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9xzy

DEPDC5 dimer (tandem DEPDC5) focused map

Method: ELECTRON MICROSCOPY Dmax: 142.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

GATOR1 complex protein DEPDC5

Homo sapiens

UniProt O75140

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 H； UniProt 1–1603 Chain H； UniProt 1–1603 Not recorded No other associated polymer ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.80 Å

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 9XZY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6CES Cryo-EM structure of GATOR1-RAG Deposited 2018-02-12 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–1603（1603 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6CET Cryo-EM structure of GATOR1 Deposited 2018-02-12 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–1603（1603 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7T3A GATOR1-RAG-RAGULATOR - Inhibitory Complex Deposited 2021-12-07 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 1–1603（1603 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7T3B GATOR1-RAG-RAGULATOR - GAP Complex Deposited 2021-12-07 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 1–1603（1603 aa）
Mutation：Y775A GDP GUANOSINE-5'-DIPHOSPHATE × 2 AF3 ALUMINUM FLUORIDE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7T3C GATOR1-RAG-RAGULATOR - Dual Complex Deposited 2021-12-07 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain A 1–1603（1603 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 3 AF3 ALUMINUM FLUORIDE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8FW5 Chimeric HsGATOR1-SpGtr-SpLam complex Deposited 2023-01-20 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–1603（1603 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 2 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
9O5A The KICSTOR-GATOR1 complex Deposited 2025-04-09 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 1–1603（1603 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9O5D The KICSTOR-GATOR1-SAMTOR complex Deposited 2025-04-10 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–1603（1603 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
9O5E The dimeric KICSTOR-GATOR1 supercomplex Deposited 2025-04-10 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain H 1–1603（1603 aa）
Chain J 1–1603（1603 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
9V0J Cryo-EM structure of GATOR1-KICSTOR complex Deposited 2025-05-18 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–1603（1603 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DEPD5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain H； PDBConstruct 19–1621； UniProt 1–1603 Author chain H； PDBConstruct 1782–3384； UniProt 1–1603

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 9xzy

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9xzy
Deposition date deposition_date2025-08-28
Structure title titleDEPDC5 dimer (tandem DEPDC5) focused map
Keywords keywordsLysosome, GATOR1, KICSTOR, cell growth, amino acid sensing, mTOR, KPTN, ITFG2, C12orf66, SZT2, NPRL2, NPRL3, DEPDC5, CELL CYCLE; CELL CYCLE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier40.71 Å
Radius of gyration Rg (electron density) rg_electron40.20 Å
Forward intensity I(0) i0701072000.00
Molecular weight molecular_weight222940.0 kDa
Excluded volume excluded_volume280880 ų
Envelope volume envelope_volume368880 ų
Hydration-shell volume shell_volume74195 ų
Envelope diameter envelope_diameter152.1 Å
Shell Rg shell_rg47.46 Å
Envelope Rg envelope_rg39.85 Å
Shape Rg shape_rg40.16 Å
Total Rg total_rg40.73 Å
Total atoms total_atoms31098
Residues n_residues1912
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 dmax142.5 Å
Rg (real space) rg_real40.55 Å
Rg uncertainty (real space) rg_real_error1.13 Å
I(0) (real space) i0_real7.0110e+08
I(0) uncertainty (real space) i0_real_error1.2230e+07
Rg (reciprocal space) rg_reciprocal40.71 Å
I(0) (reciprocal space) i0_reciprocal701200000.0000
Solution quality estimate total_estimate0.8600
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary51.1 Å
Skewness Skewness skewness0.205
Kurtosis Kurtosis kurtosis-0.273
Angular range angular_range— – 0.1950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha77100000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.730; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.986
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)