2r17

Functional architecture of the retromer cargo-recognition complex

Method: X-RAY DIFFRACTION D_max: 122.1 Å Quality: GOOD

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

Vacuolar protein sorting-associated protein 29

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 1–182	Non-standard monomer：Yes (specific site not provided by mmCIF)	Vacuolar protein sorting-associated protein 35 × 1 （Q96QK1）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–182	Non-standard monomer：Yes (specific site not provided by mmCIF)	Vacuolar protein sorting-associated protein 35 × 1 （Q96QK1） 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

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 2R17	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1W24 Crystal Structure Of human Vps29 Deposited 2004-06-26	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–182（182 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；25%PEG4000, 10%ETHYENE GLYCOL, 100MM HEPES PH7.5, pH 7.50	Resolution 2.10 Å R-free 0.244
5GTU Structural and mechanistic insights into regulation of the retromer coat by TBC1d5 Deposited 2016-08-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–182（181 aa） Fragment：UNP residues 2-182	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；289 K；0.1M Bis-Tris, pH6.0, 2% Tacsimate, pH 6.0, 15~20% PEG3350	Resolution 1.50 Å R-free 0.186
5OSH Structure of retromer VPS29-VPS35C subunits complexed with RidL N-terminal domain (1-236) Deposited 2017-08-17	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–182（182 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–182（182 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–182（182 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1–182（182 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 mutation/modification 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 1–182（182 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 mutation/modification 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 1–182（182 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–182（182 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 1–182（182 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
5WYH Crystal structure of RidL(1-200) complexed with VPS29 Deposited 2017-01-13	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–182（181 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Tris pH8.0, 20% PEG 8000	Resolution 2.46 Å R-free 0.225
5WYH Crystal structure of RidL(1-200) complexed with VPS29 Deposited 2017-01-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–182（181 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Tris pH8.0, 20% PEG 8000	Resolution 2.46 Å R-free 0.225
6XS5 Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D1 Deposited 2020-07-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–182（182 aa）	Not recorded	GOL GLYCEROL × 2 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；3.5 M Sodium Formate	Resolution 2.01 Å R-free 0.225
6XS7 Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-D2 Deposited 2020-07-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–182（182 aa）	Not recorded	GOL GLYCEROL × 2 FMT FORMIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 30% PEG2000 MME	Resolution 1.58 Å R-free 0.191
6XS9 Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L1 Deposited 2020-07-15	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 1–182（182 aa）	Not recorded	MLI MALONATE ION × 2 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.4 M sodium malonate	Resolution 2.69 Å R-free 0.282
6XS9 Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L1 Deposited 2020-07-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–182（182 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1 O4B 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.4 M sodium malonate	Resolution 2.69 Å R-free 0.282
6XSA Crystal structure of human Vps29 complexed with RaPID-derived cyclic peptide RT-L2 Deposited 2020-07-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–182（182 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M HEPES, 1 M succinic and 1% PEG2000 MME	Resolution 1.83 Å R-free 0.227
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 experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–182（182 aa） Chain D 1–182（182 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
8ESE Crystal structure of human Vps29 bound to a peptide from Vps35L Deposited 2022-10-13	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Z 1–182（182 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M Bis-tris pH 5.5 and 25% (w/v) PEG3350	Resolution 1.35 Å R-free 0.241
8P0V Structure of the human Commander complex coiled coils, DENND10 and partial Retriever subcomplex Deposited 2023-05-10	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain N 1–182（182 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.50 Å
8P0X Structure of the human Commander complex Retriever Subcomplex Deposited 2023-05-11	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain N 1–182（182 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.50 Å
8R02 Crystal structure of the retromer complex VPS29/VPS35 with the ligand bis-1,3-phenyl guanylhydrazone, 2a Deposited 2023-10-30	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–182（182 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–182（182 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–182（182 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–182（182 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–182（182 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–182（182 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–182（182 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–182（182 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
8SYM Human VPS29/VPS35L Complex (Locally refined map) Deposited 2023-05-25	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–186（186 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7；10 mM HEPES (pH 7.0), 150 mM NaCl, 2 mM MgCl2, 2 mM DTT, and 5% (v/v) glycerol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
8SYN Human VPS35L/VPS29/VPS26C Complex Deposited 2023-05-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–186（186 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7；10 mM HEPES (pH 7.0), 150 mM NaCl, 2 mM MgCl2, 2 mM DTT, and 5% (v/v) glycerol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
8SYO Human Retriever VPS35L/VPS29/VPS26C Complex (Composite Map) Deposited 2023-05-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–186（186 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7；10 mM HEPES (pH 7.0), 150 mM NaCl, 2 mM MgCl2, 2 mM DTT, and 5% (v/v) glycerol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
9AU7 Human Retriever VPS35L/VPS29/VPS26C complex bound to SNX17 peptide (Composite Map) Deposited 2024-02-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–186（186 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

20 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPS29_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–183； UniProt 1–182 Author chain B； PDBConstruct 2–183； UniProt 1–182

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 483–780	Non-standard monomer：Yes (specific site not provided by mmCIF)	Vacuolar protein sorting-associated protein 29 × 1 （Q9UBQ0）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 483–780	Non-standard monomer：Yes (specific site not provided by mmCIF)	Vacuolar protein sorting-associated protein 29 × 1 （Q9UBQ0） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 2R17	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5F0J Structure of retromer VPS26-VPS35 subunits bound to SNX3 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 × 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 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 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 construct Different mutation/modification 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 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 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 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 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 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 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPS35_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–298； UniProt 483–780 Author chain D； PDBConstruct 1–298； UniProt 483–780

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	2r17
Deposition date deposition_date	2007-08-22
Structure title title	Functional architecture of the retromer cargo-recognition complex
Keywords keywords	Protein Transport, Membrane, Phosphorylation; 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	37.30 Å
Radius of gyration Rg (electron density) rg_electron	37.59 Å
Forward intensity I(0) i0	174772000.00
Molecular weight molecular_weight	108450.0 kDa
Excluded volume excluded_volume	136150 Å³
Envelope volume envelope_volume	174580 Å³
Hydration-shell volume shell_volume	40894 Å³
Envelope diameter envelope_diameter	128.9 Å
Shell Rg shell_rg	40.75 Å
Envelope Rg envelope_rg	37.65 Å
Shape Rg shape_rg	37.57 Å
Total Rg total_rg	37.88 Å
Total atoms total_atoms	7591
Residues n_residues	924
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	122.1 Å
Rg (real space) rg_real	37.72 Å
Rg uncertainty (real space) rg_real_error	1.18 Å
I(0) (real space) i0_real	1.7480e+08
I(0) uncertainty (real space) i0_real_error	3.2680e+06
Rg (reciprocal space) rg_reciprocal	37.47 Å
I(0) (reciprocal space) i0_reciprocal	174700000.0000
Solution quality estimate total_estimate	0.8001
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	32.0 Å
Skewness Skewness skewness	0.550
Kurtosis Kurtosis kurtosis	-0.419
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	38920000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.770; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.860; Smooth: 0.227

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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	Vacuolar protein sorting-associated protein 29
Molecular weight formula_weight	20850.5 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	7640

MMLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKP

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 35
Molecular weight formula_weight	34517.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

DFADEQSLVGRFIHLLRSEDPDQQYLILNTARKHFGAGGNQRIRFTLPPLVFAAYQLAFRYKENSKVDDKWEKKCQKIFSFAHQTISALIKAELAELPLRLFLQGALAAGEIGFENHETVAYEFMSQAFSLYEDEISDSKAQLAAITLIIGTFERMKCFSEENHEPLRTQCALAASKLLKKPDQGRAVSTCAHLFWSGRNTDKNGEELHGGKRVMECLKKALKIANQCMDPSLQVQLFIEILNRYIYFYEKENDAVTIQVLNQLIQKIREDLPNLESSEETEQINKHFHNTLEHLRLR

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 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	49

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2r17a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
Family Family family	d.159.1.7 — YfcE-like

Domain ID domain_id	d2r17b_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
Family Family family	d.159.1.7 — YfcE-like

CATH v4.4 (4 domains)

Domain ID domain_id	2r17A00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

Domain ID domain_id	2r17B00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

Domain ID domain_id	2r17C00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	660 — Vacuolar protein sorting-associated protein 35, helical subcomplex Vps35-C

Domain ID domain_id	2r17D00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	660 — Vacuolar protein sorting-associated protein 35, helical subcomplex Vps35-C

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8. Citations (1)

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Unit-cell length a length_a	66.250 Å
Unit-cell length b length_b	128.471 Å
Unit-cell length c length_c	140.452 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	2.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2160
R_work r_work	0.2160
R_free r_free	0.2680

fit	/app/data/saxs_computation/r1/2r17/2r17.fit
pddf	/app/data/pr_computation/r1/2r17/2r17.pr.out
profile	/app/data/saxs_computation/r1/2r17/2r17.dat

Functional architecture of the retromer cargo-recognition complex

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

Vacuolar protein sorting-associated protein 29

State in the Current Structure

Other States of the Same Protein in the Database

Vacuolar protein sorting-associated protein 35

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

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)