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- PDB-7x2u: Structure of a human NHE3-CHP1 complex in the autoinhibited state -

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Basic information

Entry
Database: PDB / ID: 7x2u
TitleStructure of a human NHE3-CHP1 complex in the autoinhibited state
Components
  • Calcineurin B homologous protein 1
  • Sodium/hydrogen exchanger 3
KeywordsMEMBRANE PROTEIN / Sodium/proton antiporter
Function / homology
Function and homology information


negative regulation of phosphatase activity / positive regulation of sodium:proton antiporter activity / Sodium/Proton exchangers / Hyaluronan degradation / : / membrane docking / positive regulation of protein transport / negative regulation of protein autophosphorylation / transporter complex / positive regulation of phospholipid biosynthetic process ...negative regulation of phosphatase activity / positive regulation of sodium:proton antiporter activity / Sodium/Proton exchangers / Hyaluronan degradation / : / membrane docking / positive regulation of protein transport / negative regulation of protein autophosphorylation / transporter complex / positive regulation of phospholipid biosynthetic process / potassium:proton antiporter activity / sodium:proton antiporter activity / membrane organization / microtubule bundle formation / cellular response to acidic pH / sodium ion import across plasma membrane / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of NF-kappaB transcription factor activity / negative regulation of protein import into nucleus / small GTPase-mediated signal transduction / endoplasmic reticulum-Golgi intermediate compartment / negative regulation of protein phosphorylation / protein kinase inhibitor activity / brush border / positive regulation of protein targeting to membrane / potassium channel regulator activity / negative regulation of protein kinase activity / transport vesicle / monoatomic ion transport / cytoplasmic microtubule organization / negative regulation of protein ubiquitination / potassium ion transmembrane transport / phosphatidylinositol binding / protein export from nucleus / regulation of intracellular pH / PDZ domain binding / brush border membrane / potassium ion transport / kinase binding / recycling endosome membrane / calcium-dependent protein binding / microtubule cytoskeleton / early endosome membrane / microtubule binding / membrane fusion / early endosome / protein stabilization / apical plasma membrane / membrane raft / Golgi membrane / focal adhesion / calcium ion binding / cell surface / endoplasmic reticulum / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Na+/H+ exchanger, isoforms 3/5 / : / Na+/H+ antiporter like fold - #20 / Na+/H+ antiporter like fold / Na+/H+ exchanger / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane / EF-hand domain pair / EF-hand, calcium binding motif ...Na+/H+ exchanger, isoforms 3/5 / : / Na+/H+ antiporter like fold - #20 / Na+/H+ antiporter like fold / Na+/H+ exchanger / Cation/H+ exchanger, CPA1 family / Cation/H+ exchanger / Sodium/hydrogen exchanger, transmembrane / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-85R / Chem-PGT / Sodium/hydrogen exchanger 3 / Calcineurin B homologous protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsDong, Y. / Li, H. / Gao, Y. / Zhang, X.C. / Zhao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030304 China
CitationJournal: Sci Adv / Year: 2022
Title: Structure of a human NHE3-CHP1 complex in the autoinhibited state
Authors: Dong, Y. / Li, H. / Ilie, A. / Gao, Y. / Boucher, A. / Zhang, X.C. / Orlowski, J. / Zhao, Y.
History
DepositionFeb 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.0Apr 20, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 20, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 20, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 20, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 20, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 20, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 20, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN
Revision 1.2Jun 26, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update
Revision 1.3Jul 2, 2025Group: Data collection / Structure summary / Category: em_admin / em_software / pdbx_entry_details
Item: _em_admin.last_update / _em_software.name / _pdbx_entry_details.has_protein_modification
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sodium/hydrogen exchanger 3
B: Sodium/hydrogen exchanger 3
C: Calcineurin B homologous protein 1
D: Calcineurin B homologous protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,03016
Polymers183,8984
Non-polymers9,13212
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area21140 Å2
ΔGint-201 kcal/mol
Surface area58580 Å2

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Components

#1: Protein Sodium/hydrogen exchanger 3 / Na(+)/H(+) exchanger 3 / NHE-3 / Solute carrier family 9 member 3


Mass: 70537.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC9A3, NHE3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P48764
#2: 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: 21411.910 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-85R / [(2~{R})-2-hexadecanoyloxy-3-[oxidanyl-[(2~{S},3~{S},5~{R},6~{S})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propyl] hexadecanoate


Mass: 811.032 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H79O13P / Feature type: SUBJECT OF INVESTIGATION
#4: 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.: 10 / Source method: obtained synthetically / Formula: C40H79O10P / Comment: phospholipid*YM
Has ligand of interestY
Has protein modificationN

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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

ComponentName: Human NHE3-CHP1 complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 defocus max: 22000 nm / Nominal defocus min: 12000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37572 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0112120
ELECTRON MICROSCOPYf_angle_d0.72516366
ELECTRON MICROSCOPYf_dihedral_angle_d12.3481713
ELECTRON MICROSCOPYf_chiral_restr0.051882
ELECTRON MICROSCOPYf_plane_restr0.0042023

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