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7dl2

Cryo-EM structure of human TSC complex

Method: ELECTRON MICROSCOPY Dmax: 266.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Hamartin

Homo sapiens

UniProt Q92574

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain C； UniProt 1–1164 Chain D； UniProt 1–1164 Not recorded Isoform 7 of Tuberin × 2 （P49815） TBC1 domain family member 7 × 1 （Q9P0N9） unknown protein × 1 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 7DL2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4Z6Y Structure of the TBC1D7-TSC1 complex Deposited 2015-04-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 938–993（56 aa） Fragment：UNP RESIDUES 938-993
Chain F 938–993（56 aa） Fragment：UNP RESIDUES 938-993
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；8% PEG 6000, 4% 2-methyl-2,4-pentanediol (MPD), 0.1M HEPES, pH7.5
Resolution 2.81 Å R-free 0.255
4Z6Y Structure of the TBC1D7-TSC1 complex Deposited 2015-04-06 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 938–993（56 aa） Fragment：UNP RESIDUES 938-993
Chain H 938–993（56 aa） Fragment：UNP RESIDUES 938-993
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；8% PEG 6000, 4% 2-methyl-2,4-pentanediol (MPD), 0.1M HEPES, pH7.5
Resolution 2.81 Å R-free 0.255
5EJC Crystal structural of the TSC1-TBC1D7 complex Deposited 2015-11-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 939–992（54 aa） Fragment：UNP residues 939-992
Chain F 939–992（54 aa） Fragment：UNP residues 939-992
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；200 mM NaCl, 20mM CaCl2 and 15% PEG-3350
Resolution 3.10 Å R-free 0.239
5EJC Crystal structural of the TSC1-TBC1D7 complex Deposited 2015-11-01 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 939–992（54 aa） Fragment：UNP residues 939-992
Chain D 939–992（54 aa） Fragment：UNP residues 939-992
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；200 mM NaCl, 20mM CaCl2 and 15% PEG-3350
Resolution 3.10 Å R-free 0.239
9C9I Structure of the TSC1:WIPI3 complex Deposited 2024-06-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 648–681（34 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M ammonium tartrate, 20 % PEG3350, and 0.25 M sodium acetate.
Resolution 3.18 Å R-free 0.255
9C9I Structure of the TSC1:WIPI3 complex Deposited 2024-06-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 648–681（34 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M ammonium tartrate, 20 % PEG3350, and 0.25 M sodium acetate.
Resolution 3.18 Å R-free 0.255
9C9I Structure of the TSC1:WIPI3 complex Deposited 2024-06-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 648–681（34 aa）
Chain X 648–681（34 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M ammonium tartrate, 20 % PEG3350, and 0.25 M sodium acetate.
Resolution 3.18 Å R-free 0.255
9C9I Structure of the TSC1:WIPI3 complex Deposited 2024-06-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 648–681（34 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；0.2 M ammonium tartrate, 20 % PEG3350, and 0.25 M sodium acetate.
Resolution 3.18 Å R-free 0.255
9CE3 Structure of the TSC:WIPI3 lysosomal recruitment complex Deposited 2024-06-26 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–1164（1164 aa）
Chain D 1–1164（1164 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES (pH 7.6), 250 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

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

View Construct and Data Evidence
UniProt name TSC1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain C； PDBConstruct 1–1164； UniProt 1–1164 Author chain D； PDBConstruct 1–1164； UniProt 1–1164

Isoform 7 of Tuberin

Homo sapiens

UniProt P49815

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 1–1692 Chain B； UniProt 1–1692 Not recorded Hamartin × 2 （Q92574） TBC1 domain family member 7 × 1 （Q9P0N9） unknown protein × 1 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 7DL2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9CE3 Structure of the TSC:WIPI3 lysosomal recruitment complex Deposited 2024-06-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 2–1784（1783 aa）
Chain B 2–1784（1783 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES (pH 7.6), 250 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TSC2_HUMAN
Isoform P49815-7
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–1692； UniProt 1–1692 Author chain B； PDBConstruct 1–1692； UniProt 1–1692

TBC1 domain family member 7

Homo sapiens

UniProt Q9P0N9

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain E； UniProt 21–287 Not recorded Hamartin × 2 （Q92574） Isoform 7 of Tuberin × 2 （P49815） unknown protein × 1 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 7DL2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3QWL Crystal structure of human TBC1 domain family member 7 Deposited 2011-02-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–293（293 aa）
Not recorded UNX UNKNOWN LIGAND × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；20% PEG-1500, 0.2M magnesium chloride, 0.1M TRIS. 1:10 dispase-1 added in situ., pH 8.5, vapor diffusion, sitting drop, temperature 289K
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；Selenomethionyl derivative protein. 30% PEG-1500, 0.2M sodium chloride, 0.1M HEPES. 1:10 dispase-1 added in situ., pH 7.5, vapor diffusion, sitting drop, temperature 289K
Resolution 1.90 Å R-free 0.259
4Z6Y Structure of the TBC1D7-TSC1 complex Deposited 2015-04-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 21–293（273 aa） Fragment：UNP RESIDUES 21-293
Chain E 21–293（273 aa） Fragment：UNP RESIDUES 21-293
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；8% PEG 6000, 4% 2-methyl-2,4-pentanediol (MPD), 0.1M HEPES, pH7.5
Resolution 2.81 Å R-free 0.255
4Z6Y Structure of the TBC1D7-TSC1 complex Deposited 2015-04-06 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 21–293（273 aa） Fragment：UNP RESIDUES 21-293
Chain G 21–293（273 aa） Fragment：UNP RESIDUES 21-293
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；287 K；8% PEG 6000, 4% 2-methyl-2,4-pentanediol (MPD), 0.1M HEPES, pH7.5
Resolution 2.81 Å R-free 0.255
5EJC Crystal structural of the TSC1-TBC1D7 complex Deposited 2015-11-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 18–293（276 aa） Fragment：UNP residues 18-293
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；200 mM NaCl, 20mM CaCl2 and 15% PEG-3350
Resolution 3.10 Å R-free 0.239
5EJC Crystal structural of the TSC1-TBC1D7 complex Deposited 2015-11-01 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 18–293（276 aa） Fragment：UNP residues 18-293
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；200 mM NaCl, 20mM CaCl2 and 15% PEG-3350
Resolution 3.10 Å R-free 0.239
9CE3 Structure of the TSC:WIPI3 lysosomal recruitment complex Deposited 2024-06-26 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–293（293 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；20 mM HEPES (pH 7.6), 250 mM NaCl, 2 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBCD7_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain E； PDBConstruct 1–267； UniProt 21–287

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 7dl2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7dl2
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7dl2
Deposition date deposition_date2020-11-25
Structure title titleCryo-EM structure of human TSC complex
Keywords keywordsTSC complex, Regulator of cell growth, GTPase-activating protein, Elongated arch-shaped fold, GENE REGULATION; GENE REGULATION
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier— Å
Radius of gyration Rg (electron density) rg_electron103.10 Å
Forward intensity I(0) i01527390000.00
Molecular weight molecular_weight330470.0 kDa
Excluded volume excluded_volume414260 ų
Envelope volume envelope_volume900080 ų
Hydration-shell volume shell_volume85159 ų
Envelope diameter envelope_diameter390.5 Å
Shell Rg shell_rg59.51 Å
Envelope Rg envelope_rg116.00 Å
Shape Rg shape_rg103.40 Å
Total Rg total_rg101.50 Å
Total atoms total_atoms23285
Residues n_residues3089
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 dmax266.4 Å
Rg (real space) rg_real90.41 Å
Rg uncertainty (real space) rg_real_error1.52 Å
I(0) (real space) i0_real1.4460e+09
I(0) uncertainty (real space) i0_real_error3.3080e+07
Rg (reciprocal space) rg_reciprocal86.05 Å
I(0) (reciprocal space) i0_reciprocal1461000000.0000
Solution quality estimate total_estimate0.8149
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary53.3 Å
Skewness Skewness skewness0.386
Kurtosis Kurtosis kurtosis-0.904
Angular range angular_range— – 0.0750 Å−1
Current regularization parameter α current_alpha0.5206
Highest regularization parameter α highest_alpha29690000.0000
Real-space data points n_real_points16
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.011; Oscil: 0.687; Stabil: 0.974; Sysdev: 1.000; Positv: 1.000; Valcen: 0.645; Smooth: 0.001
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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8. Citations (1)

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9. Files and Curves (10)