8fw5

Chimeric HsGATOR1-SpGtr-SpLam complex

Method: ELECTRON MICROSCOPY Dmax: 182.7 Å Quality: GOOD

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

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 × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain A; UniProt 1–1603 Not recorded GATOR complex protein NPRL2 × 1 (Q8WTW4) GATOR complex protein NPRL3 × 1 (Q12980) GTP-binding protein Gtr1 × 1 GTP-binding protein Gtr2 × 1 Schizosaccharomyces pombe LAM1, Human LAMTOR1 ortholog × 1 Schizosaccharomyces pombe LAM2, Human LAMTOR2 ortholog × 1 Schizosaccharomyces pombe LAM3, Human LAMTOR3 ortholog × 1 Schizosaccharomyces pombe LAM4, Human LAMTOR5 ortholog × 1 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

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.

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 A; PDBConstruct 1–1603; UniProt 1–1603

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 × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain B; UniProt 1–380 Not recorded GATOR complex protein DEPDC5 × 1 (O75140) GATOR complex protein NPRL3 × 1 (Q12980) GTP-binding protein Gtr1 × 1 GTP-binding protein Gtr2 × 1 Schizosaccharomyces pombe LAM1, Human LAMTOR1 ortholog × 1 Schizosaccharomyces pombe LAM2, Human LAMTOR2 ortholog × 1 Schizosaccharomyces pombe LAM3, Human LAMTOR3 ortholog × 1 Schizosaccharomyces pombe LAM4, Human LAMTOR5 ortholog × 1 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

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.

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 2
Chains and sequence ranges Author chain B; PDBConstruct 22–401; 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 × 9 PDB declaration: nonameric(9) Consistent with protein copy count Chain C; UniProt 1–569 Not recorded GATOR complex protein DEPDC5 × 1 (O75140) GATOR complex protein NPRL2 × 1 (Q8WTW4) GTP-binding protein Gtr1 × 1 GTP-binding protein Gtr2 × 1 Schizosaccharomyces pombe LAM1, Human LAMTOR1 ortholog × 1 Schizosaccharomyces pombe LAM2, Human LAMTOR2 ortholog × 1 Schizosaccharomyces pombe LAM3, Human LAMTOR3 ortholog × 1 Schizosaccharomyces pombe LAM4, Human LAMTOR5 ortholog × 1 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

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.

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 3
Chains and sequence ranges Author chain C; PDBConstruct 22–590; UniProt 1–569

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 8fw5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8fw5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8fw5
Deposition date deposition_date2023-01-20
Structure title titleChimeric HsGATOR1-SpGtr-SpLam complex
Keywords keywordsmTOR complex 1 (mTORC1), Rag GTPase, Gtr GTPase, LAMTOR, GATOR1, nutrient sensing, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier53.89
Radius of gyration Rg (electron density) rg_electron53.47
Forward intensity I(0) i01451290000.00
Molecular weight molecular_weight324700.0 kDa
Excluded volume excluded_volume408970 ų
Envelope volume envelope_volume609220 ų
Hydration-shell volume shell_volume95448 ų
Envelope diameter envelope_diameter190.7
Shell Rg shell_rg56.98
Envelope Rg envelope_rg52.27
Shape Rg shape_rg53.45
Total Rg total_rg53.65
Total atoms total_atoms22853
Residues n_residues2832
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 dmax182.7
Rg (real space) rg_real53.84
Rg uncertainty (real space) rg_real_error1.81
I(0) (real space) i0_real1.4510e+09
I(0) uncertainty (real space) i0_real_error2.9750e+07
Rg (reciprocal space) rg_reciprocal53.92
I(0) (reciprocal space) i0_reciprocal1451000000.0000
Solution quality estimate total_estimate0.8879
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary63.0
Skewness Skewness skewness0.247
Kurtosis Kurtosis kurtosis-0.477
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha107700000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.871

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (12)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id8fw5D01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id8fw5D02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology450 — Beta-Lactamase
Homologous superfamily homologous superfamily190
Domain ID domain_id8fw5E01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily300 — P-loop containing nucleotide triphosphate hydrolases
Domain ID domain_id8fw5E02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology450 — Beta-Lactamase
Homologous superfamily homologous superfamily190

8. Citations (1)

9. Files and Curves (10)