3g2u

VHS Domain of human GGA1 complexed with Sotilin C-terminal Peptide

Method: X-RAY DIFFRACTION D_max: 62.9 Å Quality: EXCELLENT

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

ADP-ribosylation factor-binding protein GGA1

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–147	Fragment：VHS Domain (N-terminal domain)	C-terminal fragment of Sortilin × 1 （Q99523） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–147	Fragment：VHS Domain (N-terminal domain)	C-terminal fragment of Sortilin × 1 （Q99523） 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

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 3G2U	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1J2J Crystal structure of GGA1 GAT N-terminal region in complex with ARF1 GTP form Deposited 2003-01-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 166–210（45 aa） Fragment：GAT N-terminal region	Not recorded	MG MAGNESIUM ION × 1 IOD IODIDE ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, KI, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.227
1JWF Crystal Structure of human GGA1 VHS domain. Deposited 2001-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–147（147 aa） Fragment：VHS DOMAIN(N-terminal domain)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 3350, potassium dihydrogen phosphate, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.261
1JWG VHS Domain of human GGA1 complexed with cation-independent M6PR C-terminal Peptide Deposited 2001-09-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–147（147 aa） Fragment：VHS DOMAIN(N-terminal domain)	Not recorded	IOD IODIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 3350, ammonium iodide, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.261
1JWG VHS Domain of human GGA1 complexed with cation-independent M6PR C-terminal Peptide Deposited 2001-09-04	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–147（147 aa） Fragment：VHS DOMAIN(N-terminal domain)	Not recorded	IOD IODIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 3350, ammonium iodide, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.261
1NA8 Crystal structure of ADP-ribosylation factor binding protein GGA1 Deposited 2002-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 494–639（146 aa） Fragment：appendage domain, Residues 494-639 of SWS Q9UJY5 Chain B 494–639（146 aa） Fragment：appendage domain, Residues 494-639 of SWS Q9UJY5	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；289 K；sodium citrate, ammonium sulphate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.30 Å R-free 0.279
1NAF Crystal structure of the human GGA1 GAT domain Deposited 2002-11-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 165–314（150 aa） Fragment：GAT domain, Residues 165-314 of SWS Q9UJY5	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；289 K；sodium acetate, lithium sulphate, NaH2PO4/K2HPO4, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.80 Å R-free 0.283
1NWM GAT domain of human GGA1 Deposited 2003-02-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 166–302（137 aa） Fragment：GAT domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；298.15 K；polyethylene glycol 4000, iso-propanol, sodium citrate, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K	Resolution 2.40 Å R-free 0.286
1O3X Crystal structure of human GGA1 GAT domain Deposited 2003-05-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 166–305（140 aa） Fragment：Gat domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；MPD, PEG6000, Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.290
1OM9 Structure of the GGA1-appendage in complex with the p56 binding peptide Deposited 2003-02-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 494–639（146 aa） Fragment：appendage domain, Residues 494-639 of SWS Q9UJY5	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；288 K；100 mM sodium citrate, 100 mM MgCl2 and 35% PEG 400, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 2.50 Å R-free 0.262
1OM9 Structure of the GGA1-appendage in complex with the p56 binding peptide Deposited 2003-02-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 494–639（146 aa） Fragment：appendage domain, Residues 494-639 of SWS Q9UJY5	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；288 K；100 mM sodium citrate, 100 mM MgCl2 and 35% PEG 400, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 2.50 Å R-free 0.262
1OM9 Structure of the GGA1-appendage in complex with the p56 binding peptide Deposited 2003-02-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 494–639（146 aa） Fragment：appendage domain, Residues 494-639 of SWS Q9UJY5 Chain B 494–639（146 aa） Fragment：appendage domain, Residues 494-639 of SWS Q9UJY5	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；288 K；100 mM sodium citrate, 100 mM MgCl2 and 35% PEG 400, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K	Resolution 2.50 Å R-free 0.262
1OXZ Crystal Structure of the Human GGA1 GAT domain Deposited 2003-04-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 141–326（186 aa） Fragment：GAT domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；lithium sulfate, MES, ethylene glycol , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.285
1PY1 Complex of GGA1-VHS domain and beta-secretase C-terminal phosphopeptide Deposited 2003-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–157（156 aa） Fragment：VHS Domain (Residues 2-157) Chain B 2–157（156 aa） Fragment：VHS Domain (Residues 2-157)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；PEG 3350, AMMONIUM SULFATE, CACODYLATE, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.288
1PY1 Complex of GGA1-VHS domain and beta-secretase C-terminal phosphopeptide Deposited 2003-07-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 2–157（156 aa） Fragment：VHS Domain (Residues 2-157) Chain D 2–157（156 aa） Fragment：VHS Domain (Residues 2-157)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；PEG 3350, AMMONIUM SULFATE, CACODYLATE, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.288
1UJJ VHS domain of human GGA1 complexed with C-terminal peptide from BACE Deposited 2003-08-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–147（147 aa） Fragment：VHS domain, N-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；293 K；PEG 5000MME, di-Ammonium hydrogen phosphate, Tris-HCl, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.295
1UJJ VHS domain of human GGA1 complexed with C-terminal peptide from BACE Deposited 2003-08-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–147（147 aa） Fragment：VHS domain, N-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.6；293 K；PEG 5000MME, di-Ammonium hydrogen phosphate, Tris-HCl, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.295
1UJK VHS domain of human GGA1 complexed with C-terminal phosphopeptide from BACE Deposited 2003-08-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–147（147 aa） Fragment：VHS domain, N-terminal domain	Not recorded	IOD IODIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG5000MME, Ammonium Iodide, 1,6-hexanediol, MES-NaOH, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.245
1UJK VHS domain of human GGA1 complexed with C-terminal phosphopeptide from BACE Deposited 2003-08-05	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–147（147 aa） Fragment：VHS domain, N-terminal domain	Not recorded	IOD IODIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG5000MME, Ammonium Iodide, 1,6-hexanediol, MES-NaOH, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.245
1UJK VHS domain of human GGA1 complexed with C-terminal phosphopeptide from BACE Deposited 2003-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–147（147 aa） Fragment：VHS domain, N-terminal domain Chain B 1–147（147 aa） Fragment：VHS domain, N-terminal domain	Not recorded	IOD IODIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG5000MME, Ammonium Iodide, 1,6-hexanediol, MES-NaOH, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.245
1X79 Crystal structure of human GGA1 GAT domain complexed with the GAT-binding domain of Rabaptin5 Deposited 2004-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 210–302（93 aa）	Not recorded	SO4 SULFATE ION × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；AMMONIUM SULFATE, TRIS, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.41 Å R-free 0.283
2DWX Co-crystal Structure Analysis of GGA1-GAE with the WNSF motif Deposited 2006-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639 Chain P 376–388（13 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.55 Å R-free 0.287
2DWX Co-crystal Structure Analysis of GGA1-GAE with the WNSF motif Deposited 2006-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.55 Å R-free 0.287
2DWX Co-crystal Structure Analysis of GGA1-GAE with the WNSF motif Deposited 2006-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639 Chain Q 376–388（13 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.55 Å R-free 0.287
2DWX Co-crystal Structure Analysis of GGA1-GAE with the WNSF motif Deposited 2006-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.55 Å R-free 0.287
2DWY Crystal Structure Analysis of GGA1-GAE Deposited 2006-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.257
2DWY Crystal Structure Analysis of GGA1-GAE Deposited 2006-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.257
2DWY Crystal Structure Analysis of GGA1-GAE Deposited 2006-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.257
2DWY Crystal Structure Analysis of GGA1-GAE Deposited 2006-08-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.257
2DWY Crystal Structure Analysis of GGA1-GAE Deposited 2006-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639 Chain D 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.257
2DWY Crystal Structure Analysis of GGA1-GAE Deposited 2006-08-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639 Chain B 507–639（133 aa） Fragment：GAE DOMAIN, RESIDUES 507-639	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG3350, DI-AMMONIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.30 Å R-free 0.257
3G2S VHS Domain of human GGA1 complexed with SorLA C-terminal Peptide Deposited 2009-02-01	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–147（147 aa） Fragment：VHS Domain (N-terminal domain)	Not recorded	No recorded non-water small molecule	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 1.70 Å R-free 0.226
3G2S VHS Domain of human GGA1 complexed with SorLA C-terminal Peptide Deposited 2009-02-01	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–147（147 aa） Fragment：VHS Domain (N-terminal domain)	Not recorded	HEZ HEXANE-1,6-DIOL × 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 1.70 Å R-free 0.226
3G2T VHS Domain of human GGA1 complexed with SorLA C-terminal Phosphopeptide Deposited 2009-02-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–147（147 aa） Fragment：VHS Domain (N-terminal domain)	Not recorded	IOD IODIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；18%(w/v) PEG 5000 MME, 0.2M NH4I, 0.1M TRIS-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.00 Å R-free 0.233
3G2T VHS Domain of human GGA1 complexed with SorLA C-terminal Phosphopeptide Deposited 2009-02-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–147（147 aa） Fragment：VHS Domain (N-terminal domain)	Not recorded	IOD IODIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；292 K；18%(w/v) PEG 5000 MME, 0.2M NH4I, 0.1M TRIS-HCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 2.00 Å R-free 0.233
3G2V VHS Domain of human GGA1 complexed with Sotilin C-terminal Phosphopeptide Deposited 2009-02-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–147（147 aa） Fragment：VHS Domain (N-terminal domain)	Not recorded	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–147（147 aa） Fragment：VHS Domain (N-terminal domain)	Not recorded	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
3G2W VHS Domain of human GGA1 complexed with a DXXLL hinge peptide Deposited 2009-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–147（147 aa） Fragment：VHS Domain (N-terminal domain) Chain C 351–364（14 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	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 2.40 Å R-free 0.259
3G2W VHS Domain of human GGA1 complexed with a DXXLL hinge peptide Deposited 2009-02-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1–147（147 aa） Fragment：VHS Domain (N-terminal domain) Chain D 351–364（14 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	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 2.40 Å R-free 0.259

19 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GGA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–149； UniProt 1–147 Author chain B； PDBConstruct 3–149； UniProt 1–147

C-terminal fragment of Sortilin

OrganismNot specified

UniProt Q99523

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 819–831	Not recorded	ADP-ribosylation factor-binding protein GGA1 × 1 （Q9UJY5） 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 819–831	Not recorded	ADP-ribosylation factor-binding protein GGA1 × 1 （Q9UJY5） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 3G2U	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 oligomeric state 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
3G2V VHS Domain of human GGA1 complexed with Sotilin C-terminal Phosphopeptide Deposited 2009-02-01	Different mutation/modification 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 mutation/modification 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 construct Different oligomeric state 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
8T8S Sortilin-PGRN peptide complex Deposited 2023-06-23	Different construct Different oligomeric state 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 × 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 conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 79–756（678 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
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 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 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	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–13； UniProt 819–831 Author chain D； PDBConstruct 1–13； UniProt 819–831

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3g2u
Deposition date deposition_date	2009-02-01
Structure title title	VHS Domain of human GGA1 complexed with Sotilin C-terminal Peptide
Keywords keywords	ADP-ribosylation factor binding protein GGA1, VHS, acidic-cluster dileucine signal, Sortilin, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	20.46 Å
Radius of gyration Rg (electron density) rg_electron	19.49 Å
Forward intensity I(0) i0	20773100.00
Molecular weight molecular_weight	34267.0 kDa
Excluded volume excluded_volume	42662 Å³
Envelope volume envelope_volume	49304 Å³
Hydration-shell volume shell_volume	21052 Å³
Envelope diameter envelope_diameter	64.4 Å
Shell Rg shell_rg	25.79 Å
Envelope Rg envelope_rg	19.56 Å
Shape Rg shape_rg	19.49 Å
Total Rg total_rg	20.37 Å
Total atoms total_atoms	2371
Residues n_residues	294
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	62.9 Å
Rg (real space) rg_real	20.35 Å
Rg uncertainty (real space) rg_real_error	0.35 Å
I(0) (real space) i0_real	2.0770e+07
I(0) uncertainty (real space) i0_real_error	2.3600e+05
Rg (reciprocal space) rg_reciprocal	20.37 Å
I(0) (reciprocal space) i0_reciprocal	20770000.0000
Solution quality estimate total_estimate	0.9025
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.0 Å
Skewness Skewness skewness	0.180
Kurtosis Kurtosis kurtosis	-0.482
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3973000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.982

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	ADP-ribosylation factor-binding protein GGA1
Molecular weight formula_weight	16958.6 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	2518

GSMEPAMEPETLEARINRATNPLNKELDWASINGFCEQLNEDFEGPPLATRLLAHKIQSPQEWEAIQALTVLETCMKSCGKRFHDEVGKFRFLNELIKVVSPKYLGSRTSEKVKNKILELLYSWTVGLPEEVKIAEAYQMLKKQGIVKS

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	Escherichia coli

Entity 2 Entity 2 polymer

Description description	C-terminal fragment of Sortilin
Molecular weight formula_weight	1495.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

SGYHDDSDEDLLE

Entity 3 Entity 3 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3g2ua_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.9 — ENTH/VHS domain
Family Family family	a.118.9.2 — VHS domain

Domain ID domain_id	d3g2ub_
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.9 — ENTH/VHS domain
Family Family family	a.118.9.2 — VHS domain

CATH v4.4 (2 domains)

Domain ID domain_id	3g2uA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	3g2uB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	90 —

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8. Citations (1)

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Unit-cell length a length_a	48.486 Å
Unit-cell length b length_b	72.728 Å
Unit-cell length c length_c	103.767 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.301 Å
Low-resolution limit resolution_low	37.601 Å
R factor r_factor	0.2010
R_work r_work	0.1990
R_free r_free	0.2460

fit	/app/data/saxs_computation/g2/3g2u/3g2u.fit
pddf	/app/data/pr_computation/g2/3g2u/3g2u.pr.out
profile	/app/data/saxs_computation/g2/3g2u/3g2u.dat

VHS Domain of human GGA1 complexed with Sotilin C-terminal Peptide

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

ADP-ribosylation factor-binding protein GGA1

State in the Current Structure

Other States of the Same Protein in the Database

C-terminal fragment of Sortilin

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)