8ese

Crystal structure of human Vps29 bound to a peptide from Vps35L

Method: X-RAY DIFFRACTION D_max: 51.2 Å Quality: EXCELLENT

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

VPS35 endosomal protein-sorting factor-like

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 X； UniProt 16–38	Not recorded	Vacuolar protein sorting-associated protein 29 × 1 （Q9UBQ0）	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

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	B3KT69_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 1–23； UniProt 16–38

Vacuolar protein sorting-associated protein 29

Homo sapiens

UniProt Q9UBQ0

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 Z； UniProt 1–182	Not recorded	VPS35 endosomal protein-sorting factor-like × 1 （B3KT69）	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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8ESE	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 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
2R17 Functional architecture of the retromer cargo-recognition complex Deposited 2007-08-22	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）	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 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）	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
5GTU Structural and mechanistic insights into regulation of the retromer coat by TBC1d5 Deposited 2016-08-23	Different construct 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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）	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 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
8P0V Structure of the human Commander complex coiled coils, DENND10 and partial Retriever subcomplex Deposited 2023-05-10	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 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 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 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 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 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 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 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 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 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 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 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 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 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 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VPS29_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain Z； PDBConstruct 3–184； UniProt 1–182

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	8ese
Deposition date deposition_date	2022-10-13
Structure title title	Crystal structure of human Vps29 bound to a peptide from Vps35L
Keywords keywords	Commander, Retriever, Vps29, Vps35L, ENDOCYTOSIS; ENDOCYTOSIS
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	17.11 Å
Radius of gyration Rg (electron density) rg_electron	15.80 Å
Forward intensity I(0) i0	8320370.00
Molecular weight molecular_weight	22301.0 kDa
Excluded volume excluded_volume	28381 Å³
Envelope volume envelope_volume	31544 Å³
Hydration-shell volume shell_volume	16383 Å³
Envelope diameter envelope_diameter	50.9 Å
Shell Rg shell_rg	22.28 Å
Envelope Rg envelope_rg	16.10 Å
Shape Rg shape_rg	15.79 Å
Total Rg total_rg	16.94 Å
Total atoms total_atoms	3160
Residues n_residues	198
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	51.2 Å
Rg (real space) rg_real	16.97 Å
Rg uncertainty (real space) rg_real_error	0.24 Å
I(0) (real space) i0_real	8.3200e+06
I(0) uncertainty (real space) i0_real_error	9.1990e+04
Rg (reciprocal space) rg_reciprocal	16.99 Å
I(0) (reciprocal space) i0_reciprocal	8320000.0000
Solution quality estimate total_estimate	0.9053
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.042
Kurtosis Kurtosis kurtosis	-0.509
Angular range angular_range	— – 0.4650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1849000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	VPS35 endosomal protein-sorting factor-like
Molecular weight formula_weight	2635.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	3589

EFASCRLEAVPLEFGDYHPLKPI

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Vacuolar protein sorting-associated protein 29
Molecular weight formula_weight	20726.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z

GHMLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVRGDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFEAFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYKKP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	191

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	8eseZ01
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

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8. Citations (1)

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Unit-cell length a length_a	43.719 Å
Unit-cell length b length_b	55.285 Å
Unit-cell length c length_c	82.644 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	4

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

Resolution resolution	1.350 Å
Low-resolution limit resolution_low	45.950 Å
R factor r_factor	0.2165
R_work r_work	0.2153
R_free r_free	0.2413

fit	/app/data/saxs_computation/es/8ese/8ese.fit
pddf	/app/data/pr_computation/es/8ese/8ese.pr.out
profile	/app/data/saxs_computation/es/8ese/8ese.dat

Crystal structure of human Vps29 bound to a peptide from Vps35L

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

VPS35 endosomal protein-sorting factor-like

State in the Current Structure

Other States of the Same Protein in the Database

Vacuolar protein sorting-associated protein 29

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)