SAXSdb — 5f0j

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

Vacuolar protein sorting-associated protein 35

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 14–470	Fragment：Residues 14-470	Vacuolar protein sorting-associated protein 26A × 1 （O75436） Sorting nexin-3 × 1 （O60493） SO4 SULFATE ION × 6 GOL GLYCEROL × 5 EDO 1,2-ETHANEDIOL × 24	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.9 M AmSO4, 0.1 M MES pH 6.0	Resolution 2.70 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 5F0J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2R17 Functional architecture of the retromer cargo-recognition complex Deposited 2007-08-22	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 483–780（298 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 8；291 K；20% PEG 3350, 1M NaCl,50mM Tris, pH 8.0, hanging drop, temperature 291K	Resolution 2.80 Å R-free 0.268
2R17 Functional architecture of the retromer cargo-recognition complex Deposited 2007-08-22	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 483–780（298 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 8；291 K；20% PEG 3350, 1M NaCl,50mM Tris, pH 8.0, hanging drop, temperature 291K	Resolution 2.80 Å R-free 0.268
5F0K Structure of VPS35 N terminal region Deposited 2015-11-27	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 14–470（457 aa） Fragment：Residues 14-470	Not recorded	EDO 1,2-ETHANEDIOL × 5 GOL GLYCEROL × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；1.7 M AmSO4, 2% PEG 1000, 0.1 M Hepes pH 7.6	Resolution 3.07 Å R-free 0.255
5F0K Structure of VPS35 N terminal region Deposited 2015-11-27	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 14–470（457 aa） Fragment：Residues 14-470	Not recorded	EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；1.7 M AmSO4, 2% PEG 1000, 0.1 M Hepes pH 7.6	Resolution 3.07 Å R-free 0.255
5F0K Structure of VPS35 N terminal region Deposited 2015-11-27	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 14–470（457 aa） Fragment：Residues 14-470	Not recorded	EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；1.7 M AmSO4, 2% PEG 1000, 0.1 M Hepes pH 7.6	Resolution 3.07 Å R-free 0.255
5F0K Structure of VPS35 N terminal region Deposited 2015-11-27	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 14–470（457 aa） Fragment：Residues 14-470	Not recorded	EDO 1,2-ETHANEDIOL × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；1.7 M AmSO4, 2% PEG 1000, 0.1 M Hepes pH 7.6	Resolution 3.07 Å R-free 0.255
5F0K Structure of VPS35 N terminal region Deposited 2015-11-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 14–470（457 aa） Fragment：Residues 14-470	Not recorded	EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；291 K；1.7 M AmSO4, 2% PEG 1000, 0.1 M Hepes pH 7.6	Resolution 3.07 Å R-free 0.255
5F0L Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 Deposited 2015-11-27	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 14–470（457 aa） Fragment：Residues 14-470	Not recorded	SO4 SULFATE ION × 10 GOL GLYCEROL × 6 EDO 1,2-ETHANEDIOL × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.75 M AmSO4, 0.1 M MES pH 6.0, 15% Glycerol	Resolution 3.20 Å R-free 0.259
5F0M Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled) Deposited 2015-11-27	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 14–470（457 aa） Fragment：Residues 14-470	Not recorded	SO4 SULFATE ION × 6 GOL GLYCEROL × 5 EDO 1,2-ETHANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.8 M AmSO4, 0.1 M MES pH 6.0, 5% Glycerol	Resolution 3.10 Å R-free 0.254
5F0P Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled) Deposited 2015-11-27	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 14–470（457 aa） Fragment：Residues 14-470	Not recorded	SO4 SULFATE ION × 6 GOL GLYCEROL × 4 EDO 1,2-ETHANEDIOL × 20 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.8 M AmSO4, 0.1 M MES pH 6.0, 10% Glycerol	Resolution 2.78 Å R-free 0.261
5OSH Structure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236) Deposited 2017-08-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 482–780（299 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M sodium chloride 0.1 M Tris pH 8.0 4-8% PEG6000.	Resolution 4.30 Å R-free 0.311
5OSH Structure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236) Deposited 2017-08-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 482–780（299 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M sodium chloride 0.1 M Tris pH 8.0 4-8% PEG6000.	Resolution 4.30 Å R-free 0.311
5OSH Structure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236) Deposited 2017-08-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 482–780（299 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M sodium chloride 0.1 M Tris pH 8.0 4-8% PEG6000.	Resolution 4.30 Å R-free 0.311
5OSH Structure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236) Deposited 2017-08-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 482–780（299 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M sodium chloride 0.1 M Tris pH 8.0 4-8% PEG6000.	Resolution 4.30 Å R-free 0.311
5OSI Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176) Deposited 2017-08-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 471–781（311 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl, 20% PEG3350 0.1 M Tris pH 8.5	Resolution 2.52 Å R-free 0.267
5OSI Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176) Deposited 2017-08-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 471–781（311 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl, 20% PEG3350 0.1 M Tris pH 8.5	Resolution 2.52 Å R-free 0.267
5OSI Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176) Deposited 2017-08-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 471–781（311 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl, 20% PEG3350 0.1 M Tris pH 8.5	Resolution 2.52 Å R-free 0.267
5OSI Structure of retromer VPS29-VPS35C subunits complexed with RidL harpin loop (163-176) Deposited 2017-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain K 471–781（311 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl, 20% PEG3350 0.1 M Tris pH 8.5	Resolution 2.52 Å R-free 0.267
7BLN VPS35/VPS29 arch of metazoan membrane-assembled retromer:SNX3 complex modelled with human proteins Deposited 2021-01-18	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 × 4 PDB declaration: tetrameric	Chain A 1–796（796 aa） Chain C 1–796（796 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.90 Å
7BLO VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 complex modelled with human proteins Deposited 2021-01-18	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 × 8 PDB declaration: octameric	Chain A 12–363（352 aa） Chain C 12–363（352 aa）	Not recorded	PIB 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.50 Å
8R02 Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl guanylhydrazone, 2a Deposited 2023-10-30	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 476–780（305 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；20% PEG 3350, 150 mM NaK tartrate, 100 mM NaCl, pH 7.4	Resolution 2.50 Å R-free 0.264
8R02 Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl guanylhydrazone, 2a Deposited 2023-10-30	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 476–780（305 aa）	Not recorded	XFZ Bis-1,3-phenyl guanylhydrazon × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；20% PEG 3350, 150 mM NaK tartrate, 100 mM NaCl, pH 7.4	Resolution 2.50 Å R-free 0.264
8R0J Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl guanylhydrazone, 2a Deposited 2023-10-31	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 476–780（305 aa）	Not recorded	XFZ Bis-1,3-phenyl guanylhydrazon × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；18% PEG 3350, 150 mM NaK tartrate, pH 7.4;	Resolution 2.40 Å R-free 0.250
8R0J Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl guanylhydrazone, 2a Deposited 2023-10-31	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 476–780（305 aa）	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；293 K；18% PEG 3350, 150 mM NaK tartrate, pH 7.4;	Resolution 2.40 Å R-free 0.250
8RKS Structure of VPS29-VPS35 bound to the LFa motif R21 of Fam21. Deposited 2023-12-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 471–781（311 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl, 20% PEG3350 0.1 M Tris pH 8.5	Resolution 3.10 Å R-free 0.288
8RKS Structure of VPS29-VPS35 bound to the LFa motif R21 of Fam21. Deposited 2023-12-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 471–781（311 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl, 20% PEG3350 0.1 M Tris pH 8.5	Resolution 3.10 Å R-free 0.288
8RKS Structure of VPS29-VPS35 bound to the LFa motif R21 of Fam21. Deposited 2023-12-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 471–781（311 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl, 20% PEG3350 0.1 M Tris pH 8.5	Resolution 3.10 Å R-free 0.288
8RKS Structure of VPS29-VPS35 bound to the LFa motif R21 of Fam21. Deposited 2023-12-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 471–781（311 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.1 M NaCl, 20% PEG3350 0.1 M Tris pH 8.5	Resolution 3.10 Å R-free 0.288

12 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPS35_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–462； UniProt 14–470

Vacuolar protein sorting-associated protein 26A

Homo sapiens

UniProt O75436

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 2–326	Non-standard monomer：Yes (specific site not provided by mmCIF)	Vacuolar protein sorting-associated protein 35 × 1 （Q96QK1） Sorting nexin-3 × 1 （O60493） SO4 SULFATE ION × 6 GOL GLYCEROL × 5 EDO 1,2-ETHANEDIOL × 24	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.9 M AmSO4, 0.1 M MES pH 6.0	Resolution 2.70 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 5F0J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2FAU Crystal structure of human vps26 Deposited 2005-12-08	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 1–327（327 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；300 K；8% PEG 8000 100mM Na cacodylate pH 6.5 15% glycerol 10mM DTT 1mM TmCl3, VAPOR DIFFUSION, SITTING DROP, temperature 300K	Resolution 2.10 Å R-free 0.284
5F0L Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 Deposited 2015-11-27	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 B 1–317（317 aa）	Not recorded	SO4 SULFATE ION × 10 GOL GLYCEROL × 6 EDO 1,2-ETHANEDIOL × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.75 M AmSO4, 0.1 M MES pH 6.0, 15% Glycerol	Resolution 3.20 Å R-free 0.259
5F0M Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled) Deposited 2015-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 2–321（320 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 6 GOL GLYCEROL × 5 EDO 1,2-ETHANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.8 M AmSO4, 0.1 M MES pH 6.0, 5% Glycerol	Resolution 3.10 Å R-free 0.254
5F0P Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled) Deposited 2015-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–321（321 aa） Fragment：Residues 1-321	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 6 GOL GLYCEROL × 4 EDO 1,2-ETHANEDIOL × 20 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.8 M AmSO4, 0.1 M MES pH 6.0, 10% Glycerol	Resolution 2.78 Å R-free 0.261
7BLO VPS26 dimer region of metazoan membrane-assembled retromer:SNX3 complex modelled with human proteins Deposited 2021-01-18	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 × 8 PDB declaration: octameric	Chain F 8–301（294 aa） Chain J 8–301（294 aa）	Not recorded	PIB 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 9.50 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VP26A_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–328； UniProt 2–326

Sorting nexin-3

Homo sapiens

UniProt O60493

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 1–162	Not recorded	Vacuolar protein sorting-associated protein 35 × 1 （Q96QK1） Vacuolar protein sorting-associated protein 26A × 1 （O75436） SO4 SULFATE ION × 6 GOL GLYCEROL × 5 EDO 1,2-ETHANEDIOL × 24	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.9 M AmSO4, 0.1 M MES pH 6.0	Resolution 2.70 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 5F0J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2MXC Solution structure of the full length sorting nexin 3 Deposited 2014-12-20	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 2–162（161 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.100；Pressure 1.000 NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] SNX3FL, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2YPS Crystal structure of the PX domain of human sorting nexin 3 Deposited 2012-10-31	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 24–155（132 aa） Fragment：PX DOMAIN, RESIDUES 24-155	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 3.5M FORMATE	Resolution 2.60 Å R-free 0.255
2YPS Crystal structure of the PX domain of human sorting nexin 3 Deposited 2012-10-31	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 24–155（132 aa） Fragment：PX DOMAIN, RESIDUES 24-155	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 3.5M FORMATE	Resolution 2.60 Å R-free 0.255
2YPS Crystal structure of the PX domain of human sorting nexin 3 Deposited 2012-10-31	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 24–155（132 aa） Fragment：PX DOMAIN, RESIDUES 24-155	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 3.5M FORMATE	Resolution 2.60 Å R-free 0.255
2YPS Crystal structure of the PX domain of human sorting nexin 3 Deposited 2012-10-31	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 24–155（132 aa） Fragment：PX DOMAIN, RESIDUES 24-155	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 3.5M FORMATE	Resolution 2.60 Å R-free 0.255
5F0L Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 Deposited 2015-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–162（162 aa） Fragment：Residues 14-470	Not recorded	SO4 SULFATE ION × 10 GOL GLYCEROL × 6 EDO 1,2-ETHANEDIOL × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.75 M AmSO4, 0.1 M MES pH 6.0, 15% Glycerol	Resolution 3.20 Å R-free 0.259
5F0M Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled) Deposited 2015-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–162（162 aa） Fragment：Residues 14-470	Not recorded	SO4 SULFATE ION × 6 GOL GLYCEROL × 5 EDO 1,2-ETHANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.8 M AmSO4, 0.1 M MES pH 6.0, 5% Glycerol	Resolution 3.10 Å R-free 0.254
5F0P Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled) Deposited 2015-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–162（162 aa） Fragment：Residues 1-162	Not recorded	SO4 SULFATE ION × 6 GOL GLYCEROL × 4 EDO 1,2-ETHANEDIOL × 20 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.8 M AmSO4, 0.1 M MES pH 6.0, 10% Glycerol	Resolution 2.78 Å R-free 0.261

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

View Construct and Data Evidence

UniProt name	SNX3_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 6–167； UniProt 1–162

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	5f0j
Deposition date deposition_date	2015-11-27
Structure title title	Structure of retromer VPS26-VPS35 subunits bound to SNX3
Keywords keywords	protein transport, retromer, sorting nexin, 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	39.67 Å
Radius of gyration Rg (electron density) rg_electron	40.34 Å
Forward intensity I(0) i0	179612000.00
Molecular weight molecular_weight	109190.0 kDa
Excluded volume excluded_volume	137120 Å³
Envelope volume envelope_volume	189440 Å³
Hydration-shell volume shell_volume	43484 Å³
Envelope diameter envelope_diameter	163.0 Å
Shell Rg shell_rg	40.42 Å
Envelope Rg envelope_rg	41.31 Å
Shape Rg shape_rg	40.37 Å
Total Rg total_rg	40.23 Å
Total atoms total_atoms	7637
Residues n_residues	911
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	152.3 Å
Rg (real space) rg_real	40.26 Å
Rg uncertainty (real space) rg_real_error	2.13 Å
I(0) (real space) i0_real	1.7960e+08
I(0) uncertainty (real space) i0_real_error	3.5740e+06
Rg (reciprocal space) rg_reciprocal	39.89 Å
I(0) (reciprocal space) i0_reciprocal	179500000.0000
Solution quality estimate total_estimate	0.7880
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.1 Å
Skewness Skewness skewness	0.666
Kurtosis Kurtosis kurtosis	0.298
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22780000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.600; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.584; Smooth: 0.856

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Vacuolar protein sorting-associated protein 35
Molecular weight formula_weight	53288.3 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	7732

GAMGSKLLDEAIQAVKVQSFQMKRCLDKNKLMDALKHASNMLGELRTSMLSPKSYYELYMAISDELHYLEVYLTDEFAKGRKVADLYELVQYAGNIIPRLYLLITVGVVYVKSFPQSRKDILKDLVEMCRGVQHPLRGLFLRNYLLQCTRNILPDEGEPTDEETTGDISDSMDFVLLNFAEMNKLWVRMQHQGHSRDREKRERERQELRILVGTNLVRLSQLEGVNVERYKQIVLTGILEQVVNCRDALAQEYLMECIIQVFPDEFHLQTLNPFLRACAELHQNVNVKNIIIALIDRLALFAHREDGPGIPADIKLFDIFSQQVATVIQSRQDMPSEDVVSLQVSLINLAMKCYPDRVDYVDKVLETTVEIFNKLNLEHIATSSAVSKELTRLLKIPVDTYNNILTVLKLKHFHPLFEYFDYESRKSMSCYVLSNVLDYNTEIVSQDQVDSIMNLVSTLIQD

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Vacuolar protein sorting-associated protein 26A
Molecular weight formula_weight	40239.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGMSFLGGFFGPICEIDIVLNDGETRKMAEMKTEDGKVEKHYLFYDGESVSGKVNLAFKQPGKRLEHQGIRIEFVGQIELFNDKSNTHEFVNLVKELALPGELTQSRSYDFEFMQVEKPYESYIGANVRLRYFLKVTIVRRLTDLVKEYDLIVHQLATYPDVNNSIKMEVGIEDCLHIEFEYNKSKYHLKDVIVGKIYFLLVRIKIQHMELQLIKKEITGIGPSTTTETETIAKYEIMDGAPVKGESIPIRLFLAGYDPTPTMRDVNKKFSVRYFLNLVLVDEEDRRYFKQQEIILWRKAPEKLRKQRTNFHQRFESPESQASAEQPEMGLVPRGSHHHHH

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 BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Sorting nexin-3
Molecular weight formula_weight	19193.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GAMGSMAETVADTRRLITKPQNLNDAYGPPSNFLEIDVSNPQTVGVGRGRFTTYEIRVKTNLPIFKLKESTVRRRYSDFEWLRSELERESKVVVPPLPGKAFLRQLPFRGDDGIFDDNFIEERKQGLEQFINKVAGHPLAQNERCLHMFLQDEIIDKSYTPSKIRHA

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 BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	95

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5f0jB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	640 —

Domain ID domain_id	5f0jB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	640 —

Domain ID domain_id	5f0jC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1520 — PX Domain
Homologous superfamily homologous superfamily	10 — Phox-like domain

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8. Citations (1)

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Unit-cell length a length_a	372.820 Å
Unit-cell length b length_b	75.580 Å
Unit-cell length c length_c	57.530 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.87 °
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	2.700 Å
Low-resolution limit resolution_low	56.980 Å
R factor r_factor	0.2091
R_work r_work	0.2072
R_free r_free	0.2461

fit	/app/data/saxs_computation/f0/5f0j/5f0j.fit
pddf	/app/data/pr_computation/f0/5f0j/5f0j.pr.out
profile	/app/data/saxs_computation/f0/5f0j/5f0j.dat

Structure of retromer VPS26-VPS35 subunits bound to SNX3

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

Vacuolar protein sorting-associated protein 35

State in the Current Structure

Other States of the Same Protein in the Database

Vacuolar protein sorting-associated protein 26A

State in the Current Structure

Other States of the Same Protein in the Database

Sorting nexin-3

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 (7)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)