8V4S

Cryo-EM structure of the rat P2X7 receptor in the apo closed state purified in the absence of sodium


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

High-affinity agonism at the P2X 7 receptor is mediated by three residues outside the orthosteric pocket.

Oken, A.C.Lisi, N.E.Krishnamurthy, I.McCarthy, A.E.Godsey, M.H.Glasfeld, A.Mansoor, S.E.

(2024) Nat Commun 15: 6662-6662

  • DOI: https://doi.org/10.1038/s41467-024-50771-6
  • Primary Citation of Related Structures:  
    8TR5, 8TRJ, 8V4S

  • PubMed Abstract: 

    P2X receptors are trimeric ATP-gated ion channels that activate diverse signaling cascades. Due to its role in apoptotic pathways, selective activation of P2X 7 is a potential experimental tool and therapeutic approach in cancer biology. However, mechanisms of high-affinity P2X 7 activation have not been defined. We report high-resolution cryo-EM structures of wild-type rat P2X 7 bound to the high-affinity agonist BzATP as well as significantly improved apo receptor structures in the presence and absence of sodium. Apo structures define molecular details of pore architecture and reveal how a partially hydrated Na + ion interacts with the conductance pathway in the closed state. Structural, electrophysiological, and direct binding data of BzATP reveal that three residues just outside the orthosteric ATP-binding site are responsible for its high-affinity agonism. This work provides insights into high-affinity agonism for any P2X receptor and lays the groundwork for development of subtype-specific agonists applicable to cancer therapeutics.


  • Organizational Affiliation

    Department of Chemical Physiology & Biochemistry, Oregon Health & Science University, Portland, OR, 97239, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
P2X purinoceptor 7
A, B, C
595RattusMutation(s): 0 
Gene Names: P2rx7
Membrane Entity: Yes 
UniProt
Find proteins for Q64663 (Rattus norvegicus)
Explore Q64663 
Go to UniProtKB:  Q64663
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ64663
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
D [auth A],
O [auth B],
Z [auth C]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
PLM (Subject of Investigation/LOI)
Query on PLM

Download Ideal Coordinates CCD File 
FA [auth C]
GA [auth C]
HA [auth C]
IA [auth C]
J [auth A]
FA [auth C],
GA [auth C],
HA [auth C],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
CA [auth C]
DA [auth C]
EA [auth C]
G [auth A]
H [auth A]
CA [auth C],
DA [auth C],
EA [auth C],
G [auth A],
H [auth A],
I [auth A],
R [auth B],
S [auth B],
T [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
E [auth A]
F [auth A]
P [auth B]
AA [auth C],
BA [auth C],
E [auth A],
F [auth A],
P [auth B],
Q [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.49 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesR00HL138129
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2GM149551

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-08-21
    Changes: Advisory, Data collection, Database references, Derived calculations