SAXSdb — 9y7x

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

Glycine receptor subunit alpha-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 × 5 PDB declaration: pentameric（5） Consistent with protein copy count	Chain A； UniProt 1–452 Chain B； UniProt 1–452 Chain C； UniProt 1–452 Chain D； UniProt 1–452 Chain E； UniProt 1–452	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 GLY GLYCINE × 5	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.55 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 9Y7X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5BKF Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer, Glycine bound, desensitized state Deposited 2021-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 28–343（316 aa） Chain A 409–452（44 aa） Chain B 28–343（316 aa） Chain B 409–452（44 aa） Chain C 28–343（316 aa） Chain C 409–452（44 aa） Chain D 28–343（316 aa） Chain D 409–452（44 aa）	Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 GLY GLYCINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
5BKG Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer, glycine bound, (semi)open state Deposited 2021-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 28–343（316 aa） Chain A 409–452（44 aa） Chain B 28–343（316 aa） Chain B 409–452（44 aa） Chain C 28–343（316 aa） Chain C 409–452（44 aa） Chain D 28–343（316 aa） Chain D 409–452（44 aa）	Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 GLY GLYCINE × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7KUY Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer, strychnine bound state Deposited 2020-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 28–343（316 aa） Chain A 409–452（44 aa） Chain B 28–343（316 aa） Chain B 409–452（44 aa） Chain C 28–343（316 aa） Chain C 409–452（44 aa） Chain D 28–343（316 aa） Chain D 409–452（44 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 SY9 STRYCHNINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7L31 Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer, strychnine bound state, 3.8 Angstrom Deposited 2020-12-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 28–343（316 aa） Chain A 409–452（44 aa） Chain B 28–343（316 aa） Chain B 409–452（44 aa） Chain C 28–343（316 aa） Chain C 409–452（44 aa） Chain D 28–343（316 aa） Chain D 409–452（44 aa）	Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted Mutation：second cytoplasmic domain deleted	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 9 SY9 STRYCHNINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9Y7P Homomeric Glycine Receptor alpha2 with 1 mM Glycine in a Desensitized State Deposited 2025-09-11	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–452（452 aa） Chain B 1–452（452 aa） Chain C 1–452（452 aa） Chain D 1–452（452 aa） Chain E 1–452（452 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 GLY GLYCINE × 5 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
9Y7W Homomeric Glycine Receptor alpha2 with 1 mM Glycine in an Open State Deposited 2025-09-11	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–452（452 aa） Chain B 1–452（452 aa） Chain C 1–452（452 aa） Chain D 1–452（452 aa） Chain E 1–452（452 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 GLY GLYCINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.19 Å
9Y7Z Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine in a Desensitized State Deposited 2025-09-11	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–452（452 aa） Chain B 1–452（452 aa） Chain C 1–452（452 aa） Chain D 1–452（452 aa） Chain E 1–452（452 aa）	Not recorded	PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 GLY GLYCINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.78 Å
9Y80 Homomeric Glycine Receptor alpha2 with PTX in a Desensitized State Deposited 2025-09-11	Different ligand/ion	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–452（452 aa） Chain B 1–452（452 aa） Chain C 1–452（452 aa） Chain D 1–452（452 aa） Chain E 1–452（452 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 GLY GLYCINE × 5 RI5 (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione × 1 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 15	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.55 Å
9Y8Z Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine in an Apo State Deposited 2025-09-11	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–452（452 aa） Chain B 1–452（452 aa） Chain C 1–452（452 aa） Chain D 1–452（452 aa） Chain E 1–452（452 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 30 CLR CHOLESTEROL × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
9Y94 Homomeric Glycine Receptor alpha2 with PTX in an Open State Deposited 2025-09-13	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–452（452 aa） Chain B 1–452（452 aa） Chain C 1–452（452 aa） Chain D 1–452（452 aa） Chain E 1–452（452 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 GLY GLYCINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9Y95 Homomeric Glycine Receptor alpha2 with PTX in an Apo State Deposited 2025-09-13	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–452（452 aa） Chain B 1–452（452 aa） Chain C 1–452（452 aa） Chain D 1–452（452 aa） Chain E 1–452（452 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 PX4 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 20 RI5 (1aR,2aR,3S,6R,6aS,8aS,8bR,9R)-2a-hydroxy-8b-methyl-9-(prop-1-en-2-yl)hexahydro-3,6-methano-1,5,7-trioxacyclopenta[ij]c yclopropa[a]azulene-4,8(3H)-dione × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
9Y96 Homomeric Glycine Receptor alpha2 with 1 mM Glycine in a Closed State Deposited 2025-09-13	Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–452（452 aa） Chain B 1–452（452 aa） Chain C 1–452（452 aa） Chain D 1–452（452 aa） Chain E 1–452（452 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10 GLY GLYCINE × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.36 Å

12 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GLRA2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–452； UniProt 1–452 Author chain B； PDBConstruct 1–452； UniProt 1–452 Author chain C； PDBConstruct 1–452； UniProt 1–452 Author chain D； PDBConstruct 1–452； UniProt 1–452 Author chain E； PDBConstruct 1–452； UniProt 1–452

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	9y7x
Deposition date deposition_date	2025-09-11
Structure title title	Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine in an Open State
Keywords keywords	homopentamer, ion channel, ligand gated ion channel, TRANSPORT PROTEIN; TRANSPORT 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	39.69 Å
Radius of gyration Rg (electron density) rg_electron	39.14 Å
Forward intensity I(0) i0	555526000.00
Molecular weight molecular_weight	201610.0 kDa
Excluded volume excluded_volume	255860 Å³
Envelope volume envelope_volume	338500 Å³
Hydration-shell volume shell_volume	70617 Å³
Envelope diameter envelope_diameter	132.2 Å
Shell Rg shell_rg	46.17 Å
Envelope Rg envelope_rg	38.66 Å
Shape Rg shape_rg	39.17 Å
Total Rg total_rg	39.46 Å
Total atoms total_atoms	14199
Residues n_residues	1732
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	128.0 Å
Rg (real space) rg_real	39.60 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	5.5550e+08
I(0) uncertainty (real space) i0_real_error	9.1670e+06
Rg (reciprocal space) rg_reciprocal	39.66 Å
I(0) (reciprocal space) i0_reciprocal	555600000.0000
Solution quality estimate total_estimate	0.8108
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	48.0 Å
Skewness Skewness skewness	0.337
Kurtosis Kurtosis kurtosis	-0.272
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	78980000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.847; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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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	Glycine receptor subunit alpha-2
Molecular weight formula_weight	53782.8 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	14199

MNRQLVNILTALFAFFLETNHFRTAFCKDHDSRSGKQPSQTLSPSDFLDKLMGRTSGYDARIRPNFKGPPVNVTCNIFINSFGSVTETTMDYRVNIFLRQQWNDSRLAYSEYPDDSLDLDPSMLDSIWKPDLFFANEKGANFHDVTTDNKLLRISKNGKVLYSIRLTLTLSCPMDLKNFPMDVQTCTMQLESFGYTMNDLIFEWLSDGPVQVAEGLTLPQFILKEEKELGYCTKHYNTGKFTCIEVKFHLERQMGYYLIQMYIPSLLIVILSWVSFWINMDAAPARVALGITTVLTMTTQSSGSRASLPKVSYVKAIDIWMAVCLLFVFAALLEYAAVNFVSRQHKEFLRLRRRQKRQNKEEDVTRESRFNFSGYGMGHCLQVKDGTAVKATPANPLPQPPKDGDAIKKKFVDRAKRIDTISRAAFPLAFLIFNIFYWITYKIIRHEDVHKKLVPRGSHHHHHHHH

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	Spodoptera aff. frugiperda 1 BOLD-2017

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	10

Entity 3 Entity 3 non-polymer

Description description	GLYCINE
Molecular weight formula_weight	75.1 kDa
Source method src_method	syn
Copy count entity_count	5

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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	3.550 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.55 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	16416

fit	/app/data/saxs_computation/y7/9y7x/9y7x.fit
pddf	/app/data/pr_computation/y7/9y7x/9y7x.pr.out
profile	/app/data/saxs_computation/y7/9y7x/9y7x.dat

Homomeric Glycine Receptor alpha2 with 0.1 mM Glycine in an Open State

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

Glycine receptor subunit alpha-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

Refinement Refinement

冷冻电镜 EM 3D