9zm0

Crystal structure of monomeric Atg23

Method: X-RAY DIFFRACTION Dmax: 115.0 Å Quality: REASONABLE

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

Autophagy-related protein 23

Saccharomyces cerevisiae

UniProt Q06671

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 1–95 Chain A; UniProt 212–381 Non-standard monomer:Yes (specific site not provided by mmCIF) unidentified Atg23 fragment × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;0.02 M xylitol, D-fructose, D-sorbitol, myo-inositol, L-rhamnose each; 9% PEG8000, 18% 1,5-pentanediol, 0.07 M MOPSO, 0.03 M Bis-Tris Resolution 2.10 Å R-free 0.298

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 ATG23_YEAST
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 6–100; UniProt 1–95 Author chain A; PDBConstruct 105–274; UniProt 212–381

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 9zm0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9zm0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9zm0
Deposition date deposition_date2025-12-09
最后修订 last_revision2026-01-07
Structure title titleCrystal structure of monomeric Atg23
Keywords keywordsAutophagy, Degradation, Membrane Tethering, PROTEIN TRANSPORT; PROTEIN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.86
Radius of gyration Rg (electron density) rg_electron30.96
Forward intensity I(0) i015532400.00
Molecular weight molecular_weight28943.0 kDa
Excluded volume excluded_volume35655 ų
Envelope volume envelope_volume48949 ų
Hydration-shell volume shell_volume16033 ų
Envelope diameter envelope_diameter118.6
Shell Rg shell_rg31.24
Envelope Rg envelope_rg31.45
Shape Rg shape_rg30.90
Total Rg total_rg31.17
Total atoms total_atoms2001
Residues n_residues244
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 dmax115.0
Rg (real space) rg_real31.64
Rg uncertainty (real space) rg_real_error1.73
I(0) (real space) i0_real1.5530e+07
I(0) uncertainty (real space) i0_real_error2.9220e+05
Rg (reciprocal space) rg_reciprocal31.31
I(0) (reciprocal space) i0_reciprocal15530000.0000
Solution quality estimate total_estimate0.6436
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary20.3
Skewness Skewness skewness0.650
Kurtosis Kurtosis kurtosis-0.424
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1564000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.161; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.014; Smooth: 0.865

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

8. Citations (1)

9. Files and Curves (10)