SAXSdb — 8w8s

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

Probable G-protein coupled receptor 101

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain R； UniProt 1–508	Not recorded	U7D 1-(4-methylpyridin-2-yl)-3-[3-(trifluoromethyl)phenyl]thiourea × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.30 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 8W8S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8W8Q Cryo-EM structure of the GPR101-Gs complex Deposited 2023-09-04	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 1–508（508 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.89 Å
8W8R Cryo-EM structure of the AA-14-bound GPR101-Gs complex Deposited 2023-09-04	Different oligomeric state	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–508（508 aa）	Not recorded	U7D 1-(4-methylpyridin-2-yl)-3-[3-(trifluoromethyl)phenyl]thiourea × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GP101_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain R； PDBConstruct 1–508； UniProt 1–508

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	8w8s
Deposition date deposition_date	2023-09-04
Structure title title	Cryo-EM structure of the AA14-bound GPR101 complex
Keywords keywords	GPCR, orphan receptor, GPR101, constitutive activity, cryo-EM, structural protein, 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	22.19 Å
Radius of gyration Rg (electron density) rg_electron	21.08 Å
Forward intensity I(0) i0	14379600.00
Molecular weight molecular_weight	32066.0 kDa
Excluded volume excluded_volume	41762 Å³
Envelope volume envelope_volume	52764 Å³
Hydration-shell volume shell_volume	21287 Å³
Envelope diameter envelope_diameter	77.4 Å
Shell Rg shell_rg	27.32 Å
Envelope Rg envelope_rg	21.44 Å
Shape Rg shape_rg	21.08 Å
Total Rg total_rg	22.13 Å
Total atoms total_atoms	2265
Residues n_residues	281
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	74.6 Å
Rg (real space) rg_real	22.19 Å
Rg uncertainty (real space) rg_real_error	0.61 Å
I(0) (real space) i0_real	1.4380e+07
I(0) uncertainty (real space) i0_real_error	2.1620e+05
Rg (reciprocal space) rg_reciprocal	22.19 Å
I(0) (reciprocal space) i0_reciprocal	14380000.0000
Solution quality estimate total_estimate	0.8000
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.6 Å
Skewness Skewness skewness	0.338
Kurtosis Kurtosis kurtosis	-0.347
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2378000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.813; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Probable G-protein coupled receptor 101
Molecular weight formula_weight	56774.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R
Atom count atom_count	2265

MTSTCTNSTRESNSSHTCMPLSKMPISLAHGIIRSTVLVIFLAASFVGNIVLALVLQRKPQLLQVTNRFIFNLLVTDLLQISLVAPWVVATSVPLFWPLNSHFCTALVSLTHLFAFASVNTIVVVSVDRYLSIIHPLSYPSKMTQRRGYLLLYGTWIVAILQSTPPLYGWGQAAFDERNALCSMIWGASPSYTILSVVSFIVIPLIVMIACYSVVFCAARRQHALLYNVKRHSLEVRVKDCVENEDEEGAEKKEEFQDESEFRRQHEGEVKAKEGRMEAKDGSLKAKEGSTGTSESSVEARGSEEVRESSTVASDGSMEGKEGSTKVEENSMKADKGRTEVNQCSIDLGEDDMEFGEDDINFSEDDVEAVNIPESLPPSRRNSNSNPPLPRCYQCKAAKVIFIIIFSYVLSLGPYCFLAVLAVWVDVETQVPQWVITIIIWLFFLQCCIHPYVYGYMHKTIKKEIQDMLKKFFCKEKPPKEDSHPDLPGTEGGTEGKIVPSYDSATFP

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 frugiperda

Entity 2 Entity 2 non-polymer

Description description	1-(4-methylpyridin-2-yl)-3-[3-(trifluoromethyl)phenyl]thiourea
Molecular weight formula_weight	311.3 kDa
Source method src_method	syn
Copy count entity_count	2

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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	3.30 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	3646024

fit	/app/data/saxs_computation/w8/8w8s/8w8s.fit
pddf	/app/data/pr_computation/w8/8w8s/8w8s.pr.out
profile	/app/data/saxs_computation/w8/8w8s/8w8s.dat

Cryo-EM structure of the AA14-bound GPR101 complex

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

Probable G-protein coupled receptor 101

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)