SAXSdb — 8zfb

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

G-protein coupled receptor 4

Xenopus tropicalis

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain R； UniProt 1–353	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.2 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.78 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 8ZFB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8ZD1 Cryo-EM structure of the xGPR4-Gs complex in pH6.2 Deposited 2024-04-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 13–301（289 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
8ZF4 Cryo-EM structure of the receptor of xGPR4-Gs complex in pH6.2 Deposited 2024-05-07	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain R 1–353（353 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å
8ZF6 Cryo-EM structure of the xGPR4-Gs complex in pH6.7 Deposited 2024-05-07	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–353（353 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.98 Å
8ZF7 Cryo-EM structure of the receptor of xGPR4-Gs complex in pH6.7 Deposited 2024-05-07	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain R 1–353（353 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
8ZFA Cryo-EM structure of the xtGPR4-Gs complex in pH7.2 Deposited 2024-05-07	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–353（353 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å
9JVM Cryo-EM structure of the receptor of xGPR4-apo in pH8.0 Deposited 2024-10-09	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain R 1–353（353 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.36 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A6I8PUB9_XENTR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain R； PDBConstruct 1–353； UniProt 1–353

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	8zfb
Deposition date deposition_date	2024-05-07
Structure title title	Cryo-EM structure of the receptor of xtGPR4-Gs complex in pH7.2
Keywords keywords	pH7.2, xtGPR4, receptor, 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	21.67 Å
Radius of gyration Rg (electron density) rg_electron	20.44 Å
Forward intensity I(0) i0	14513300.00
Molecular weight molecular_weight	29591.0 kDa
Excluded volume excluded_volume	37524 Å³
Envelope volume envelope_volume	46314 Å³
Hydration-shell volume shell_volume	19453 Å³
Envelope diameter envelope_diameter	72.6 Å
Shell Rg shell_rg	26.42 Å
Envelope Rg envelope_rg	20.93 Å
Shape Rg shape_rg	20.41 Å
Total Rg total_rg	21.45 Å
Total atoms total_atoms	2088
Residues n_residues	286
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	70.2 Å
Rg (real space) rg_real	21.72 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.4510e+07
I(0) uncertainty (real space) i0_real_error	1.9570e+05
Rg (reciprocal space) rg_reciprocal	21.71 Å
I(0) (reciprocal space) i0_reciprocal	14510000.0000
Solution quality estimate total_estimate	0.8655
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.395
Kurtosis Kurtosis kurtosis	-0.363
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2531000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.676

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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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	3.78 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	167112

Description description	G-protein coupled receptor 4
Molecular weight formula_weight	38083.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	R
Atom count atom_count	2088

Cryo-EM structure of the receptor of xtGPR4-Gs complex in pH7.2

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

G-protein coupled receptor 4

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Xenopus tropicalis
通用名 common_name	tropical clawed frog
NCBI Class编号 ncbi_taxonomy_id	8364
宿主生物 host_organism	Spodoptera frugiperda

fit	/app/data/saxs_computation/zf/8zfb/8zfb.fit
pddf	/app/data/pr_computation/zf/8zfb/8zfb.pr.out
profile	/app/data/saxs_computation/zf/8zfb/8zfb.dat