6NUF

Structure of Calcineurin in complex with NHE1 peptide

  • Classification: HYDROLASE/Calcium Binding Protein
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): Yes 

  • Deposited: 2019-01-31 Released: 2019-07-03 
  • Deposition Author(s): Wang, X., Page, R., Peti, W.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular basis for the binding and selective dephosphorylation of Na+/H+exchanger 1 by calcineurin.

Hendus-Altenburger, R.Wang, X.Sjogaard-Frich, L.M.Pedraz-Cuesta, E.Sheftic, S.R.Bendsoe, A.H.Page, R.Kragelund, B.B.Pedersen, S.F.Peti, W.

(2019) Nat Commun 10: 3489-3489

  • DOI: https://doi.org/10.1038/s41467-019-11391-7
  • Primary Citation of Related Structures:  
    6NUC, 6NUF, 6NUU

  • PubMed Abstract: 

    Very little is known about how Ser/Thr protein phosphatases specifically recruit and dephosphorylate substrates. Here, we identify how the Na + /H + -exchanger 1 (NHE1), a key regulator of cellular pH homeostasis, is regulated by the Ser/Thr phosphatase calcineurin (CN). NHE1 activity is increased by phosphorylation of NHE1 residue T779, which is specifically dephosphorylated by CN. While it is known that Ser/Thr protein phosphatases prefer pThr over pSer, we show that this preference is not key to this exquisite CN selectivity. Rather a combination of molecular mechanisms, including recognition motifs, dynamic charge-charge interactions and a substrate interaction pocket lead to selective dephosphorylation of pT779. Our data identify T779 as a site regulating NHE1-mediated cellular acid extrusion and provides a molecular understanding of NHE1 substrate selection by CN, specifically, and how phosphatases recruit specific substrates, generally.


  • Organizational Affiliation

    Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, DK-2200, Copenhagen N, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform372Homo sapiensMutation(s): 0 
Gene Names: PPP3CACALNACNA
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q08209 (Homo sapiens)
Explore Q08209 
Go to UniProtKB:  Q08209
PHAROS:  Q08209
GTEx:  ENSG00000138814 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ08209
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Calcineurin subunit B type 1156Homo sapiensMutation(s): 0 
Gene Names: PPP3R1CNA2CNB
UniProt & NIH Common Fund Data Resources
Find proteins for P63098 (Homo sapiens)
Explore P63098 
Go to UniProtKB:  P63098
PHAROS:  P63098
GTEx:  ENSG00000221823 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP63098
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/hydrogen exchanger 148Homo sapiensMutation(s): 2 
Gene Names: SLC9A1APNH1NHE1
UniProt & NIH Common Fund Data Resources
Find proteins for P19634 (Homo sapiens)
Explore P19634 
Go to UniProtKB:  P19634
PHAROS:  P19634
GTEx:  ENSG00000090020 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19634
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
F [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
D [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
K [auth B],
L [auth B],
M [auth B],
N [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.477α = 90
b = 126.808β = 90
c = 127.431γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SAINTdata reduction
SADABSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01NS091336
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM098482

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description