8ZTF | pdb_00008ztf

Structure of calcium preference ATP-gated channel P2X1 in the Pre-open state in the presence of 10mM Calcium ion

PDB DOI: https://doi.org/10.2210/pdb8ZTF/pdb
EM Map EMD-60460: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-06-07 Released: 2025-06-11
Deposition Author(s): Zhang, H., Xu, H.E.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.43 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis of ion permeation, calcium selectivity, and pore blocking at the P2X1 receptor

Zhang, H., Xu, H.E.

To be published.

Macromolecule Content

Total Structure Weight: 138.17 kDa
Atom Count: 7,978
Modeled Residue Count: 990
Deposited Residue Count: 1,197
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P2X purinoceptor 1	A, B, C	399	Mus musculus	Mutation(s): 0 Gene Names: P2rx1
UniProt
Find proteins for P51576 (Mus musculus) Explore P51576 Go to UniProtKB: P51576
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51576
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: P51576-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth A] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B]	D [auth A], H [auth A], K [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain H [auth A] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth A] Focus chain K [auth B]
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C]	E [auth A] F [auth A] G [auth A] L [auth B] M [auth B] E [auth A], F [auth A], G [auth A], L [auth B], M [auth B], N [auth B], R [auth C], S [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain P [auth B] SDF format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B]	O [auth B], P [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain O [auth B] Focus chain P [auth B] Interactions & Density Focus chain O [auth B] Focus chain P [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain Q [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain Q [auth C]	I [auth A], J [auth B], Q [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain Q [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain Q [auth C]