SAXSdb — 2jye

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

Granulin A

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 A； UniProt 281–337	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.8；298 K；Pressure ambient NMR measurement conditions：pH 6.8；288 K；Pressure ambient NMR sample composition：10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 100% D2O \| 100% D2O	Resolution not provided

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 2JYE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1G26 THE SOLUTION STRUCTURE OF A WELL-FOLDED PEPTIDE BASED ON THE 31-RESIDUE AMINO-TERMINAL SUBDOMAIN OF HUMAN GRANULIN A Deposited 2000-10-17	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 281–311（31 aa） Fragment：N-TERMINAL DOMAIN (RESIDUES 1-31)	Mutation：D1V, K3H, S9I, Q20P	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；288 K；Pressure ambient NMR measurement conditions pH 5；298 K；Pressure ambient NMR sample composition 0.5 mM HGA 1-31 (D1V, K3H, S9I, Q20P); 20 mM sodium acetate-d3, 10% D2O, 90% H2O \| 10% D2O, 90% H2O NMR sample composition 0.5 mM HGA 1-31 (D1V, K3H, S9I, Q20P); 20 mM sodium acetate-d3, 100% D2O \| 100% D2O	Resolution not provided
2JYT Human Granulin C, isomer 1 Deposited 2007-12-19	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 364–417（54 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Pressure ambient NMR measurement conditions pH 6.8；288 K；Pressure ambient NMR sample composition 10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM HgrnC1, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM HgrnC1, 100% D2O \| 100% D2O	Resolution not provided
2JYU Human Granulin C, isomer 2 Deposited 2007-12-19	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 364–417（54 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Pressure ambient NMR measurement conditions pH 6.8；288 K；Pressure ambient NMR sample composition 10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM HgrnC2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM HgrnC2, 100% D2O \| 100% D2O	Resolution not provided
2JYV Human Granulin F Deposited 2007-12-19	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 123–179（57 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Pressure ambient NMR measurement conditions pH 6.8；288 K；Pressure ambient NMR sample composition 10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM [U-100% 15N] HgrnF, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 10 mM sodium phosphate, 150 mM sodium chloride, 0.2 mM EDTA, 0.5-1.0 mM [U-100% 15N] HgrnF, 100% D2O \| 100% D2O	Resolution not provided
6NUG hGRNA4-28_3s Deposited 2019-02-01	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 284–307（24 aa） Fragment：residues 284-307	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；290 K；Pressure 1 NMR sample composition 0.5 mM hGRNA4-28_3s, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
8T8R Sortilin-PGRN peptide complex Deposited 2023-06-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 578–593（16 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20.00 %w/ PEG 3350, 0.20 M Sodium citrate	Resolution 2.87 Å R-free 0.287
8T8S Sortilin-PGRN peptide complex Deposited 2023-06-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 578–593（16 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.10 M Tris, 30.00 %w/v PEG 3000, 0.20 M NaCl	Resolution 2.99 Å R-free 0.275
8T8S Sortilin-PGRN peptide complex Deposited 2023-06-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 578–593（16 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7；293 K；0.10 M Tris, 30.00 %w/v PEG 3000, 0.20 M NaCl	Resolution 2.99 Å R-free 0.275

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

View Construct and Data Evidence

UniProt name	GRN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–59； UniProt 281–337

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	2jye
Deposition date deposition_date	2007-12-13
Structure title title	Human Granulin A
Keywords keywords	Granulin A, epithelin, human, stack of hairpins, Alternative splicing, Cytokine, Glycoprotein, Polymorphism, Secreted; CYTOKINE
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	14.55 Å
Radius of gyration Rg (electron density) rg_electron	14.33 Å
Forward intensity I(0) i0	123157000.00
Molecular weight molecular_weight	79029.0 kDa
Excluded volume excluded_volume	93592 Å³
Envelope volume envelope_volume	34039 Å³
Hydration-shell volume shell_volume	16362 Å³
Envelope diameter envelope_diameter	63.0 Å
Shell Rg shell_rg	23.89 Å
Envelope Rg envelope_rg	18.55 Å
Shape Rg shape_rg	14.42 Å
Total Rg total_rg	14.58 Å
Total atoms total_atoms	10270
Residues n_residues	720
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	60.1 Å
Rg (real space) rg_real	14.68 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	1.2320e+08
I(0) uncertainty (real space) i0_real_error	1.4720e+06
Rg (reciprocal space) rg_reciprocal	14.67 Å
I(0) (reciprocal space) i0_reciprocal	123200000.0000
Solution quality estimate total_estimate	0.7344
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.2 Å
Skewness Skewness skewness	0.611
Kurtosis Kurtosis kurtosis	0.206
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	523300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.427; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.266; Smooth: 0.997

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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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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2jyeA01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	25 — Laminin
Homologous superfamily homologous superfamily	160 — Granulin

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8. Citations (1)

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Description description	Granulin A
Molecular weight formula_weight	7920.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	10270

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	Escherichia coli

fit	/app/data/saxs_computation/jy/2jye/2jye.fit
pddf	/app/data/pr_computation/jy/2jye/2jye.pr.out
profile	/app/data/saxs_computation/jy/2jye/2jye.dat

Human Granulin A

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

Granulin A

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)