9au7

Human Retriever VPS35L/VPS29/VPS26C complex bound to SNX17 peptide (Composite Map)

Method: ELECTRON MICROSCOPY Dmax: 157.5 Å Quality: GOOD

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

VPS35 endosomal protein-sorting factor-like

Homo sapiens

UniProt Q7Z3J2

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 1–963 Not recorded Vacuolar protein sorting-associated protein 29 × 1 (Q9UBQ0) Vacuolar protein sorting-associated protein 26C × 1 (O14972) Sorting nexin-17 × 1 (Q15036) ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.40 Å

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.

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

View Construct and Data Evidence
UniProt name VP35L_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–963; UniProt 1–963

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 1–186 Not recorded VPS35 endosomal protein-sorting factor-like × 1 (Q7Z3J2) Vacuolar protein sorting-associated protein 26C × 1 (O14972) Sorting nexin-17 × 1 (Q15036) ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.40 Å

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.

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 Q9UBQ0-2
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–186; UniProt 1–186

Vacuolar protein sorting-associated protein 26C

Homo sapiens

UniProt O14972

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 1–297 Not recorded VPS35 endosomal protein-sorting factor-like × 1 (Q7Z3J2) Vacuolar protein sorting-associated protein 29 × 1 (Q9UBQ0) Sorting nexin-17 × 1 (Q15036) ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.40 Å

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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VP26C_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–297; UniProt 1–297

Sorting nexin-17

OrganismNot specified

UniProt Q15036

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 451–470 Not recorded VPS35 endosomal protein-sorting factor-like × 1 (Q7Z3J2) Vacuolar protein sorting-associated protein 29 × 1 (Q9UBQ0) Vacuolar protein sorting-associated protein 26C × 1 (O14972) ELECTRON MICROSCOPY cryo-EM buffer:pH 7 cryo-EM vitrification conditions:Cryogen ETHANE Resolution 3.40 Å

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.

5 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SNX17_HUMAN
Isoform
PDB entities 4
Chains and sequence ranges Author chain D; PDBConstruct 1–20; UniProt 451–470

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 9au7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9au7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9au7
Deposition date deposition_date2024-02-28
Structure title titleHuman Retriever VPS35L/VPS29/VPS26C complex bound to SNX17 peptide (Composite Map)
Keywords keywordsRetreiver, CCC, Endosomal recycling, Sorting Nexin, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodELECTRON MICROSCOPY

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier46.66
Radius of gyration Rg (electron density) rg_electron46.92
Forward intensity I(0) i0204922000.00
Molecular weight molecular_weight122320.0 kDa
Excluded volume excluded_volume155130 ų
Envelope volume envelope_volume233720 ų
Hydration-shell volume shell_volume43101 ų
Envelope diameter envelope_diameter158.9
Shell Rg shell_rg48.47
Envelope Rg envelope_rg45.59
Shape Rg shape_rg46.91
Total Rg total_rg47.02
Total atoms total_atoms17304
Residues n_residues1079
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax157.5
Rg (real space) rg_real47.08
Rg uncertainty (real space) rg_real_error2.07
I(0) (real space) i0_real2.0490e+08
I(0) uncertainty (real space) i0_real_error4.4500e+06
Rg (reciprocal space) rg_reciprocal46.67
I(0) (reciprocal space) i0_reciprocal204800000.0000
Solution quality estimate total_estimate0.8019
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary32.4
Skewness Skewness skewness0.329
Kurtosis Kurtosis kurtosis-0.854
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17080000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.662; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.651; Smooth: 0.785

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

8. Citations (1)

9. Files and Curves (10)