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- PDB-5ejc: Crystal structural of the TSC1-TBC1D7 complex -

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Basic information

Entry
Database: PDB / ID: 5ejc
TitleCrystal structural of the TSC1-TBC1D7 complex
Components
  • Hamartin
  • TBC1 domain family member 7
KeywordsSIGNALING PROTEIN / TSC1 / TBC1D7
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 / TBC/RABGAPs / protein folding chaperone complex / 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 / SAD / Resolution: 3.1 Å
AuthorsWang, Z. / Qin, J. / Gong, W. / Xu, W.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Defense (DOD, United States)W81XWH-13-1-0059 (TS120073) United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis of the Interaction between Tuberous Sclerosis Complex 1 (TSC1) and Tre2-Bub2-Cdc16 Domain Family Member 7 (TBC1D7).
Authors: Qin, J. / Wang, Z. / Hoogeveen-Westerveld, M. / Shen, G. / Gong, W. / Nellist, M. / Xu, W.
History
DepositionNov 1, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2May 11, 2016Group: Database references
Revision 1.3Apr 10, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,6116
Polymers89,6116
Non-polymers00
Water00
1
A: TBC1 domain family member 7
E: Hamartin
F: Hamartin


Theoretical massNumber of molelcules
Total (without water)44,8053
Polymers44,8053
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-25 kcal/mol
Surface area17400 Å2
MethodPISA
2
B: TBC1 domain family member 7
C: Hamartin
D: Hamartin


Theoretical massNumber of molelcules
Total (without water)44,8053
Polymers44,8053
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3880 Å2
ΔGint-23 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.395, 66.704, 98.370
Angle α, β, γ (deg.)90.000, 91.910, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13C
23E
14C
24F
15D
25E
16D
26F
17E
27F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALCYSCYSAA22 - 2865 - 269
21VALVALCYSCYSBB22 - 2865 - 269
12GLYGLYARGARGCC939 - 9682 - 31
22GLYGLYARGARGDD939 - 9682 - 31
13GLYGLYARGARGCC939 - 9682 - 31
23GLYGLYARGARGEE939 - 9682 - 31
14GLYGLYARGARGCC939 - 9682 - 31
24GLYGLYARGARGFF939 - 9682 - 31
15GLYGLYLEULEUDD939 - 9692 - 32
25GLYGLYLEULEUEE939 - 9692 - 32
16GLYGLYGLUGLUDD939 - 9702 - 33
26GLYGLYGLUGLUFF939 - 9702 - 33
17GLYGLYLEULEUEE939 - 9692 - 32
27GLYGLYLEULEUFF939 - 9692 - 32

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

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


Mass: 32257.348 Da / Num. of mol.: 2 / Fragment: UNP residues 18-293
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: 6273.984 Da / Num. of mol.: 4 / Fragment: UNP residues 939-992
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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 200 mM NaCl, 20mM CaCl2 and 15% PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2014
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 21259 / % possible obs: 99.7 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.067 / Rrim(I) all: 0.128 / Χ2: 1.313 / Net I/av σ(I): 11.744 / Net I/σ(I): 7.9 / Num. measured all: 74730
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.193.10.75817160.7260.4890.9050.98698.6
3.19-3.293.40.55417690.8880.3480.6561.09799.5
3.29-3.413.60.45517480.8740.2780.5341.21299.9
3.41-3.553.60.37417570.9290.2290.4391.39299.9
3.55-3.713.60.24317670.9560.1490.2861.60799.8
3.71-3.913.60.19517880.9810.120.2291.54599.7
3.91-4.153.60.14817490.9840.0920.1741.45899.7
4.15-4.473.60.12417690.9860.0770.1461.43899.7
4.47-4.923.50.10317740.9890.0640.1221.31299.6
4.92-5.633.50.10317750.9860.0650.1221.31899.9
5.63-7.093.50.08417990.990.0530.11.28199.8
7.09-503.50.04518480.9960.0280.0531.00399.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.928 / SU B: 55.132 / SU ML: 0.385 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 1094 5.2 %RANDOM
Rwork0.2196 ---
obs0.2206 20089 96.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 185.71 Å2 / Biso mean: 99.257 Å2 / Biso min: 65.58 Å2
Baniso -1Baniso -2Baniso -3
1-4.09 Å20 Å21.74 Å2
2--4.89 Å20 Å2
3----9.07 Å2
Refinement stepCycle: final / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5467 0 0 0 5467
Num. residues----671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195580
X-RAY DIFFRACTIONr_bond_other_d0.0030.025490
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.9927530
X-RAY DIFFRACTIONr_angle_other_deg0.974312658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1865665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50123.828256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.152151006
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8211540
X-RAY DIFFRACTIONr_chiral_restr0.0540.2839
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216114
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021242
X-RAY DIFFRACTIONr_mcbond_it2.1697.7362678
X-RAY DIFFRACTIONr_mcbond_other2.1597.7342677
X-RAY DIFFRACTIONr_mcangle_it3.72611.593337
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A170670.07
12B170670.07
21C13050.22
22D13050.22
31C13870.21
32E13870.21
41C13750.17
42F13750.17
51D14850.14
52E14850.14
61D14150.21
62F14150.21
71E14120.2
72F14120.2
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 55 -
Rwork0.361 922 -
all-977 -
obs--59.79 %
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)
10.34690.0094-0.52820.06590.02492.3309-0.29060.02930.0102-0.02080.0997-0.04380.3009-0.16060.19090.27680.01190.03070.25420.00440.189217.4224-37.9704231.8326
21.2760.32070.55360.13450.08571.6624-0.01250.02140.12480.053-0.03410.1373-0.13380.37090.04660.1967-0.11980.08510.1556-0.03260.232358.10822.8803215.2291
36.97-3.9842-2.92634.70112.89761.88610.31960.1583-0.0956-0.6199-0.36310.2151-0.3598-0.19680.04350.11560.0261-0.03610.0777-0.01740.176228.4684-11.0007203.0588
46.9648-1.3711-5.06211.35232.1915.07440.2044-0.1511-0.21760.0167-0.1732-0.0328-0.0874-0.0902-0.03120.0866-0.05360.00080.0727-0.01580.159431.6211-10.2001210.6551
59.3061-1.6485-2.3250.85850.56051.00350.6295-0.4970.188-0.0857-0.2464-0.0982-0.12210.0421-0.38310.1142-0.0534-0.04210.22440.02560.288333.4307-25.6052210.1945
610.5524-5.8393-1.2693.74881.04040.43680.36180.0212-0.1102-0.3134-0.1697-0.0876-0.069-0.1018-0.1920.1478-0.0017-0.0780.07030.05140.236536.6488-28.7182201.7236
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 289
2X-RAY DIFFRACTION2B21 - 287
3X-RAY DIFFRACTION3C939 - 969
4X-RAY DIFFRACTION4D938 - 971
5X-RAY DIFFRACTION5E939 - 970
6X-RAY DIFFRACTION6F939 - 977

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