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9uww

Cryo-EM structure of the human P2X2 receptor in the apo closed state

Method: ELECTRON MICROSCOPY Dmax: 120.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

P2X purinoceptor 2

Homo sapiens

UniProt Q9UBL9

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 × 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

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 9UWW 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 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 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 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
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 experimental conditions 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 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 × 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 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 × 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 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 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 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 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 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 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 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 × 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 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 × 9 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9ON6 The pre-open state 2 structure of human P2X2 receptor channel in lipid nanodiscs with free ATP and sodium Deposited 2025-05-14 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 × 9 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9UWX Cryo-EM structure of the human P2X2 receptor in the ATP-bound open state Deposited 2025-05-13 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 7.5
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 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 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 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 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 ligand/ion Different experimental conditions 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.

SAXS scattering curve SAXS Profile

SAXS profile for 9uww

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9uww
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9uww
Deposition date deposition_date2025-05-13
Structure title titleCryo-EM structure of the human P2X2 receptor in the apo closed state
Keywords keywordsP2X ion channal, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.02 Å
Radius of gyration Rg (electron density) rg_electron35.04 Å
Forward intensity I(0) i0184159000.00
Molecular weight molecular_weight112540.0 kDa
Excluded volume excluded_volume142370 ų
Envelope volume envelope_volume193920 ų
Hydration-shell volume shell_volume47813 ų
Envelope diameter envelope_diameter123.9 Å
Shell Rg shell_rg39.82 Å
Envelope Rg envelope_rg35.64 Å
Shape Rg shape_rg34.93 Å
Total Rg total_rg35.76 Å
Total atoms total_atoms7924
Residues n_residues987
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax120.1 Å
Rg (real space) rg_real35.18 Å
Rg uncertainty (real space) rg_real_error1.28 Å
I(0) (real space) i0_real1.8420e+08
I(0) uncertainty (real space) i0_real_error3.0370e+06
Rg (reciprocal space) rg_reciprocal35.08 Å
I(0) (reciprocal space) i0_reciprocal184100000.0000
Solution quality estimate total_estimate0.8451
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.0 Å
Skewness Skewness skewness0.581
Kurtosis Kurtosis kurtosis0.048
Angular range angular_range— – 0.2250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha27380000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.716; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.850
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)