Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

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

 6U9V

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

• PDB DOI:  https://doi.org/10.2210/pdb6U9V/pdb
• EM Map EMD-20702: EMDB EMDataResource

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


• Deposited: 2019-09-09 Released: 2019-10-23 
• Deposition Author(s): Mansoor, S.E., McCarthy, A.E.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

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

Literature

Full-Length P2X7Structures Reveal How Palmitoylation Prevents Channel Desensitization.

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

(2019) Cell 179: 659-670.e13

• PubMed: 31587896 
• DOI: https://doi.org/10.1016/j.cell.2019.09.017
• Primary Citation of 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.

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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. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P2X purinoceptor 7	A, B, C	609	Rattus norvegicus	Mutation(s): 0  Gene Names: P2rx7 Membrane Entity: Yes
UniProt
Find proteins for Q64663 (Rattus norvegicus) Explore Q64663  Go to UniProtKB:  Q64663

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, E, F, G, H, I	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	J, K, L	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q3G	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)	M [auth A], MA [auth C], Z [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
PLM	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	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)	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

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	J, K, L	alpha-maltose	Oligosaccharide / Nutrient		Ligand Interaction

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-10-23 
Deposition Author(s): Mansoor, S.E., McCarthy, A.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	K99HL138129

Revision History  

• 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