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5ejc

Crystal structural of the TSC1-TBC1D7 complex

Method: X-RAY DIFFRACTION Dmax: 110.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 18–293 Fragment：UNP residues 18-293 Non-standard monomer：Yes (specific site not provided by mmCIF) Hamartin × 2 （Q92574） 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 18–293 Fragment：UNP residues 18-293 Non-standard monomer：Yes (specific site not provided by mmCIF) Hamartin × 2 （Q92574） 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

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 5EJC 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 mutation/modification Different oligomeric state Different ligand/ion 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 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 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
7DL2 Cryo-EM structure of human TSC complex Deposited 2020-11-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 21–287（267 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
9CE3 Structure of the TSC:WIPI3 lysosomal recruitment complex Deposited 2024-06-26 Different construct Different mutation/modification Different oligomeric state Different experimental method 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 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TBCD7_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–276； UniProt 18–293 Author chain B； PDBConstruct 1–276； UniProt 18–293

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain E； UniProt 939–992 Chain F； UniProt 939–992 Fragment：UNP residues 939-992 TBC1 domain family member 7 × 1 （Q9P0N9） 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
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain C； UniProt 939–992 Chain D； UniProt 939–992 Fragment：UNP residues 939-992 TBC1 domain family member 7 × 1 （Q9P0N9） 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

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 5EJC 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 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 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
7DL2 Cryo-EM structure of human TSC complex Deposited 2020-11-25 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
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 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
9C9I Structure of the TSC1:WIPI3 complex Deposited 2024-06-14 Different construct Different mutation/modification Different oligomeric state 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 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 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 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 construct Different oligomeric state Different experimental method 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 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TSC1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 2–55； UniProt 939–992 Author chain D； PDBConstruct 2–55； UniProt 939–992 Author chain E； PDBConstruct 2–55； UniProt 939–992 Author chain F； PDBConstruct 2–55； UniProt 939–992

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 5ejc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5ejc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5ejc
Deposition date deposition_date2015-11-01
Structure title titleCrystal structural of the TSC1-TBC1D7 complex
Keywords keywordsTSC1, TBC1D7, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.30 Å
Radius of gyration Rg (electron density) rg_electron34.03 Å
Forward intensity I(0) i091475900.00
Molecular weight molecular_weight78452.0 kDa
Excluded volume excluded_volume98808 ų
Envelope volume envelope_volume134080 ų
Hydration-shell volume shell_volume33786 ų
Envelope diameter envelope_diameter113.2 Å
Shell Rg shell_rg40.00 Å
Envelope Rg envelope_rg33.12 Å
Shape Rg shape_rg33.94 Å
Total Rg total_rg34.81 Å
Total atoms total_atoms5467
Residues n_residues655
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 dmax110.7 Å
Rg (real space) rg_real34.39 Å
Rg uncertainty (real space) rg_real_error0.83 Å
I(0) (real space) i0_real9.1480e+07
I(0) uncertainty (real space) i0_real_error1.4410e+06
Rg (reciprocal space) rg_reciprocal34.34 Å
I(0) (reciprocal space) i0_reciprocal91470000.0000
Solution quality estimate total_estimate0.8911
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary31.3 Å
Skewness Skewness skewness0.292
Kurtosis Kurtosis kurtosis-0.735
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14310000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.905; Smooth: 0.930
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id5ejcA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily750 — Ypt/Rab-GAP domain of gyp1p, domain 1
Domain ID domain_id5ejcA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily680 — Ypt/Rab-GAP domain of gyp1p, domain 2
Domain ID domain_id5ejcA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily80 — Ypt/Rab-GAP domain of gyp1p, domain 3
Domain ID domain_id5ejcB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily750 — Ypt/Rab-GAP domain of gyp1p, domain 1
Domain ID domain_id5ejcB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily680 — Ypt/Rab-GAP domain of gyp1p, domain 2
Domain ID domain_id5ejcB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily80 — Ypt/Rab-GAP domain of gyp1p, domain 3
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8. Citations (1)

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9. Files and Curves (10)