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- PDB-5gt7: Crystal Structure of Arg-bound CASTOR1 -

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Basic information

Entry
Database: PDB / ID: 5gt7
TitleCrystal Structure of Arg-bound CASTOR1
ComponentsGATS-like protein 3
KeywordsSIGNALING PROTEIN / arginine binding / mTOR / GATSL2 / CASTOR1 / GATOR2 / ACT domain
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
ARGININE / MALONATE ION / Cytosolic arginine sensor for mTORC1 subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.048 Å
AuthorsGuo, L. / Deng, D.
Funding support China, 1items
OrganizationGrant numberCountry
MOST2016YFA0502700 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Crystal structures of arginine sensor CASTOR1 in arginine-bound and ligand free states
Authors: Zhou, Y. / Wang, C. / Xiao, Q. / Guo, L.
History
DepositionAug 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.2Mar 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)148,71614
Polymers147,4034
Non-polymers1,31310
Water9,098505
1
A: GATS-like protein 3
B: GATS-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3587
Polymers73,7022
Non-polymers6575
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-7 kcal/mol
Surface area26110 Å2
MethodPISA
2
C: GATS-like protein 3
D: GATS-like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3587
Polymers73,7022
Non-polymers6575
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-6 kcal/mol
Surface area27200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.833, 83.146, 97.289
Angle α, β, γ (deg.)90.000, 116.390, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 2 or (resid 4 and (name...
21(chain B and (resseq 2 or (resid 4 and (name...
31(chain C and (resseq 2 or (resid 4 and (name...
41(chain D and (resseq 2 or (resid 4 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 2 or (resid 4 and (name...A0
211(chain B and (resseq 2 or (resid 4 and (name...B0
311(chain C and (resseq 2 or (resid 4 and (name...C0
411(chain D and (resseq 2 or (resid 4 and (name...D0

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Components

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


Mass: 36850.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GATSL3, CASTOR1 / Production host: Spodoptera frugiperda (fall armyworm) / 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-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 2.5 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 5 % (w/v) PEG3350, 0.1 M Na Malonate pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1.0011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0011 Å / Relative weight: 1
ReflectionResolution: 2.048→50 Å / Num. obs: 82993 / % possible obs: 99.5 % / Redundancy: 6.1 % / Biso Wilson estimate: 35.46 Å2 / Rmerge(I) obs: 0.091 / Net I/av σ(I): 18.612 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.05-2.125.90.8840.69198.8
2.12-2.2160.6330.819199
2.21-2.3160.4630.894199.1
2.31-2.436.10.3440.938199.5
2.43-2.586.20.260.966199.5
2.58-2.786.30.1780.984199.5
2.78-3.066.30.1180.992199.8
3.06-3.516.30.0830.995199.9
3.51-4.4260.0660.9961100
4.42-506.10.050.995199.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHENIX(1.10.1_2155: ???)refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.048→33.029 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.32
RfactorNum. reflection% reflection
Rfree0.2112 4521 5.45 %
Rwork0.1847 --
obs0.1862 82969 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.09 Å2 / Biso mean: 46.6482 Å2 / Biso min: 17.5 Å2
Refinement stepCycle: final / Resolution: 2.048→33.029 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9492 0 54 505 10051
Biso mean--61.27 42.68 -
Num. residues----1223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039862
X-RAY DIFFRACTIONf_angle_d0.67413448
X-RAY DIFFRACTIONf_chiral_restr0.0481580
X-RAY DIFFRACTIONf_plane_restr0.0041722
X-RAY DIFFRACTIONf_dihedral_angle_d12.4725923
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4993X-RAY DIFFRACTION7.676TORSIONAL
12B4993X-RAY DIFFRACTION7.676TORSIONAL
13C4993X-RAY DIFFRACTION7.676TORSIONAL
14D4993X-RAY DIFFRACTION7.676TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0482-2.07150.3261510.27142514266595
2.0715-2.09590.28911350.26032599273499
2.0959-2.12140.3181390.26052581272099
2.1214-2.14830.27451570.2432563272099
2.1483-2.17650.29261560.23632591274799
2.1765-2.20640.24521540.23752604275899
2.2064-2.23790.25611360.22632599273599
2.2379-2.27130.26011620.21822601276399
2.2713-2.30670.24971190.20662618273799
2.3067-2.34460.251080.207226242732100
2.3446-2.3850.26171320.20712661279399
2.385-2.42830.2641470.211725792726100
2.4283-2.4750.24491410.20882599274099
2.475-2.52550.29331480.21492640278899
2.5255-2.58040.25281520.205626072759100
2.5804-2.64040.23921430.19622629277299
2.6404-2.70640.22711580.198826082766100
2.7064-2.77960.2331340.200226472781100
2.7796-2.86130.23291530.197226092762100
2.8613-2.95360.23111680.187826012769100
2.9536-3.05910.1951960.186225822778100
3.0591-3.18150.22761970.183625952792100
3.1815-3.32610.24231550.180926142769100
3.3261-3.50130.17891650.172526182783100
3.5013-3.72040.20891690.178926312800100
3.7204-4.00720.2141360.17126562792100
4.0072-4.40960.16381320.152626642796100
4.4096-5.04580.13931630.135626392802100
5.0458-6.34970.19971480.178826662814100
6.3497-33.03350.18361670.180327092876100

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