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5f0m

Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled)

Method: X-RAY DIFFRACTION Dmax: 150.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Vacuolar protein sorting-associated protein 35

Homo sapiens

UniProt Q96QK1

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 × 4 PDB declaration: tetrameric（4） 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） Natural resistance-associated macrophage protein 2 × 1 （P49281） 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

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 5F0M 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
5F0J Structure of retromer VPS26-VPS35 subunits bound to SNX3 Deposited 2015-11-27 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 14–470（457 aa） Fragment：Residues 14-470
Not recorded 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
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 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
5F0P Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled) Deposited 2015-11-27 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 2–321 Non-standard monomer：Yes (specific site not provided by mmCIF) Vacuolar protein sorting-associated protein 35 × 1 （Q96QK1） Sorting nexin-3 × 1 （O60493） Natural resistance-associated macrophage protein 2 × 1 （P49281） 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

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 5F0M 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
5F0J Structure of retromer VPS26-VPS35 subunits bound to SNX3 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 × 3 PDB declaration: trimeric
Chain B 2–326（325 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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
5F0L Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 Deposited 2015-11-27 Different construct Different mutation/modification 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
5F0P Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled) Deposited 2015-11-27 Different construct 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 2–321； UniProt 2–321

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain C； UniProt 1–162 Fragment：Residues 14-470 Vacuolar protein sorting-associated protein 35 × 1 （Q96QK1） Vacuolar protein sorting-associated protein 26A × 1 （O75436） Natural resistance-associated macrophage protein 2 × 1 （P49281） 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

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 5F0M 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
5F0J Structure of retromer VPS26-VPS35 subunits bound to SNX3 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 × 3 PDB declaration: trimeric
Chain C 1–162（162 aa）
Not recorded 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
5F0L Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 Deposited 2015-11-27 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
5F0P Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled) Deposited 2015-11-27 Different construct 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

Natural resistance-associated macrophage protein 2

Homo sapiens

UniProt P49281

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain D； UniProt 549–560 Fragment：UNP residues 549-560 Non-standard monomer：Yes (specific site not provided by mmCIF) Vacuolar protein sorting-associated protein 35 × 1 （Q96QK1） Vacuolar protein sorting-associated protein 26A × 1 （O75436） Sorting nexin-3 × 1 （O60493） 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

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 5F0M Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5F0L Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 Deposited 2015-11-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 545–568（24 aa） Fragment：UNP residues 545-568
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
5F0P Structure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1(L557M) (SeMet labeled) Deposited 2015-11-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 549–560（12 aa）
Mutation：L557M 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
9F6N Human divalent metal transporter 1 (DMT1/SLC11A2) in complex with manganese, in an occluded state Deposited 2024-05-02 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 2–590（589 aa）
Not recorded MN MANGANESE (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.60 Å
9F6O Human divalent metal transporter 1 (DMT1/SLC11A2) in complex with sybody 1, in an occluded state Deposited 2024-05-02 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 × 2 PDB declaration: dimeric
Chain A 2–590（589 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.90 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NRAM2_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–12； UniProt 549–560

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

SAXS profile for 5f0m

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5f0m
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5f0m
Deposition date deposition_date2015-11-27
Structure title titleStructure of retromer VPS26-VPS35 subunits bound to SNX3 and DMT1 (SeMet labeled)
Keywords keywordsprotein transport, retromer, sorting nexin; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.54 Å
Radius of gyration Rg (electron density) rg_electron40.17 Å
Forward intensity I(0) i0175093000.00
Molecular weight molecular_weight107800.0 kDa
Excluded volume excluded_volume135400 ų
Envelope volume envelope_volume187520 ų
Hydration-shell volume shell_volume43163 ų
Envelope diameter envelope_diameter160.2 Å
Shell Rg shell_rg40.23 Å
Envelope Rg envelope_rg41.22 Å
Shape Rg shape_rg40.20 Å
Total Rg total_rg40.07 Å
Total atoms total_atoms7544
Residues n_residues904
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax150.4 Å
Rg (real space) rg_real40.12 Å
Rg uncertainty (real space) rg_real_error1.80 Å
I(0) (real space) i0_real1.7510e+08
I(0) uncertainty (real space) i0_real_error2.9810e+06
Rg (reciprocal space) rg_reciprocal39.76 Å
I(0) (reciprocal space) i0_reciprocal175000000.0000
Solution quality estimate total_estimate0.7924
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.4 Å
Skewness Skewness skewness0.665
Kurtosis Kurtosis kurtosis0.285
Angular range angular_range— – 0.2000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha21290000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.620; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.606; Smooth: 0.832
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id5f0mB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily640 —
Domain ID domain_id5f0mB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily640 —
Domain ID domain_id5f0mC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1520 — PX Domain
Homologous superfamily homologous superfamily10 — Phox-like domain
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8. Citations (1)

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9. Files and Curves (10)