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- PDB-5gv2: Crystal structure of Arginine-bound CASTOR1 from Homo sapiens -

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Basic information

Entry
Database: PDB / ID: 5gv2
TitleCrystal structure of Arginine-bound CASTOR1 from Homo sapiens
ComponentsGATS-like protein 3
KeywordsSIGNALING PROTEIN / CASTOR1 / Arginine / Dimer
Function / homology
Function and homology information


molecular sensor activity / cellular response to L-arginine / Amino acids regulate mTORC1 / arginine binding / negative regulation of TORC1 signaling / protein sequestering activity / positive regulation of TORC1 signaling / 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 / VC0802-like / VC0802-like ...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 / VC0802-like / VC0802-like / ACT-like domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ARGININE / Cytosolic arginine sensor for mTORC1 subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsGai, Z.C. / Wu, G.
CitationJournal: Cell Discov / Year: 2016
Title: Structural mechanism for the arginine sensing and regulation of CASTOR1 in the mTORC1 signaling pathway
Authors: Gai, Z. / Wang, Q. / Yang, C. / Wang, L. / Deng, W. / Wu, G.
History
DepositionSep 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Mar 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,3014
Polymers77,1012
Non-polymers2002
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-12 kcal/mol
Surface area27440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.547, 76.834, 95.223
Angle α, β, γ (deg.)90.00, 96.21, 90.00
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: 38550.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GATSL3, CASTOR1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WTX7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#3: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 45.38 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Magnesium acetate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.06→94.7 Å / Num. obs: 135965 / % possible obs: 99.7 % / Redundancy: 3.3 % / Net I/σ(I): 5.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→94.66 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.421 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.281 / ESU R Free: 0.215 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23828 1678 5.1 %RANDOM
Rwork0.18998 ---
obs0.1925 31497 78.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.632 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0 Å20.21 Å2
2--0.34 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.06→94.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4793 0 13 149 4955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194914
X-RAY DIFFRACTIONr_bond_other_d0.0030.024735
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.9676688
X-RAY DIFFRACTIONr_angle_other_deg1.132310883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5815602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.66923.223211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.73815799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8711534
X-RAY DIFFRACTIONr_chiral_restr0.120.2786
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215434
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021106
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_it3.0362.9762438
X-RAY DIFFRACTIONr_mcbond_other3.0372.9772437
X-RAY DIFFRACTIONr_mcangle_it4.824.4283030
X-RAY DIFFRACTIONr_mcangle_other4.8194.4273031
X-RAY DIFFRACTIONr_scbond_it3.7043.3332476
X-RAY DIFFRACTIONr_scbond_other3.7043.3332476
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7984.853659
X-RAY DIFFRACTIONr_long_range_B_refined8.21323.5235241
X-RAY DIFFRACTIONr_long_range_B_other8.20623.4875209
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.064→2.118 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 44 -
Rwork0.217 938 -
obs--31.79 %

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