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3fog

Crystal structure of the PX domain of sorting nexin-17 (SNX17)

Method: X-RAY DIFFRACTION Dmax: 45.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sorting nexin-17

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–108 Fragment：residues 1-115 NA SODIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；20% PEG 3350, 0.2M sodium fluoride, 0.1M bis-Tris propane, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.80 Å R-free 0.279

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 3FOG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3LUI Crystal structure of the SNX17 PX domain with bound sulphate Deposited 2010-02-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–112（112 aa） Fragment：SNX17 PX domain (residues 1-112)
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.8M lithium sulphate, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.80 Å R-free 0.245
3LUI Crystal structure of the SNX17 PX domain with bound sulphate Deposited 2010-02-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–112（112 aa） Fragment：SNX17 PX domain (residues 1-112)
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.8M lithium sulphate, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.80 Å R-free 0.245
3LUI Crystal structure of the SNX17 PX domain with bound sulphate Deposited 2010-02-17 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–112（112 aa） Fragment：SNX17 PX domain (residues 1-112)
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；1.8M lithium sulphate, 0.1M Tris, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.80 Å R-free 0.245
4GXB Structure of the SNX17 atypical FERM domain bound to the NPxY motif of P-selectin Deposited 2012-09-04 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 A 111–388（278 aa） Fragment：FERM domain, UNP residues 111-388
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；0.1M sodium acetate, 0.2M magnesium chloride, 15% PEG4000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 1.80 Å R-free 0.204
4TKN Structure of the SNX17 FERM domain bound to the second NPxF motif of KRIT1 Deposited 2014-05-27 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 A 108–391（284 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 5% PEG 400
Resolution 3.00 Å R-free 0.268
4TKN Structure of the SNX17 FERM domain bound to the second NPxF motif of KRIT1 Deposited 2014-05-27 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 B 108–391（284 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 5% PEG 400
Resolution 3.00 Å R-free 0.268
4TKN Structure of the SNX17 FERM domain bound to the second NPxF motif of KRIT1 Deposited 2014-05-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 108–391（284 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 5% PEG 400
Resolution 3.00 Å R-free 0.268
7RM8 Solution NMR structure of PDLIM7 PDZ bound to SNX17 peptide Deposited 2021-07-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 457–470（14 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；298 K；Ionic strength (raw mmCIF value) 75 mM NaCl；Pressure 1
NMR sample composition 1 mM [U-13C; U-15N] PDLIM7_SNX17_Fusion, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
9AU7 Human Retriever VPS35L/VPS29/VPS26C complex bound to SNX17 peptide (Composite Map) Deposited 2024-02-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 451–470（20 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

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 1
Chains and sequence ranges Author chain A； PDBConstruct 1–108； UniProt 1–108

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 3fog

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3fog
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3fog
Deposition date deposition_date2008-12-30
Structure title titleCrystal structure of the PX domain of sorting nexin-17 (SNX17)
Keywords keywordshelix, Structural Genomics, Structural Genomics Consortium, SGC, Cytoplasm, Endosome, Phosphoprotein, Protein transport, Transport; 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_guinier14.64 Å
Radius of gyration Rg (electron density) rg_electron13.36 Å
Forward intensity I(0) i02792960.00
Molecular weight molecular_weight11582.0 kDa
Excluded volume excluded_volume14497 ų
Envelope volume envelope_volume16764 ų
Hydration-shell volume shell_volume10888 ų
Envelope diameter envelope_diameter43.7 Å
Shell Rg shell_rg18.83 Å
Envelope Rg envelope_rg13.65 Å
Shape Rg shape_rg13.36 Å
Total Rg total_rg14.62 Å
Total atoms total_atoms819
Residues n_residues102
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 dmax45.4 Å
Rg (real space) rg_real14.54 Å
Rg uncertainty (real space) rg_real_error0.22 Å
I(0) (real space) i0_real2.7930e+06
I(0) uncertainty (real space) i0_real_error2.8690e+04
Rg (reciprocal space) rg_reciprocal14.55 Å
I(0) (reciprocal space) i0_reciprocal2793000.0000
Solution quality estimate total_estimate0.8942
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.8 Å
Skewness Skewness skewness0.087
Kurtosis Kurtosis kurtosis-0.402
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha399400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.949
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3foga1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.189 — PX domain
Superfamily Superfamily superfamilyd.189.1 — PX domain
Family Family familyd.189.1.0 — automated matches
Domain ID domain_idd3foga2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id3fogA00
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)