9wt3

NRBF2 coiled coil domain promotes autophagy by strengthening association with Vps15 in the PI3KC3 complex

Method: X-RAY DIFFRACTION Dmax: 91.4 Å Quality: GOOD

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

Nuclear receptor-binding factor 2

Mus musculus

UniProt Q8VCQ3

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 165–210 Chain B; UniProt 165–210 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;289 K;3.916 M NaCl and 0.1 M Tris buffer (pH 7.0) Resolution 2.25 Å R-free 0.263
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 165–210 Chain D; UniProt 165–210 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;289 K;3.916 M NaCl and 0.1 M Tris buffer (pH 7.0) Resolution 2.25 Å R-free 0.263
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 165–210 Chain H; UniProt 165–210 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;289 K;3.916 M NaCl and 0.1 M Tris buffer (pH 7.0) Resolution 2.25 Å R-free 0.263
4 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 165–210 Chain G; UniProt 165–210 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;289 K;3.916 M NaCl and 0.1 M Tris buffer (pH 7.0) Resolution 2.25 Å R-free 0.263

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 NRBF2_MOUSE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 5–50; UniProt 165–210 Author chain B; PDBConstruct 5–50; UniProt 165–210 Author chain C; PDBConstruct 5–50; UniProt 165–210 Author chain D; PDBConstruct 5–50; UniProt 165–210 Author chain E; PDBConstruct 5–50; UniProt 165–210 Author chain F; PDBConstruct 5–50; UniProt 165–210 Author chain G; PDBConstruct 5–50; UniProt 165–210 Author chain H; PDBConstruct 5–50; UniProt 165–210

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 9wt3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9wt3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9wt3
Deposition date deposition_date2025-09-15
Structure title titleNRBF2 coiled coil domain promotes autophagy by strengthening association with Vps15 in the PI3KC3 complex
Keywords keywordsPI3KC3 complex, NRBF2, Autophagy, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.00
Radius of gyration Rg (electron density) rg_electron24.71
Forward intensity I(0) i028866700.00
Molecular weight molecular_weight41739.0 kDa
Excluded volume excluded_volume53018 ų
Envelope volume envelope_volume71041 ų
Hydration-shell volume shell_volume25023 ų
Envelope diameter envelope_diameter95.2
Shell Rg shell_rg30.58
Envelope Rg envelope_rg24.85
Shape Rg shape_rg24.67
Total Rg total_rg25.61
Total atoms total_atoms2936
Residues n_residues356
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 dmax91.4
Rg (real space) rg_real25.00
Rg uncertainty (real space) rg_real_error0.98
I(0) (real space) i0_real2.8870e+07
I(0) uncertainty (real space) i0_real_error4.9220e+05
Rg (reciprocal space) rg_reciprocal25.00
I(0) (reciprocal space) i0_reciprocal28870000.0000
Solution quality estimate total_estimate0.8297
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.4
Skewness Skewness skewness0.387
Kurtosis Kurtosis kurtosis-0.018
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2120000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.620; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.939; Smooth: 0.982

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)