99653
#2: Protein Sodium/hydrogen exchanger 1 / APNH / Na(+)/H(+) antiporter / amiloride-sensitive / Na(+)/H(+) exchanger 1 / NHE-1 / Solute ...APNH / Na(+)/H(+) antiporter / amiloride-sensitive / Na(+)/H(+) exchanger 1 / NHE-1 / Solute carrier family 9 member 1


Mass: 57100.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A1, APNH1, NHE1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P19634
#3: Chemical
ChemComp-PGT / (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / PHOSPHATIDYLGLYCEROL / 1-PALMITOYL-2-OLEOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)](SODIUM SALT)


Mass: 751.023 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
#4: Chemical ChemComp-HG0 / N-[bis(azanyl)methylidene]-3-methylsulfonyl-4-propan-2-yl-benzamide


Mass: 283.347 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N3O3S / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Human NHE1-CHP1 complex under pH 7.5, bound by cariporideCOMPLEX#1-#20RECOMBINANT
2Sodium/protein exchanger 1 (NHE1) under pH 7.5, bound by cariporideCOMPLEX#11RECOMBINANT
3Calcineurin B homologous protein 1 (CHP1) under pH 7.5COMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.23 MDaNO
220.182 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Homo sapiens (human)9606HEK293
32Homo sapiens (human)9606HEK293
Buffer solutionpH: 7.5
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The NHE1-CHP1 complex was reconstituted into lipid nanodiscs.
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 13000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3855
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 32 / Used frames/image: 1-32

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Processing

EM software
IDNameVersionCategory
1Gautomatch0.56particle selection
2Topaz0.2.3particle selection
3SerialEM3.6image acquisition
5GctfCTF correction
8Coot0.89model fitting
10PHENIX1.18model refinement
11RELION3.1initial Euler assignment
12cryoSPARC2.15initial Euler assignment
13RELION3.1final Euler assignment
15cryoSPARC2.153D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61460 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL

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