SAXSdb — 9xqr

▼

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

P2X purinoceptor 1

Mus musculus

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 1–399 Chain B； UniProt 1–399 Chain C； UniProt 1–399	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 1 MG MAGNESIUM ION × 3 A1D8Z 3,5-bis(trifluoromethyl)aniline × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.3 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.14 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 9XQR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8ZT1 sStructure of calcium preference ATP-gated channel P2X1 in complex with BTFA Deposited 2024-06-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–399（399 aa） Chain B 1–399（399 aa） Chain C 1–399（399 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 A1D8Z 3,5-bis(trifluoromethyl)aniline × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 CA CALCIUM ION × 2 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8ZT2 Structure of calcium preference ATP-gated channel Apo-P2X1 in the Desensitized state 1 Deposited 2024-06-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–399（399 aa） Chain B 1–399（399 aa） Chain C 1–399（399 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MG MAGNESIUM ION × 3 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.31 Å
8ZT5 Structure of calcium preference ATP-gated channel P2X1 in the Desensitized state 2 in the presence of 1mM Calcium ion Deposited 2024-06-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–399（399 aa） Chain B 1–399（399 aa） Chain C 1–399（399 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MG MAGNESIUM ION × 3 CA CALCIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.35 Å
8ZT8 Structure of calcium preference ATP-gated channel P2X1 in the Desensitized state 3 in the presence of 5mM Calcium ion Deposited 2024-06-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–399（399 aa） Chain B 1–399（399 aa） Chain C 1–399（399 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MG MAGNESIUM ION × 3 CA CALCIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.34 Å
8ZTA Structure of calcium preference ATP-gated channel P2X1 in the Desensitized state 4 in the presence of 10mM Calcium ion Deposited 2024-06-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–399（399 aa） Chain B 1–399（399 aa） Chain C 1–399（399 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MG MAGNESIUM ION × 3 CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.58 Å
8ZTD Structure of calcium preference ATP-gated channel P2X1 in the Desensitized state 5 in the presence of 10 mM Calcium ion Deposited 2024-06-07	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–399（399 aa） Chain B 1–399（399 aa） Chain C 1–399（399 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 MG MAGNESIUM ION × 3 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.63 Å
8ZTF Structure of calcium preference ATP-gated channel P2X1 in the Pre-open state in the presence of 10mM Calcium ion Deposited 2024-06-07	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–399（399 aa） Chain B 1–399（399 aa） Chain C 1–399（399 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 MG MAGNESIUM ION × 3 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.43 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	P2RX1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–399； UniProt 1–399 Author chain B； PDBConstruct 1–399； UniProt 1–399 Author chain C； PDBConstruct 1–399； UniProt 1–399

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9xqr
Deposition date deposition_date	2025-11-18
Structure title title	Cryo-EM structure of P1X1 in complex with BTFA
Keywords keywords	ION CHANNEL, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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

Radius of gyration Rg (Guinier) rg_guinier	33.26 Å
Radius of gyration Rg (electron density) rg_electron	33.07 Å
Forward intensity I(0) i0	383603000.00
Molecular weight molecular_weight	105610.0 kDa
Excluded volume excluded_volume	102390 Å³
Envelope volume envelope_volume	188780 Å³
Hydration-shell volume shell_volume	48029 Å³
Envelope diameter envelope_diameter	119.4 Å
Shell Rg shell_rg	39.24 Å
Envelope Rg envelope_rg	33.82 Å
Shape Rg shape_rg	33.07 Å
Total Rg total_rg	33.43 Å
Total atoms total_atoms	7992
Residues n_residues	997
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

▼

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

Maximum dimension Dmax dmax	114.0 Å
Rg (real space) rg_real	33.41 Å
Rg uncertainty (real space) rg_real_error	0.81 Å
I(0) (real space) i0_real	3.8360e+08
I(0) uncertainty (real space) i0_real_error	5.4850e+06
Rg (reciprocal space) rg_reciprocal	33.35 Å
I(0) (reciprocal space) i0_reciprocal	383600000.0000
Solution quality estimate total_estimate	0.8398
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.0 Å
Skewness Skewness skewness	0.562
Kurtosis Kurtosis kurtosis	0.081
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	35010000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.717; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.780

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	P2X purinoceptor 1
Molecular weight formula_weight	48413.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,C,A
Atom count atom_count	7995

MARRLQDELSAFFFEYDTPRMVLVRNKKVGVIFRLIQLVVLVYVIGWVFVYEKGYQTSSGLISSVSVKLKGLAVTQLQGLGPQVWDVADYVFPAHGDSSFVVMTNFIMTPQQAQGHCAENPEGGICQDDSGCTPGKAERKAQGIRTGNCVPFNGTVKTCEIFGWCPVEVDDKIPSPALLHEAENFTLFIKNSISFPRFKVNRRNLVEEVNGTYMKKCLYHKILHPLCPVFSLGYVVRESGQDFRSLAEKGGVVGITIDWECDLDWHVRHCKPIYQFHGLYGEKNLSPGFNFRFARHFVQNGTNRRHLFKVFGIRFDILVDGKAGKFDIIPTMTTIGSGIGIFGVATVLCDLLLLHILPKRHYYKQKKFKYAEDMGPGEGERDPAATSSTLGLQENMRTSKLLEVLFQGPHHHHHHHHHHDYKDDDDK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 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	3

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	3,5-bis(trifluoromethyl)aniline
Molecular weight formula_weight	229.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3

▶

8. Citations (1)

▶

Resolution resolution	3.14 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	218684

fit	/app/data/saxs_computation/xq/9xqr/9xqr.fit
pddf	/app/data/pr_computation/xq/9xqr/9xqr.pr.out
profile	/app/data/saxs_computation/xq/9xqr/9xqr.dat

Cryo-EM structure of P1X1 in complex with BTFA