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- PDB-5i2c: Arginine-bound CASTOR1 from Homo sapiens -

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Basic information

Entry
Database: PDB / ID: 5i2c
TitleArginine-bound CASTOR1 from Homo sapiens
ComponentsGATS-like protein 3
KeywordsSIGNALING PROTEIN / signaling / arginine / ACT / mTOR
Function / homology
Function and homology information


cellular response to L-arginine / small molecule sensor activity / Amino acids regulate mTORC1 / arginine binding / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / cellular response to amino acid starvation / protein sequestering activity / identical protein binding / cytosol
Similarity search - Function
CASTOR family / CASTOR1, N-terminal / : / Cytosolic arginine sensor for mTORC1 subunit 1 N-terminal domain / Cytosolic arginine sensor for mTORC1 subunit 1/2, ACT-like / CASTOR, ACT domain / ACT domain / ACT-like domain
Similarity search - Domain/homology
ACETATE ION / ARGININE / Cytosolic arginine sensor for mTORC1 subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.801 Å
AuthorsSaxton, R.A. / Knockenhauer, K.E. / Schwartz, T.U.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA103866 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI47389 United States
Department of Defense (DOD, United States)W81XWH-07- 0448 United States
CitationJournal: Nature / Year: 2016
Title: Mechanism of arginine sensing by CASTOR1 upstream of mTORC1.
Authors: Saxton, R.A. / Chantranupong, L. / Knockenhauer, K.E. / Schwartz, T.U. / Sabatini, D.M.
History
DepositionFeb 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / 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 1.4Apr 10, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GATS-like protein 3
B: GATS-like protein 3
C: GATS-like protein 3
D: GATS-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,17412
Polymers145,2374
Non-polymers9378
Water14,340796
1
A: GATS-like protein 3
B: GATS-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0876
Polymers72,6182
Non-polymers4694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-14 kcal/mol
Surface area25220 Å2
MethodPISA
2
C: GATS-like protein 3
D: GATS-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,0876
Polymers72,6182
Non-polymers4694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-16 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.393, 82.601, 96.666
Angle α, β, γ (deg.)90.00, 116.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GATS-like protein 3


Mass: 36309.242 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GATSL3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): LOBSTR / References: UniProt: Q8WTX7
#2: Chemical
ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 796 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M sodium acetate, 0.25 M ammonium acetate, 22.5% PEG 3350
PH range: 5.0-5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.8→86.72 Å / Num. obs: 116806 / % possible obs: 97.85 % / Redundancy: 3 % / Rsym value: 0.072 / Net I/σ(I): 25.9
Reflection shellResolution: 1.8→1.85 Å / Rsym value: 0.072

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.801→86.712 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2044 2002 1.71 %
Rwork0.1717 --
obs0.1723 116806 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→86.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9009 0 64 796 9869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079288
X-RAY DIFFRACTIONf_angle_d0.84612667
X-RAY DIFFRACTIONf_dihedral_angle_d15.3445528
X-RAY DIFFRACTIONf_chiral_restr0.0571509
X-RAY DIFFRACTIONf_plane_restr0.0061602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8006-1.84560.29661350.28277694X-RAY DIFFRACTION92
1.8456-1.89550.3031360.25438243X-RAY DIFFRACTION99
1.8955-1.95130.29251480.22428193X-RAY DIFFRACTION98
1.9513-2.01430.24621370.20678208X-RAY DIFFRACTION98
2.0143-2.08630.2271470.19548066X-RAY DIFFRACTION97
2.0863-2.16980.24081420.19048269X-RAY DIFFRACTION99
2.1698-2.26860.23711450.17988245X-RAY DIFFRACTION99
2.2686-2.38820.22751430.17388171X-RAY DIFFRACTION98
2.3882-2.53780.23071380.17618179X-RAY DIFFRACTION97
2.5378-2.73380.19621510.17548281X-RAY DIFFRACTION99
2.7338-3.00890.21671470.17338314X-RAY DIFFRACTION99
3.0089-3.44430.17841420.16358206X-RAY DIFFRACTION98
3.4443-4.33950.1861440.15278373X-RAY DIFFRACTION99
4.3395-86.81270.1811470.1598362X-RAY DIFFRACTION98
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)
12.873-0.373-1.63491.37360.19522.9632-0.0817-0.0021-0.10020.09640.05060.03160.16080.03820.03370.1893-0.0206-0.00840.1188-0.00250.166750.75969.678679.4332
21.33151.3761-0.27125.2918-0.89041.76180.1206-0.22340.08120.9435-0.0535-0.0682-0.1087-0.2454-0.09730.34360.0171-0.02670.3374-0.01250.268540.92268.602690.3116
32.6691-2.4239-0.77223.90091.06312.97350.17860.2376-0.06-0.3215-0.130.1286-0.0916-0.2233-0.03960.1681-0.0092-0.00240.21140.0160.171848.534774.636262.5024
47.3272-2.08521.25352.4173-0.4874.36650.02480.31340.404-0.0273-0.08190.0348-0.2528-0.20130.05810.1992-0.02010.0210.11050.00860.23242.034184.352775.7607
52.9607-0.578-2.16591.58130.64053.49980.0923-0.16770.2782-0.00450.0398-0.1289-0.0967-0.0287-0.12630.2315-0.02840.0330.2088-0.05380.252876.485964.275752.6292
64.4473-0.6801-1.49892.0556-0.46463.6610.07470.2532-0.151-0.3175-0.0154-0.12140.20930.1423-0.07580.26120.02410.0280.1793-0.04460.195886.140755.147237.662
79.7737-6.1463-1.82444.18391.96212.5052-0.28580.49250.8815-0.06380.6293-0.3498-0.682-0.6796-0.44320.55080.06820.08590.47750.05310.428482.194663.313827.3981
84.3314-0.2061-0.13232.491-0.16493.048-0.3026-0.4362-0.36390.25240.0952-0.070.3174-0.21850.20410.3267-0.023-0.00250.1002-0.09130.238779.393146.208148.5247
93.4378-0.4255-1.52981.59211.12742.3143-0.16630.0469-0.37310.2048-0.03910.19630.3518-0.14160.18880.3014-0.03720.01380.1943-0.05750.279266.342652.760453.5804
104.334-0.0831-2.18273.8421-0.1292.1304-0.25050.0144-0.54610.10550.03830.27680.3798-0.2550.20430.4065-0.00550.03240.278-0.02640.205476.944946.269549.7933
113.07241.9354-0.26184.14081.18864.0496-0.1045-0.0565-0.47590.15790.0725-0.11220.66350.26340.03040.32640.0792-0.00450.1780.0040.245384.999641.551245.8756
122.1294-0.1761-1.13351.6224-1.05524.6857-0.05250.12840.2570.0799-0.0693-0.1931-0.18290.22870.10660.1454-0.0089-0.0460.21890.04070.27245.675843.026130.1148
131.80440.810.47096.35171.11910.35980.36020.09230.29410.463-0.4941-0.5222-0.0064-0.03240.14950.448-0.10240.05860.6390.20650.497457.122446.753419.4281
141.8090.21130.2080.73960.3274.009-0.0650.12450.19840.0846-0.02290.1644-0.5318-0.57790.09860.28770.1148-0.04060.3422-0.0060.280729.138147.621330.2735
154.4613-1.33650.73082.8871-0.14234.07790.17660.78420.0743-0.2523-0.32520.1082-0.1543-0.16260.09680.180.0232-0.00430.3860.02570.217536.229140.511214.8393
162.1074-0.5979-1.10192.1968-0.04493.67060.36530.0738-0.0543-0.0888-0.21420.20880.382-0.4948-0.13510.2869-0.0702-0.02960.3079-0.02970.235925.164736.562160.0165
171.72090.1826-0.26071.849-0.34642.6140.10360.0475-0.21360.0767-0.1410.45730.5482-0.68420.04520.3341-0.1812-0.00580.4278-0.03330.389518.494136.334769.7488
181.27230.0555-0.62272.5002-0.24414.16850.15190.08850.1432-0.1268-0.0990.0203-0.4451-0.2493-0.04830.2306-0.0024-0.01480.26250.00180.253629.063851.292864.7839
191.49460.07650.33095.87612.07612.240.0448-0.1448-0.08290.3759-0.15450.28290.3077-0.30090.09920.2314-0.0690.02540.22960.02940.222928.526345.792381.1081
202.0001-2.422724.30596.202220.44450.15880.5961-0.1467-0.15810.0333-0.5616-0.1915-0.2560.2537-0.01140.04980.20670.00410.23348.84180.694182.5773
212.0002-8.079525.028122-0.6326-0.2687-0.47140.42030.3514-0.0421.40050.75120.28080.3170.04140.01410.3535-0.0880.261490.179853.39748.0665
221.99997.944226.9242-7.25682.00010.20750.48060.2287-0.4026-0.00490.07030.6382-1.423-0.2270.25060.0185-0.01520.38380.04170.274544.313536.440819.6315
232.2041-0.4491.73857.9131-1.37821.6980.3002-0.63680.0090.25080.1818-0.0266-0.30990.5994-0.4930.3091-0.1918-0.00850.34340.05680.308526.535135.511278.1782
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 137 )
2X-RAY DIFFRACTION2chain 'A' and (resid 138 through 175 )
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 268 )
4X-RAY DIFFRACTION4chain 'A' and (resid 269 through 322 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 75 )
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 137 )
7X-RAY DIFFRACTION7chain 'B' and (resid 138 through 153 )
8X-RAY DIFFRACTION8chain 'B' and (resid 154 through 190 )
9X-RAY DIFFRACTION9chain 'B' and (resid 191 through 248 )
10X-RAY DIFFRACTION10chain 'B' and (resid 249 through 279 )
11X-RAY DIFFRACTION11chain 'B' and (resid 280 through 322 )
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 137 )
13X-RAY DIFFRACTION13chain 'C' and (resid 138 through 173 )
14X-RAY DIFFRACTION14chain 'C' and (resid 174 through 268 )
15X-RAY DIFFRACTION15chain 'C' and (resid 269 through 322 )
16X-RAY DIFFRACTION16chain 'D' and (resid 2 through 32 )
17X-RAY DIFFRACTION17chain 'D' and (resid 33 through 153 )
18X-RAY DIFFRACTION18chain 'D' and (resid 154 through 262 )
19X-RAY DIFFRACTION19chain 'D' and (resid 263 through 323 )
20X-RAY DIFFRACTION20chain 'A' and (resid 401 through 401 )
21X-RAY DIFFRACTION21chain 'B' and (resid 401 through 401 )
22X-RAY DIFFRACTION22chain 'C' and (resid 401 through 401 )
23X-RAY DIFFRACTION23chain 'D' and (resid 401 through 401 )

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