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4gxb

Structure of the SNX17 atypical FERM domain bound to the NPxY motif of P-selectin

Method: X-RAY DIFFRACTION Dmax: 61.3 Å Quality: REASONABLE
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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 111–388 Fragment：FERM domain, UNP residues 111-388 P-selectin × 1 （Q01102） 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

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 4GXB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3FOG Crystal structure of the PX domain of sorting nexin-17 (SNX17) Deposited 2008-12-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–108（108 aa） Fragment：residues 1-115
Not recorded 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
3LUI Crystal structure of the SNX17 PX domain with bound sulphate Deposited 2010-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–112（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 oligomeric state 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 oligomeric state 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
4TKN Structure of the SNX17 FERM domain bound to the second NPxF motif of KRIT1 Deposited 2014-05-27 Different construct 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 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 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 3–280； UniProt 111–388

P-selectin

Mus musculus

UniProt Q01102

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 B； UniProt 735–768 Fragment：intracellular domain, UNP residues 735-768 Sorting nexin-17 × 1 （Q15036） 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

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 LYAM3_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 8–41； UniProt 735–768

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 4gxb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4gxb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4gxb
Deposition date deposition_date2012-09-04
Structure title titleStructure of the SNX17 atypical FERM domain bound to the NPxY motif of P-selectin
Keywords keywordsFERM domain, PROTEIN TRANSPORT-CELL ADHESION complex; PROTEIN TRANSPORT/CELL ADHESION
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_guinier20.60 Å
Radius of gyration Rg (electron density) rg_electron19.47 Å
Forward intensity I(0) i017315100.00
Molecular weight molecular_weight31747.0 kDa
Excluded volume excluded_volume39960 ų
Envelope volume envelope_volume48023 ų
Hydration-shell volume shell_volume20588 ų
Envelope diameter envelope_diameter66.7 Å
Shell Rg shell_rg26.00 Å
Envelope Rg envelope_rg19.76 Å
Shape Rg shape_rg19.45 Å
Total Rg total_rg20.50 Å
Total atoms total_atoms2232
Residues n_residues278
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 dmax61.3 Å
Rg (real space) rg_real20.55 Å
Rg uncertainty (real space) rg_real_error0.08 Å
I(0) (real space) i0_real1.6790e+07
I(0) uncertainty (real space) i0_real_error1.5750e+05
Rg (reciprocal space) rg_reciprocal20.50 Å
I(0) (reciprocal space) i0_reciprocal17320000.0000
Solution quality estimate total_estimate0.7147
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary24.9 Å
Skewness Skewness skewness0.169
Kurtosis Kurtosis kurtosis-0.461
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha9.0000
Highest regularization parameter α highest_alpha3410000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.968; Stabil: 0.922; Sysdev: 0.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.650
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id4gxbA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id4gxbA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology80 — Acyl-CoA Binding Protein
Homologous superfamily homologous superfamily60 —
Domain ID domain_id4gxbA03
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology29 — PH-domain like
Homologous superfamily homologous superfamily30 — Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB)
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8. Citations (1)

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9. Files and Curves (10)