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- PDB-5gs9: Crystal structure of CASTOR1-arginine -

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Basic information

Entry
Database: PDB / ID: 5gs9
TitleCrystal structure of CASTOR1-arginine
ComponentsGATS-like protein 3
KeywordsSIGNALING PROTEIN / arginine binding
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 / protein sequestering activity / cellular response to amino acid starvation / 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
ARGININE / Cytosolic arginine sensor for mTORC1 subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsZhang, T. / Ding, J.
CitationJournal: Cell Discov / Year: 2016
Title: Structural insight into the arginine-binding specificity of CASTOR1 in amino acid-dependent mTORC1 signaling.
Authors: Xia, J. / Wang, R. / Zhang, T. / Ding, J.
History
DepositionAug 15, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 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)150,2228
Polymers149,5224
Non-polymers7014
Water5,657314
1
A: GATS-like protein 3
B: GATS-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1114
Polymers74,7612
Non-polymers3502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-12 kcal/mol
Surface area26060 Å2
MethodPISA
2
C: GATS-like protein 3
D: GATS-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1114
Polymers74,7612
Non-polymers3502
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-14 kcal/mol
Surface area25230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.644, 83.564, 97.810
Angle α, β, γ (deg.)90.000, 116.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GATS-like protein 3 / Cellular arginine sensor for mTORC1 protein 1 / CASTOR1


Mass: 37380.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GATSL3, CASTOR1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus / References: UniProt: Q8WTX7
#2: Chemical
ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.29 Å3/Da / Density % sol: 46.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M sodium citrate (pH 5.0), 20% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: CMOS / Date: Jul 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.5→50.01 Å / Num. obs: 47062 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.085 / Net I/av σ(I): 15.857 / Net I/σ(I): 4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.5-2.596.20.4950.872199.7
2.59-2.696.70.3990.919199.9
2.69-2.826.60.2990.9491100
2.82-2.966.90.2180.9751100
2.96-3.1570.1710.9831100
3.15-3.396.70.1210.99199.9
3.39-3.736.80.0950.9941100
3.73-4.2770.0720.9961100
4.27-5.386.80.0530.9971100
5.38-506.60.0430.9991100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
REFMAC5.8.0123refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.5→50.01 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 20.935 / SU ML: 0.204 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.265 / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 2360 5 %RANDOM
Rwork0.1754 ---
obs0.1778 44415 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 127.09 Å2 / Biso mean: 52.176 Å2 / Biso min: 23.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å2-0 Å2
2---1.05 Å2-0 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 2.5→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9249 0 0 314 9563
Biso mean---47.52 -
Num. residues----1179
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0199513
X-RAY DIFFRACTIONr_angle_refined_deg1.2551.97112953
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14451157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.96223.317404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.619151553
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1321562
X-RAY DIFFRACTIONr_chiral_restr0.0740.21526
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217098
X-RAY DIFFRACTIONr_mcbond_it1.2924.6364694
X-RAY DIFFRACTIONr_mcangle_it1.7056.9265829
X-RAY DIFFRACTIONr_scbond_it1.4134.8054819
X-RAY DIFFRACTIONr_rigid_bond_restr0.4839513
X-RAY DIFFRACTIONr_sphericity_free34.63597
X-RAY DIFFRACTIONr_sphericity_bonded23.18559514
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 158 -
Rwork0.258 3290 -
all-3448 -
obs--99.62 %
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)
10.0508-0.00470.02010.0899-0.02810.09120.0007-0.00360.0032-0.00030.00070.00180.0001-0.0031-0.00140.0460.00110.01730.1136-0.00080.0068-24.05415.1965-31.7678
20.07990.0332-0.03920.106-0.0540.0961-0.003-0.0031-0.00020.00070.00380.00120.0046-0.0041-0.00080.0489-0.00090.0190.1150.00070.0074-55.6675-13.6741-3.7237
30.12270.01050.02140.0302-0.01170.1135-0.00120.00390.00620.0029-0.00030.0045-0.0175-0.010.00150.05080.00030.01560.1063-0.00370.0061-15.77-24.98117.2024
40.0167-0.01220.01920.09050.00110.3172-0.00130.00220.00050.00210.0025-0.01140.0060.0226-0.00120.0401-0.00330.01660.1136-0.00090.0086-0.2292-26.5523-26.2891
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 324
2X-RAY DIFFRACTION2B1 - 323
3X-RAY DIFFRACTION3C1 - 323
4X-RAY DIFFRACTION4D1 - 323

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