SAXSdb — 9on6

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1. Protein Identity and Related Structures Protein Identity & Related Structures

P2X purinoceptor 2

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–471 Chain B； UniProt 1–471 Chain C； UniProt 1–471	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ATP ADENOSINE-5'-TRIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer：pH 7 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9ON6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9DDV Cryo-EM structure of the human P2X2 receptor in the apo closed state Deposited 2024-08-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.71 Å
9DDW Cryo-EM structure of the human P2X2 receptor in conformation I of the ATP-bound desensitized state Deposited 2024-08-28	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.49 Å
9DDX Cryo-EM structure of the human P2X2 receptor in conformation II of the ATP-bound desensitized state Deposited 2024-08-28	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 43–361（319 aa） Chain B 43–361（319 aa） Chain C 43–361（319 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.55 Å
9OGH Human P2X2 apo structure in lipid nanodiscs Deposited 2025-04-30	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 POV (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate × 24 NA SODIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
9OHK Human P2X2 receptor channel in lipid nanodiscs with 0.5mM Suramin Deposited 2025-05-05	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 SVR 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9OIR Human P2X2 receptor channel in detergent with residual ATP Deposited 2025-05-06	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9OJK The open state structure of human P2X2 receptor channel in lipid nanodiscs with free ATP and sodium Deposited 2025-05-07	Parsed fields agree	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9OM0 The pre-desensitized state structure of human P2X2 receptor channel in lipid nanodiscs with free ATP and sodium Deposited 2025-05-13	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.58 Å
9OMR The desensitized state structure of human P2X2 receptor channel in lipid nanodiscs with free ATP and sodium Deposited 2025-05-14	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ATP ADENOSINE-5'-TRIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.68 Å
9ON5 The pre-open state 1 structure of human P2X2 receptor channel in lipid nanodiscs with free ATP and sodium Deposited 2025-05-14	Parsed fields agree	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ATP ADENOSINE-5'-TRIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
9UWW Cryo-EM structure of the human P2X2 receptor in the apo closed state Deposited 2025-05-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 PG8 1,2-DIOCTANOYL-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL) × 3 NA SODIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.19 Å
9UWX Cryo-EM structure of the human P2X2 receptor in the ATP-bound open state Deposited 2025-05-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.41 Å
9UWY Cryo-EM structure of the human P2X2 receptor in the ATP-bound desensitised state Deposited 2025-05-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–471（471 aa） Chain B 1–471（471 aa） Chain C 1–471（471 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.48 Å
9UX1 Cryo-EM structure of the human P2X2/3 heteromer receptor - class 1 (1:2) Deposited 2025-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–471（471 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.98 Å
9UX2 Cryo-EM structure of the human P2X2/3 heteromer receptor - class 2 (2:1) Deposited 2025-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–471（471 aa） Chain C 1–471（471 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.73 Å
9UX3 Cryo-EM structure of the human P2X2/3 heteromer receptor bound to AF-219 Deposited 2025-05-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–471（471 aa） Chain C 1–471（471 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 AF9 5-[2,4-bis(azanyl)pyrimidin-5-yl]oxy-2-methoxy-4-propan-2-yl-benzenesulfonamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.64 Å
9Z32 The structure of short splice variant (Q9UBL9-2) of human P2X2 receptor channel in lipid nanodiscs with Mg-ATP Deposited 2025-11-05	Different construct Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–404（404 aa） Chain B 1–404（404 aa） Chain C 1–404（404 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 ATP ADENOSINE-5'-TRIPHOSPHATE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å

17 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	P2RX2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–471； UniProt 1–471 Author chain B； PDBConstruct 1–471； UniProt 1–471 Author chain C； PDBConstruct 1–471； UniProt 1–471

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9on6
Deposition date deposition_date	2025-05-14
Structure title title	The pre-open state 2 structure of human P2X2 receptor channel in lipid nanodiscs with free ATP and sodium
Keywords keywords	ATP-gated ion channel, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.73 Å
Radius of gyration Rg (electron density) rg_electron	32.69 Å
Forward intensity I(0) i0	187027000.00
Molecular weight molecular_weight	110740.0 kDa
Excluded volume excluded_volume	139170 Å³
Envelope volume envelope_volume	184000 Å³
Hydration-shell volume shell_volume	47381 Å³
Envelope diameter envelope_diameter	114.5 Å
Shell Rg shell_rg	38.90 Å
Envelope Rg envelope_rg	33.16 Å
Shape Rg shape_rg	32.65 Å
Total Rg total_rg	33.33 Å
Total atoms total_atoms	7791
Residues n_residues	969
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	108.7 Å
Rg (real space) rg_real	32.77 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	1.8700e+08
I(0) uncertainty (real space) i0_real_error	2.8920e+06
Rg (reciprocal space) rg_reciprocal	32.75 Å
I(0) (reciprocal space) i0_reciprocal	187000000.0000
Solution quality estimate total_estimate	0.6442
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.5 Å
Skewness Skewness skewness	0.467
Kurtosis Kurtosis kurtosis	0.010
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	28050000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 0.049; Positv: 1.000; Valcen: 0.999; Smooth: 0.826

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	P2X purinoceptor 2
Molecular weight formula_weight	51815.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,B
Atom count atom_count	7791

MAAAQPKYPAGATARRLARGCWSALWDYETPKVIVVRNRRLGVLYRAVQLLILLYFVWYVFIVQKSYQESETGPESSIITKVKGITTSEHKVWDVEEYVKPPEGGSVFSIITRVEATHSQTQGTCPESIRVHNATCLSDADCVAGELDMLGNGLRTGRCVPYYQGPSKTCEVFGWCPVEDGASVSQFLGTMAPNFTILIKNSIHYPKFHFSKGNIADRTDGYLKRCTFHEASDLYCPIFKLGFIVEKAGESFTELAHKGGVIGVIINWDCDLDLPASECNPKYSFRRLDPKHVPASSGYNFRFAKYYKINGTTTRTLIKAYGIRIDVIVHGQAGKFSLIPTIINLATALTSVGVGSFLCDWILLTFMNKNKVYSHKKFDKVCTPSHPSGSWPVTLARVLGQAPPEPGHRSEDQHPSPPSGQEGQQGAECGPAFPPLRPCPISAPSEQMVDTPASEPAQASTPTDPKGLAQL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	3

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.60 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	106536

fit	/app/data/saxs_computation/on/9on6/9on6.fit
pddf	/app/data/pr_computation/on/9on6/9on6.pr.out
profile	/app/data/saxs_computation/on/9on6/9on6.dat

The pre-open state 2 structure of human P2X2 receptor channel in lipid nanodiscs with free ATP and sodium

1. Protein Identity and Related Structures Protein Identity & Related Structures

P2X purinoceptor 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D