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6cet

Cryo-EM structure of GATOR1

Method: ELECTRON MICROSCOPY Dmax: 166.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

GATOR complex protein NPRL2

Homo sapiens

UniProt Q8WTW4

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain N； UniProt 1–380 Not recorded GATOR complex protein NPRL3 × 1 （Q12980） GATOR complex protein DEPDC5 × 1 （O75140） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.40 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 6CET 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 N 1–380（380 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
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 B 1–380（380 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–380（380 aa）
Not recorded 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 B 1–380（380 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 B 1–380（380 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 H 1–380（380 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 D 1–380（380 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 D 1–380（380 aa）
Chain G 1–380（380 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 A 1–380（380 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

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NPRL2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain N； PDBConstruct 1–380； UniProt 1–380

GATOR complex protein NPRL3

Homo sapiens

UniProt Q12980

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain M； UniProt 1–569 Not recorded GATOR complex protein NPRL2 × 1 （Q8WTW4） GATOR complex protein DEPDC5 × 1 （O75140） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.40 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 6CET 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 M 1–569（569 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
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 C 1–569（569 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 oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain C 1–569（569 aa）
Not recorded 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 C 1–569（569 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 C 1–569（569 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 C 1–569（569 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 C 1–569（569 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 C 1–569（569 aa）
Chain F 1–569（569 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 B 1–569（569 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

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NPRL3_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain M； PDBConstruct 1–569； UniProt 1–569

GATOR 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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain D； UniProt 1–1603 Not recorded GATOR complex protein NPRL2 × 1 （Q8WTW4） GATOR complex protein NPRL3 × 1 （Q12980） ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.40 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 6CET 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
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
9XZY DEPDC5 dimer (tandem DEPDC5) focused map Deposited 2025-08-28 Different oligomeric state Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain H 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 3.80 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 3
Chains and sequence ranges Author chain D； PDBConstruct 1–1603； 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 6cet

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6cet
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6cet
Deposition date deposition_date2018-02-12
Structure title titleCryo-EM structure of GATOR1
Keywords keywordsmTORC1 amino-acid sensing lysosome growth control, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier47.12 Å
Radius of gyration Rg (electron density) rg_electron47.19 Å
Forward intensity I(0) i0562481000.00
Molecular weight molecular_weight198940.0 kDa
Excluded volume excluded_volume250420 ų
Envelope volume envelope_volume387900 ų
Hydration-shell volume shell_volume69915 ų
Envelope diameter envelope_diameter178.6 Å
Shell Rg shell_rg49.95 Å
Envelope Rg envelope_rg46.54 Å
Shape Rg shape_rg47.17 Å
Total Rg total_rg47.39 Å
Total atoms total_atoms14012
Residues n_residues1741
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 dmax166.3 Å
Rg (real space) rg_real47.34 Å
Rg uncertainty (real space) rg_real_error1.74 Å
I(0) (real space) i0_real5.6250e+08
I(0) uncertainty (real space) i0_real_error1.0990e+07
Rg (reciprocal space) rg_reciprocal47.13 Å
I(0) (reciprocal space) i0_reciprocal562300000.0000
Solution quality estimate total_estimate0.6304
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary55.4 Å
Skewness Skewness skewness0.472
Kurtosis Kurtosis kurtosis-0.119
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha51540000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.789; Stabil: 1.000; Sysdev: 0.006; Positv: 1.000; Valcen: 0.987; Smooth: 0.820
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)