SAXSdb — 7oj9

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

Sorting nexin-9

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 1–64	Not recorded	EEEV nsP3 peptide × 1	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR sample composition：1 mM [U-13C; U-15N] SNX9 SH3, 1 mM EEEV nsP3 peptide, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided

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 7OJ9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2RAI The PX-BAR membrane remodeling unit of Sorting Nexin 9 Deposited 2007-09-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 204–595（392 aa） Fragment：C-terminal fragment, residues 214-594 Chain B 204–595（392 aa） Fragment：C-terminal fragment, residues 214-594	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.3M Ammonium tartrate dibasic, 0.1M BIS-TRIS propane, pH 7.0 , VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.20 Å R-free 0.301
2RAJ SO4 bound PX-BAR membrane remodeling unit of Sorting Nexin 9 Deposited 2007-09-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 204–595（392 aa） Fragment：C-terminal fragment, residues 214-594	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.3M Ammonium tartrate dibasic, 0.1M BIS-TRIS propane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.45 Å R-free 0.276
2RAK PI(3)P bound PX-BAR membrane remodeling unit of Sorting Nexin 9 Deposited 2007-09-16	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 204–595（392 aa） Fragment：C-terminal fragment, residues 214-594	Not recorded	PIB 2-(BUTANOYLOXY)-1-{[(HYDROXY{[2,3,4,6-TETRAHYDROXY-5-(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL)OXY]METHYL}ETHYL BUTANOATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.3M Ammonium tartrate dibasic, 0.1M BIS-TRIS propane, pH 7.0 , VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.293
3DYT Crystal structure of Snx9PX-BAR (230-595), C2221 Deposited 2008-07-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 230–595（366 aa） Fragment：UNP residues 230-595	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；1.8M Ammonium sulfate, 0.1M Tris-HCl pH 8.5, 5% PEG 400, 0.05M MgSO4, 15% Xylitol, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 2.08 Å R-free 0.245
3DYU Crystal structure of Snx9PX-BAR (230-595), H32 Deposited 2008-07-28	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 230–595（366 aa） Fragment：UNP residues 230-595 Chain B 230–595（366 aa） Fragment：UNP residues 230-595	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；1.8M Ammonium sulfate, 0.1M Tris-HCl pH 8.5, 5% PEG 400, 0.05M MgSO4, 15% Xylitol, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 4.10 Å R-free 0.403
3DYU Crystal structure of Snx9PX-BAR (230-595), H32 Deposited 2008-07-28	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 230–595（366 aa） Fragment：UNP residues 230-595	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293.15 K；1.8M Ammonium sulfate, 0.1M Tris-HCl pH 8.5, 5% PEG 400, 0.05M MgSO4, 15% Xylitol, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 4.10 Å R-free 0.403
3LGE Crystal structure of rabbit muscle aldolase-SNX9 LC4 complex Deposited 2010-01-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain E 152–182（31 aa） Fragment：UNP residues 152-182 Chain F 152–182（31 aa） Fragment：UNP residues 152-182 Chain G 152–182（31 aa） Fragment：UNP residues 152-182 Chain H 152–182（31 aa） Fragment：UNP residues 152-182	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；PEG-MME 550, MgCl2, pH 7, Vapor Diffusion, Hanging drop, temperature 277K	Resolution 2.20 Å R-free 0.189
9R4W Solution NMR structure of SNX9 SH3 in complex with EspF Deposited 2025-05-08	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–64（64 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 150；Pressure ambient NMR sample composition 1.3 mM [U-13C; U-15N] SNX9 SH3, 1.5 mM EspF, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 1.9 mM SNX9 SH3, 1.5 mM [U-13C; U-15N] EspF, 20 mM sodium phosphate, 50 mM sodium chloride, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SNX9_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 4–67； UniProt 1–64

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7oj9
Deposition date deposition_date	2021-05-14
Structure title title	NMR solution structure of SNX9 SH3 - EEEV nsP3 peptide complex
Keywords keywords	complex, ENDOCYTOSIS; ENDOCYTOSIS
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	14.47 Å
Radius of gyration Rg (electron density) rg_electron	14.01 Å
Forward intensity I(0) i0	552218000.00
Molecular weight molecular_weight	194300.0 kDa
Excluded volume excluded_volume	241840 Å³
Envelope volume envelope_volume	32131 Å³
Hydration-shell volume shell_volume	15226 Å³
Envelope diameter envelope_diameter	61.9 Å
Shell Rg shell_rg	24.29 Å
Envelope Rg envelope_rg	19.70 Å
Shape Rg shape_rg	13.97 Å
Total Rg total_rg	14.42 Å
Total atoms total_atoms	27360
Residues n_residues	1800
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	38.0 Å
Rg (real space) rg_real	13.62 Å
Rg uncertainty (real space) rg_real_error	0.05 Å
I(0) (real space) i0_real	5.2630e+08
I(0) uncertainty (real space) i0_real_error	4.2520e+06
Rg (reciprocal space) rg_reciprocal	14.56 Å
I(0) (reciprocal space) i0_reciprocal	552200000.0000
Solution quality estimate total_estimate	0.6836
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	15.9 Å
Skewness Skewness skewness	0.279
Kurtosis Kurtosis kurtosis	-0.337
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	3.4360
Highest regularization parameter α highest_alpha	210100.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.002; Oscil: 0.979; Stabil: 0.985; Sysdev: 0.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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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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8. Citations (1)

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Description description	EEEV nsP3 peptide
Molecular weight formula_weight	2548.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	27360

Description description	Sorting nexin-9
Molecular weight formula_weight	7179.9 kDa
Source method src_method	man
Copy count entity_count	1

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

fit	/app/data/saxs_computation/oj/7oj9/7oj9.fit
pddf	/app/data/pr_computation/oj/7oj9/7oj9.pr.out
profile	/app/data/saxs_computation/oj/7oj9/7oj9.dat

NMR solution structure of SNX9 SH3 - EEEV nsP3 peptide complex

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

Sorting nexin-9

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)