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- PDB-4z6y: Structure of the TBC1D7-TSC1 complex -

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Basic information

Entry
Database: PDB / ID: 4z6y
TitleStructure of the TBC1D7-TSC1 complex
Components
  • Hamartin
  • TBC1 domain family member 7
KeywordsHYDROLASE INHIBITOR/PROTEIN BINDING / coiled coil / heterotetramer / HYDROLASE INHIBITOR-PROTEIN BINDING complex
Function / homology
Function and homology information


memory T cell differentiation / TSC1-TSC2 complex binding / TSC1-TSC2 complex / Inhibition of TSC complex formation by PKB / cellular response to decreased oxygen levels / negative regulation of cilium assembly / regulation of cell-matrix adhesion / cardiac muscle cell differentiation / cell projection organization / negative regulation of ATP-dependent activity ...memory T cell differentiation / TSC1-TSC2 complex binding / TSC1-TSC2 complex / Inhibition of TSC complex formation by PKB / cellular response to decreased oxygen levels / negative regulation of cilium assembly / regulation of cell-matrix adhesion / cardiac muscle cell differentiation / cell projection organization / negative regulation of ATP-dependent activity / Energy dependent regulation of mTOR by LKB1-AMPK / response to growth factor / ATPase inhibitor activity / negative regulation of cell size / regulation of stress fiber assembly / activation of GTPase activity / negative regulation of TOR signaling / protein folding chaperone complex / TBC/RABGAPs / negative regulation of macroautophagy / Macroautophagy / D-glucose import / associative learning / positive regulation of focal adhesion assembly / negative regulation of TORC1 signaling / lipid droplet / myelination / positive regulation of GTPase activity / Hsp70 protein binding / protein folding chaperone / GTPase activator activity / adult locomotory behavior / hippocampus development / cellular response to starvation / cell-matrix adhesion / positive regulation of protein ubiquitination / kidney development / TP53 Regulates Metabolic Genes / response to insulin / neural tube closure / Hsp90 protein binding / synapse organization / potassium ion transport / cerebral cortex development / small GTPase binding / lamellipodium / protein-folding chaperone binding / cell cortex / cytoplasmic vesicle / adaptive immune response / cell population proliferation / regulation of cell cycle / postsynaptic density / protein stabilization / ciliary basal body / lysosomal membrane / negative regulation of cell population proliferation / perinuclear region of cytoplasm / protein-containing complex / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Ypt/Rab-GAP domain of gyp1p, domain 2 / Ypt/Rab-GAP domain of gyp1p, domain 1 / TBC1 domain family member 7 / TBC1 domain family member 7, domain 2 / Ypt/Rab-GAP domain of gyp1p, domain 3 / Hamartin / Hamartin protein / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain ...Ypt/Rab-GAP domain of gyp1p, domain 2 / Ypt/Rab-GAP domain of gyp1p, domain 1 / TBC1 domain family member 7 / TBC1 domain family member 7, domain 2 / Ypt/Rab-GAP domain of gyp1p, domain 3 / Hamartin / Hamartin protein / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / Cyclin A; domain 1 / Helicase, Ruva Protein; domain 3 / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Hamartin / TBC1 domain family member 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.81 Å
AuthorsGai, Z. / Wu, G.
CitationJournal: To Be Published
Title: Structure of the TBC1D7-TSC1 complex
Authors: Gai, Z. / Wu, G.
History
DepositionApr 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: TBC1 domain family member 7
C: Hamartin
G: TBC1 domain family member 7
H: Hamartin
E: TBC1 domain family member 7
F: Hamartin
A: TBC1 domain family member 7
D: Hamartin


Theoretical massNumber of molelcules
Total (without water)152,0328
Polymers152,0328
Non-polymers00
Water37821
1
B: TBC1 domain family member 7
C: Hamartin
E: TBC1 domain family member 7
F: Hamartin


Theoretical massNumber of molelcules
Total (without water)76,0164
Polymers76,0164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-40 kcal/mol
Surface area30920 Å2
MethodPISA
2
G: TBC1 domain family member 7
H: Hamartin
A: TBC1 domain family member 7
D: Hamartin


Theoretical massNumber of molelcules
Total (without water)76,0164
Polymers76,0164
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-38 kcal/mol
Surface area31530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.991, 145.689, 114.758
Angle α, β, γ (deg.)90.00, 89.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TBC1 domain family member 7 / Cell migration-inducing protein 23


Mass: 31520.775 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 21-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBC1D7, TBC7, HSPC239 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P0N9
#2: Protein
Hamartin / Tuberous sclerosis 1 protein


Mass: 6487.284 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 938-993
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TSC1, KIAA0243, TSC / Production host: Escherichia coli (E. coli) / References: UniProt: Q92574
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 61.2 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8% PEG 6000, 4% 2-methyl-2,4-pentanediol (MPD), 0.1M HEPES, pH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.8→120 Å / Num. obs: 44658 / % possible obs: 98.3 % / Redundancy: 3.8 % / Net I/σ(I): 12.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.81→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.9 / SU B: 27.416 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 2.751 / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2260 5.1 %RANDOM
Rwork0.206 ---
obs0.209 42373 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.33 Å2
Baniso -1Baniso -2Baniso -3
1--2.48 Å20 Å20.15 Å2
2---0.26 Å20 Å2
3---2.74 Å2
Refinement stepCycle: LAST / Resolution: 2.81→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10434 0 0 21 10455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0210678
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.97914453
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.82551304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.15723.922464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.322151956
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1531567
X-RAY DIFFRACTIONr_chiral_restr0.1150.21635
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217895
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.81→2.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 131 -
Rwork0.316 2745 -
obs--87.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0023-0.16060.00160.23310.16050.1386-0.0483-0.0092-0.05840.0080.0540.0203-0.00430.0159-0.00580.02610.01720.0040.05680.02710.083242.83769.915910.5128
21.7403-0.6735-0.20630.41630.16730.07520.0924-0.18870.0420.02850.0414-0.15890.01870.0318-0.13380.1268-0.0242-0.03240.032-0.01830.155520.538626.954426.8635
31.14760.19530.10540.24760.11050.0851-0.07550.01730.07330.0040.06430.01350.02050.01030.01110.031-0.0145-0.00590.04820.02640.073342.9354-24.238546.7675
41.59921.3583-0.75121.7922-0.0520.95480.2558-0.0730.0170.05480.0818-0.2239-0.23780.2524-0.33760.2112-0.0025-0.00950.1284-0.08660.220820.7762-40.367930.2034
51.47080.0704-0.48670.22320.16990.3436-0.08740.0365-0.0962-0.01960.0278-0.00130.0089-0.00820.05960.02880.01190.00860.0465-0.03390.0647-8.622619.107147.1289
61.80061.0869-2.08810.82-1.41122.56150.06970.1230.1638-0.10670.14310.14750.0677-0.1992-0.21270.1357-0.0593-0.00810.0454-0.00620.094814.071527.632625.0658
71.46550.01170.59130.14550.11680.3718-0.0697-0.01870.1010.0110.00520.00050.00590.00180.06450.0336-0.0083-0.00820.0544-0.02620.0726-8.7869-33.287710.2457
82.6366-2.4773.2852.3409-3.10084.1088-0.153-0.3115-0.14410.15720.31270.1103-0.2061-0.4144-0.15970.05730.05140.00110.0814-0.01640.086713.6816-39.945431.4248
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B21 - 292
2X-RAY DIFFRACTION2C940 - 992
3X-RAY DIFFRACTION3G21 - 292
4X-RAY DIFFRACTION4H938 - 992
5X-RAY DIFFRACTION5E21 - 292
6X-RAY DIFFRACTION6F940 - 993
7X-RAY DIFFRACTION7A21 - 293
8X-RAY DIFFRACTION8D940 - 992

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