SAXSdb — 8t8s

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

Sortilin

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 Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 79–756	Not recorded	Paragranulin peptide × 1 （P28799） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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
2	Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 79–756	Not recorded	Paragranulin peptide × 1 （P28799） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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

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 8T8S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3F6K Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with neurotensin Deposited 2008-11-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 78–756（679 aa） Fragment：UNP residues 78-756	Not recorded	PGE TRIETHYLENE GLYCOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；19% PEG 6000, 600 mM NaCl, 3% Glycerol, 100 mM HEPES, 93 mM Tris-HCl, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.00 Å R-free 0.229
3G2U VHS Domain of human GGA1 complexed with Sotilin C-terminal Peptide Deposited 2009-02-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 819–831（13 aa）	Not recorded	IOD IODIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；15%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.30 Å R-free 0.246
3G2U VHS Domain of human GGA1 complexed with Sotilin C-terminal Peptide Deposited 2009-02-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 819–831（13 aa）	Not recorded	IOD IODIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；15%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.30 Å R-free 0.246
3G2V VHS Domain of human GGA1 complexed with Sotilin C-terminal Phosphopeptide Deposited 2009-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 819–831（13 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	IOD IODIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；16%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.10 Å R-free 0.244
3G2V VHS Domain of human GGA1 complexed with Sotilin C-terminal Phosphopeptide Deposited 2009-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 819–831（13 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	IOD IODIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；16%(w/v) PEG 5000 mmE, 0.2M NH4I, 0.3M 1,6-hexanediol, 0.1M MES-NaOH, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.10 Å R-free 0.244
4MSL Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF40431 Deposited 2013-09-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 78–756（679 aa） Fragment：Vps10p domain (UNP residues 78-756)	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 2ET N-[(7-hydroxy-4-methyl-2-oxo-2H-chromen-8-yl)methyl]-L-leucine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；292 K；0.1 M HEPES-Tris, 0.4 M sodium malonate, 26 % (w/v) PEG 3350, 8 % (v/v) glycerol, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.70 Å R-free 0.227
4N7E Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with AF38469 Deposited 2013-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 78–756（679 aa） Fragment：UNP residues 78-756	Mutation：V617M	PGE TRIETHYLENE GLYCOL × 1 2JQ 2-[(6-methylpyridin-2-yl)carbamoyl]-5-(trifluoromethyl)benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；292 K；0.1 M HEPES-Tris, 0.4 M sodium malonate, 27 % (w/v) PEG 3350, 4.5 % (v/v) glycerol, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.70 Å R-free 0.242
4PO7 Structure of the Sortilin:neurotensin complex at excess neurotensin concentration Deposited 2014-02-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 78–756（679 aa） Fragment：unp residues 78-756	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.9；292 K；20% PEG 6k, 300 mM sodium malonate, 3% glycerol and 100 mM TrisHCl, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.66 Å R-free 0.212
5MRH Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with Triazolone 1 Deposited 2016-12-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 78–756（679 aa）	Not recorded	Q9Z 3-(3-methylbutyl)-4~{H}-1,2,3-triazol-5-one × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；292 K；0.1M HEPES-Tris pH=7.3 0.4 M Sodium malonate 22 % (w/V) PEG 3350 8 (V/V) glycerol	Resolution 2.50 Å R-free 0.233
5MRI Crystal structure of the Vps10p domain of human sortilin/NTS3 in complex with Triazolone 18 Deposited 2016-12-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 78–756（679 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 Q9Y ~{N}-methyl-3-(3-methylbutyl)-5-oxidanyl-1,2,3-triazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；292 K；0.1 M HEPES-Tris pH 7.3 0.4 M Sodium malonate 6 % (V/V) glycerol 26 % (w/V) PEG 3350	Resolution 2.00 Å R-free 0.219
6EHO Dimer of the Sortilin Vps10p domain at low pH Deposited 2017-09-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 34–756（723 aa）	Mutation：R43G , R44G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；2.0 Ammonium sulphate	Resolution 3.50 Å R-free 0.272
6X3L Sortilin-Progranulin Interaction With Compound 2 Deposited 2020-05-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–756（756 aa）	Not recorded	UMJ 1-benzyl-3-tert-butyl-1H-pyrazole-5-carboxylic acid × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20-25% PEG3350, 0.4M Na Malonate, pH8, 0.1M Tris, 5% Glycerol	Resolution 2.70 Å R-free 0.269
6X48 Sortilin-Progranulin Interaction With Compound 17 Deposited 2020-05-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 86–748（663 aa）	Not recorded	UP4 N-(3,5-dichlorobenzene-1-carbonyl)-5,5-dimethyl-L-norleucine × 1 UNL UNKNOWN LIGAND × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20-25% PEG3350, 0.4M Na Malonate, pH8, 0.1M Tris, 5% Glycerol	Resolution 2.90 Å R-free 0.252
6X4H Sortilin-Progranulin Interaction With Compound 24 Deposited 2020-05-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 86–748（663 aa）	Not recorded	UOY 4-methyl-N-(6-phenoxypyridine-3-carbonyl)-L-leucine × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20-25% PEG3350, 0.4M Na Malonate, pH8, 0.1M Tris, 5% Glycerol	Resolution 2.90 Å R-free 0.253
8T8R Sortilin-PGRN peptide complex Deposited 2023-06-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 79–756（678 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
9I0N Cryo-EM structure of human sortilin ectodomain Deposited 2025-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 34–756（723 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9I0O Cryo-EM structure of human sortilin ectodomain in complex with a thyroglobulin C-terminal peptide Deposited 2025-01-15	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 34–756（723 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.36 Å
9R18 Structure of Sortilin ECD in complex with TNFa-targeting SORTAC Deposited 2025-04-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–756（756 aa）	Mutation：V650M	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 A1JCL (2~{S})-2-[[6-[3-[8-[2-[(2~{R})-4-[5-[1-[(2-cyanopyridin-3-yl)methyl]-2,2-dimethyl-3-oxidanylidene-pyrrolo[2,3-b]pyridin-6-yl]pyrimidin-2-yl]-2-methyl-piperazin-1-yl]-2-oxidanylidene-ethoxy]octylcarbamoyl]phenoxy]pyridin-3-yl]carbonylamino]-5,5-dimethyl-hexanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；292.15 K；22 % PEG6000, 1.1 M NaCl, 8% glycerol, 50 mM HEPES pH 8.0	Resolution 2.80 Å R-free 0.253

16 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SORT_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–678； UniProt 79–756 Author chain B； PDBConstruct 1–678； UniProt 79–756

Paragranulin peptide

OrganismNot specified

UniProt P28799

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 Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 578–593	Not recorded	Sortilin × 1 （Q99523） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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
2	Other combination Heteromer Protein × 2 其他Polymer 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 578–593	Not recorded	Sortilin × 1 （Q99523） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 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

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 8T8S	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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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
2JYE Human Granulin A Deposited 2007-12-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 281–337（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, 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
2JYT Human Granulin C, isomer 1 Deposited 2007-12-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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 ligand/ion 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

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

View Construct and Data Evidence

UniProt name	GRN_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–16； UniProt 578–593 Author chain D； PDBConstruct 1–16； UniProt 578–593

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	8t8s
Deposition date deposition_date	2023-06-23
Structure title title	Sortilin-PGRN peptide complex
Keywords keywords	Sortilin, Progranulin, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	39.85 Å
Radius of gyration Rg (electron density) rg_electron	39.75 Å
Forward intensity I(0) i0	353814000.00
Molecular weight molecular_weight	151570.0 kDa
Excluded volume excluded_volume	188600 Å³
Envelope volume envelope_volume	264370 Å³
Hydration-shell volume shell_volume	54960 Å³
Envelope diameter envelope_diameter	146.0 Å
Shell Rg shell_rg	46.02 Å
Envelope Rg envelope_rg	39.11 Å
Shape Rg shape_rg	39.76 Å
Total Rg total_rg	40.06 Å
Total atoms total_atoms	10664
Residues n_residues	1332
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	130.5 Å
Rg (real space) rg_real	39.84 Å
Rg uncertainty (real space) rg_real_error	1.23 Å
I(0) (real space) i0_real	3.5380e+08
I(0) uncertainty (real space) i0_real_error	6.5260e+06
Rg (reciprocal space) rg_reciprocal	39.85 Å
I(0) (reciprocal space) i0_reciprocal	353800000.0000
Solution quality estimate total_estimate	0.8891
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.7 Å
Skewness Skewness skewness	0.303
Kurtosis Kurtosis kurtosis	-0.464
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	28260000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.836

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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	Sortilin
Molecular weight formula_weight	75826.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	10691

APGEDEECGRVRDFVAKLANNTHQHVFDDLRGSVSLSWVGDSTGVILVLTTFHVPLVIMTFGQSKLYRSEDYGKNFKDITDLINNTFIRTEFGMAIGPENSGKVVLTAEVSGGSRGGRIFRSSDFAKNFVQTDLPFHPLTQMMYSPQNSDYLLALSTENGLWVSKNFGGKWEEIHKAVCLAKWGSDNTIFFTTYANGSCKADLGALELWRTSDLGKSFKTIGVKIYSFGLGGRFLFASVMADKDTTRRIHVSTDQGDTWSMAQLPSVGQEQFYSILAANDDMVFMHVDEPGDTGFGTIFTSDDRGIVYSKSLDRHLYTTTGGETDFTNVTSLRGVYITSVLSEDNSIQTMITFDQGGRWTHLRKPENSECDATAKNKNECSLHIHASYSISQKLNVPMAPLSEPNAVGIVIAHGSVGDAISVMVPDVYISDDGGYSWTKMLEGPHYYTILDSGGIIVAIEHSSRPINVIKFSTDEGQCWQTYTFTRDPIYFTGLASEPGARSMNISIWGFTESFLTSQWVSYTIDFKDILERNCEEKDYTIWLAHSTDPEDYEDGCILGYKEQFLRLRKSSVCQNGRDYVVTKQPSICLCSLEDFLCDFGYYRPENDSKCVEQPELKGHDLEFCLYGREEHLTTNGYRKIPGDKCQGGVNPVREVKDLKKKCTSNFLSPEKQNSKSNS

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Paragranulin peptide
Molecular weight formula_weight	1920.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

PRWDAPLRDPALRQLL

Entity 3 Entity 3 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	4

Entity 4 Entity 4 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	1

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	18

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8. Citations (1)

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Unit-cell length a length_a	237.030 Å
Unit-cell length b length_b	237.030 Å
Unit-cell length c length_c	89.427 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.990 Å
Low-resolution limit resolution_low	205.270 Å
R factor r_factor	0.2340
R_work r_work	0.2340
R_free r_free	0.2750

fit	/app/data/saxs_computation/t8/8t8s/8t8s.fit
pddf	/app/data/pr_computation/t8/8t8s/8t8s.pr.out
profile	/app/data/saxs_computation/t8/8t8s/8t8s.dat

Sortilin-PGRN peptide complex

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

Sortilin

State in the Current Structure

Other States of the Same Protein in the Database

Paragranulin peptide

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

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)