SAXSdb — 8hc0

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

Adhesion G-protein coupled receptor F1

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	Other combination Homooligomer Protein × 3 其他Polymer 1 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 207–566 Chain B； UniProt 150–206 Chain C； UniProt 567–580	Fragment：C-terminal Fragment：N-terminal	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；289 K；0.2 M ammonium sulfate, 0.1 M sodium acetate trihydrate pH 4.6, 30% PEG-MME 2,000, 15% glycerol	Resolution 2.90 Å R-free 0.292

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 8HC0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7WU3 Cryo-EM structure of the adhesion GPCR ADGRF1 in complex with miniGs Deposited 2022-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 251–860（610 aa）	Not recorded	K6G [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] hexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7WU4 Cryo-EM structure of the adhesion GPCR ADGRF1 in complex with miniGi Deposited 2022-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 251–860（610 aa）	Not recorded	CLR CHOLESTEROL × 1 K6G [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] hexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
7WU5 Cryo-EM structure of the adhesion GPCR ADGRF1(H565A/T567A) in complex with miniGi Deposited 2022-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 251–860（610 aa）	Mutation：H565A, T567A	CLR CHOLESTEROL × 1 K6G [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] hexadecanoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
7WXU GPR110/Gq complex Deposited 2022-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–910（910 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.85 Å
7WXW GPR110/Gs complex Deposited 2022-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–910（910 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.84 Å
7WY0 GPR110/G13 complex Deposited 2022-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–910（910 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å
7WZ7 GPR110/G12 complex Deposited 2022-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–910（910 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å
7X2V GPR110/Gi complex Deposited 2022-02-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 1–910（910 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AGRF1_HUMAN
Isoform	—
PDB entities	1, 2, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–360； UniProt 207–566 Author chain C； PDBConstruct 1–14； UniProt 567–580 Author chain B； PDBConstruct 1–57； UniProt 150–206

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	8hc0
Deposition date deposition_date	2022-11-01
Structure title title	Crystal structure of the extracellular domains of GPR110
Keywords keywords	Adhesion GPCR, GPR110, synaptamide, molecular dynamics simulations, CELL ADHESION; CELL ADHESION
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	28.41 Å
Radius of gyration Rg (electron density) rg_electron	28.22 Å
Forward intensity I(0) i0	39870500.00
Molecular weight molecular_weight	49349.0 kDa
Excluded volume excluded_volume	61851 Å³
Envelope volume envelope_volume	77494 Å³
Hydration-shell volume shell_volume	24720 Å³
Envelope diameter envelope_diameter	102.4 Å
Shell Rg shell_rg	33.06 Å
Envelope Rg envelope_rg	28.28 Å
Shape Rg shape_rg	28.25 Å
Total Rg total_rg	28.62 Å
Total atoms total_atoms	3469
Residues n_residues	430
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	99.8 Å
Rg (real space) rg_real	28.70 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	3.9870e+07
I(0) uncertainty (real space) i0_real_error	5.7870e+05
Rg (reciprocal space) rg_reciprocal	28.62 Å
I(0) (reciprocal space) i0_reciprocal	39870000.0000
Solution quality estimate total_estimate	0.8240
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	26.8 Å
Skewness Skewness skewness	0.519
Kurtosis Kurtosis kurtosis	-0.363
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	9722000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.700; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.651; Smooth: 0.956

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Adhesion G-protein coupled receptor F1
Molecular weight formula_weight	39499.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3524

SIVAGYEVVGSSSASELLSAIEHVAEKAKTALHKLFPLEDGSFRVFGKAQCNDIVFGFGSKDDEYTLPCSSGYRGNITAKCESSGWQVIRETCVLSLLEELNKNFSMIVGNATEAAVSSFVQNLSVIIRQNPSTTVGNLASVVSILSNISSLSLASHFRVSNSTMEDVISIADNILNSASVTNWTVLLREEKYASSRLLETLENISTLVPPTALPLNFSRKFIDWKGIPVNKSQLKRGYSYQIKMCPQNTSIPIRGRVLIGSDQFQRSLPETIISMASLTLGNILPVSKNGNAQVNGPVISTVIQNYSINEVFLFFSKIESNLSQPHCVFWDFSHLQWNDAGCHLVNETQDIVTCQCTHL

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	Mammalian expression vector Flag-MCS-pcDNA3.1

Entity 2 Entity 2 polymer

Description description	Adhesion G-protein coupled receptor F1
Molecular weight formula_weight	2413.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

TSFSILMSPFVPSTHHHHHHA

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	Mammalian expression vector Flag-MCS-pcDNA3.1

Entity 3 Entity 3 polymer

Description description	Adhesion G-protein coupled receptor F1
Molecular weight formula_weight	6612.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TKIWGTFKINERFTNDLLNSSSAIYSKYANGIEIQLKKAYERIQGFESVQVTQFRNG

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	Mammalian expression vector Flag-MCS-pcDNA3.1

Entity 4 Entity 4 branched

Description description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1073.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	7

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	45

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8. Citations (1)

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Unit-cell length a length_a	134.825 Å
Unit-cell length b length_b	47.993 Å
Unit-cell length c length_c	87.023 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	127.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	19.800 Å
R factor r_factor	0.2355
R_work r_work	0.2325
R_free r_free	0.2918

fit	/app/data/saxs_computation/hc/8hc0/8hc0.fit
pddf	/app/data/pr_computation/hc/8hc0/8hc0.pr.out
profile	/app/data/saxs_computation/hc/8hc0/8hc0.dat

Crystal structure of the extracellular domains of GPR110

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

Adhesion G-protein coupled receptor F1

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

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)