6U9V | pdb_00006u9v

Cryo electron microscopy structure of the ATP-gated rat P2X7 ion channel in the apo, closed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6U9V

This is version 3.0 of the entry. See complete history

Literature

Full-Length P2X7Structures Reveal How Palmitoylation Prevents Channel Desensitization.

McCarthy, A.E.Yoshioka, C.Mansoor, S.E.

(2019) Cell 179: 659-670.e13

  • DOI: https://doi.org/10.1016/j.cell.2019.09.017
  • Primary Citation Related Structures: 
    6U9V, 6U9W

  • PubMed Abstract: 

    P2X receptors are trimeric, non-selective cation channels activated by extracellular ATP. The P2X 7 receptor subtype is a pharmacological target because of involvement in apoptotic, inflammatory, and tumor progression pathways. It is the most structurally and functionally distinct P2X subtype, containing a unique cytoplasmic domain critical for the receptor to initiate apoptosis and not undergo desensitization. However, lack of structural information about the cytoplasmic domain has hindered understanding of the molecular mechanisms underlying these processes. We report cryoelectron microscopy structures of full-length rat P2X 7 receptor in apo and ATP-bound states. These structures reveal how one cytoplasmic element, the C-cys anchor, prevents desensitization by anchoring the pore-lining helix to the membrane with palmitoyl groups. They show a second cytoplasmic element with a unique fold, the cytoplasmic ballast, which unexpectedly contains a zinc ion complex and a guanosine nucleotide binding site. Our structures provide first insights into the architecture and function of a P2X receptor cytoplasmic domain.


  • Organizational Affiliation
    • Vollum Institute, Oregon Health and Science University, Portland, OR 97239, USA; Knight Cardiovascular Institute, Oregon Health and Science University, Portland, OR 97239, USA.

Macromolecule Content 

  • Total Structure Weight: 223.91 kDa 
  • Atom Count: 14,067 
  • Modeled Residue Count: 1,680 
  • Deposited Residue Count: 1,827 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
P2X purinoceptor 7
A, B, C
609Rattus norvegicusMutation(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
Glycosylation
Glycosylation Sites: 4Go to GlyGen: Q64663-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, F, G, H
D, E, F, G, H, I
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
J, K, L
2N/A
Glycosylation Resources
GlyTouCan: G07411ON
GlyCosmos: G07411ON

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q3G

Query on Q3G



Download:Ideal Coordinates CCD File
FA [auth B],
S [auth A],
SA [auth C]
O-[(R)-[(2S)-2-(hexadecanoyloxy)-3-(octadecanoyloxy)propoxy](hydroxy)phosphoryl]-D-serine
C40 H78 N O10 P
WZFUPCSEUKNOBF-PQQNNWGCSA-N
GDP
(Subject of Investigation/LOI)

Query on GDP



Download:Ideal Coordinates CCD File
M [auth A],
MA [auth C],
Z [auth B]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
PLM

Query on PLM



Download:Ideal Coordinates CCD File
GA [auth B]
HA [auth B]
IA [auth B]
JA [auth B]
KA [auth B]
GA [auth B],
HA [auth B],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
T [auth A],
TA [auth C],
U [auth A],
UA [auth C],
V [auth A],
VA [auth C],
W [auth A],
WA [auth C],
X [auth A],
XA [auth C],
Y [auth A],
YA [auth C]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
NAG

Query on NAG



Download:Ideal Coordinates CCD File
CA [auth B]
DA [auth B]
EA [auth B]
P [auth A]
PA [auth C]
CA [auth B],
DA [auth B],
EA [auth B],
P [auth A],
PA [auth C],
Q [auth A],
QA [auth C],
R [auth A],
RA [auth C]
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 B]
BA [auth B]
N [auth A]
NA [auth C]
O [auth A]
AA [auth B],
BA [auth B],
N [auth A],
NA [auth C],
O [auth A],
OA [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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 StatesK99HL138129

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-23
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2024-12-25
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary