7DSX

Structure of a human NHE1-CHP1 complex under pH 7.5, bound by cariporide


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structure and mechanism of the human NHE1-CHP1 complex.

Dong, Y.Gao, Y.Ilie, A.Kim, D.Boucher, A.Li, B.Zhang, X.C.Orlowski, J.Zhao, Y.

(2021) Nat Commun 12: 3474-3474

  • DOI: 10.1038/s41467-021-23496-z
  • Primary Citation of Related Structures:  
    7DSV, 7DSW, 7DSX

  • PubMed 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 volume homeostasis. Calcineurin B-homologous protein 1 (CHP1) is an obligate binding partner that promotes NHE1 biosynthetic maturation, cell surface expression and pH-sensitivity ...

    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.


    Organizational Affiliation

    College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China. zhaoy@ibp.ac.cn.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Calcineurin B homologous protein 1C,
A [auth D]
185Homo sapiensMutation(s): 1 
Gene Names: CHP1CHP
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q99653 (Homo sapiens)
Explore Q99653 
Go to UniProtKB:  Q99653
PHAROS:  Q99653
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99653
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Sodium/hydrogen exchanger 1D [auth A],
B
509Homo sapiensMutation(s): 0 
Gene Names: SLC9A1APNH1NHE1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P19634 (Homo sapiens)
Explore P19634 
Go to UniProtKB:  P19634
PHAROS:  P19634
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19634
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGT
Query on PGT

Download Ideal Coordinates CCD File 
E [auth B],
F [auth B],
H [auth B],
I [auth A],
J [auth A],
E [auth B],
F [auth B],
H [auth B],
I [auth A],
J [auth A],
K [auth A]
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
C40 H79 O10 P
KBPVYRBBONZJHF-AMAPPZPBSA-N
 Ligand Interaction
HG0 (Subject of Investigation/LOI)
Query on HG0

Download Ideal Coordinates CCD File 
G [auth B],
L [auth A]
N-[bis(azanyl)methylidene]-3-methylsulfonyl-4-propan-2-yl-benzamide
C12 H17 N3 O3 S
IWXNYAIICFKCTM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-23
    Type: Initial release