8SI7

Cryo-EM structure of TRPM7 in GDN detergent in complex with inhibitor VER155008 in closed state

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Mus musculus
  • Expression System: Homo sapiens
  • Mutation(s): No 
  • Membrane Protein: Yes  OPMPDBTMmpstruc

  • Deposited: 2023-04-14 Released: 2023-05-17 
  • Deposition Author(s): Nadezhdin, K.D., Neuberger, A., Sobolevsky, A.I.
  • Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS), German Research Foundation (DFG)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural mechanisms of TRPM7 activation and inhibition.

Nadezhdin, K.D.Correia, L.Narangoda, C.Patel, D.S.Neuberger, A.Gudermann, T.Kurnikova, M.G.Chubanov, V.Sobolevsky, A.I.

(2023) Nat Commun 14: 2639-2639

  • DOI: https://doi.org/10.1038/s41467-023-38362-3
  • Primary Citation of Related Structures:  
    8SI2, 8SI3, 8SI4, 8SI5, 8SI6, 8SI7, 8SI8, 8SIA, 8SIB

  • PubMed Abstract: 

    The transient receptor potential channel TRPM7 is a master regulator of the organismal balance of divalent cations that plays an essential role in embryonic development, immune responses, cell mobility, proliferation, and differentiation. TRPM7 is implicated in neuronal and cardiovascular disorders, tumor progression and has emerged as a new drug target. Here we use cryo-EM, functional analysis, and molecular dynamics simulations to uncover two distinct structural mechanisms of TRPM7 activation by a gain-of-function mutation and by the agonist naltriben, which show different conformational dynamics and domain involvement. We identify a binding site for highly potent and selective inhibitors and show that they act by stabilizing the TRPM7 closed state. The discovered structural mechanisms provide foundations for understanding the molecular basis of TRPM7 channelopathies and drug development.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transient receptor potential cation channel subfamily M member 7
A, B, C, D
1,279Mus musculusMutation(s): 0 
Gene Names: Trpm7ChakLtrpc7
EC: 2.7.11.1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q923J1 (Mus musculus)
Explore Q923J1 
Go to UniProtKB:  Q923J1
IMPC:  MGI:1929996
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ923J1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV
Query on POV

Download Ideal Coordinates CCD File 
AB [auth C]
BB [auth C]
CA [auth B]
DA [auth B]
DB [auth D]
AB [auth C],
BB [auth C],
CA [auth B],
DA [auth B],
DB [auth D],
E [auth A],
EA [auth B],
EB [auth D],
F [auth A],
FA [auth B],
FB [auth D],
G [auth A],
GA [auth B],
GB [auth D],
HA [auth B],
HB [auth D],
IA [auth B],
J [auth A],
K [auth A],
KA [auth B],
KB [auth D],
L [auth A],
LA [auth B],
LB [auth D],
M [auth A],
MA [auth C],
MB [auth D],
N [auth A],
NA [auth C],
NB [auth D],
O [auth A],
OA [auth C],
OB [auth D],
P [auth A],
PA [auth C],
PB [auth D],
QB [auth D],
R [auth A],
S [auth A],
SA [auth C],
T [auth A],
TA [auth C],
U [auth A],
UA [auth C],
VA [auth C],
W [auth B],
WA [auth C],
X [auth B],
XA [auth C],
Y [auth B],
YA [auth C],
Z [auth B]
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
3FD (Subject of Investigation/LOI)
Query on 3FD

Download Ideal Coordinates CCD File 
AA [auth B],
H [auth A],
IB [auth D],
QA [auth C]
4-[[(2R,3S,4R,5R)-5-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-3,4-dihydroxy-oxolan-2-yl]methoxymethyl]benzonitrile
C25 H23 Cl2 N7 O4
ZXGGCBQORXDVTE-UMCMBGNQSA-N
DU0
Query on DU0

Download Ideal Coordinates CCD File 
CB [auth C],
JA [auth B],
Q [auth A],
ZA [auth C]
2-[2-[(1~{S},2~{S},4~{S},5'~{R},6~{R},7~{S},8~{R},9~{S},12~{S},13~{R},16~{S})-5',7,9,13-tetramethylspiro[5-oxapentacyclo[10.8.0.0^{2,9}.0^{4,8}.0^{13,18}]icos-18-ene-6,2'-oxane]-16-yl]oxyethyl]propane-1,3-diol
C32 H52 O5
GFDJQXOBWHMOSQ-LEZUHYJESA-N
CLR
Query on CLR

Download Ideal Coordinates CCD File 
BA [auth B],
I [auth A],
JB [auth D],
RA [auth C]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
V [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.18
RECONSTRUCTIONcryoSPARC3.3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA206573
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS083660
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR01 NS107253
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)United StatesR01 AR078814
German Research Foundation (DFG)Germany464295817

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-17
    Type: Initial release
  • Version 1.1: 2023-05-24
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary