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- PDB-9kpb: Crystal structure of human CASTOR2 in apo form -

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Basic information

Entry
Database: PDB / ID: 9kpb
TitleCrystal structure of human CASTOR2 in apo form
ComponentsCytosolic arginine sensor for mTORC1 subunit 2
KeywordsSIGNALING PROTEIN / CASTOR2 / mTORC1 / CASTOR
Function / homology
Function and homology information


cellular response to L-arginine / Amino acids regulate mTORC1 / negative regulation of TORC1 signaling / 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
Cytosolic arginine sensor for mTORC1 subunit 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLiu, C. / Ding, J. / Zhang, T.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32070766 China
National Natural Science Foundation of China (NSFC)32271247 China
CitationJournal: Mol.Cell / Year: 2026
Title: CASTOR1 and CASTOR2 respond to different arginine levels to regulate mTORC1 activity.
Authors: Liu, C. / Zhang, Y. / Wang, Y. / Wu, M. / Li, Y. / Wei, J. / Shi, J. / Wang, R. / Su, L. / Yang, T. / Li, J. / Xiao, J. / Ding, J. / Zhang, T.
History
DepositionNov 22, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytosolic arginine sensor for mTORC1 subunit 2


Theoretical massNumber of molelcules
Total (without water)37,1581
Polymers37,1581
Non-polymers00
Water99155
1
A: Cytosolic arginine sensor for mTORC1 subunit 2

A: Cytosolic arginine sensor for mTORC1 subunit 2


Theoretical massNumber of molelcules
Total (without water)74,3172
Polymers74,3172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area1690 Å2
ΔGint-15 kcal/mol
Surface area25560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.516, 79.796, 62.746
Angle α, β, γ (deg.)90.00, 120.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cytosolic arginine sensor for mTORC1 subunit 2 / Cellular arginine sensor for mTORC1 protein 2 / GATS-like protein 2


Mass: 37158.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASTOR2, GATSL1, GATSL2 / Production host: Escherichia coli (E. coli) / References: UniProt: A6NHX0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.08 Å3/Da / Density % sol: 60.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1 M Succinic acid, pH 7.0, and 15% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.49→49.14 Å / Num. obs: 12429 / % possible obs: 79 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.4
Reflection shellResolution: 2.49→2.59 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 580 / CC1/2: 0.755 / % possible all: 39.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GS9

5gs9


Resolution: 2.5→32.12 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 612 5.01 %RANDOM
Rwork0.1891 ---
obs0.1918 12215 77.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→32.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 0 55 2306
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092299
X-RAY DIFFRACTIONf_angle_d0.9433131
X-RAY DIFFRACTIONf_dihedral_angle_d14.487798
X-RAY DIFFRACTIONf_chiral_restr0.057383
X-RAY DIFFRACTIONf_plane_restr0.007390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.750.3444820.2621543X-RAY DIFFRACTION41
2.75-3.150.29011400.24792652X-RAY DIFFRACTION72
3.15-3.970.25471910.1883650X-RAY DIFFRACTION98
3.97-32.120.20541990.1653758X-RAY DIFFRACTION99
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)
15.63931.19241.90121.8649-0.21456.7224-0.2052-0.2604-0.0772-0.16450.14690.3384-0.4553-1.02910.04290.39460.144-0.00680.39310.03420.34221.78713.436913.0202
25.60950.69522.1622.80920.6114.91210.2285-0.0526-0.0983-0.39230.14471.065-0.2048-1.7698-0.20280.38180.0492-0.11180.80880.06660.539813.06458.96322.3421
32.3946-0.13962.27742.34150.71068.62480.08960.2273-0.262-0.22910.269-0.16970.54480.1239-0.33230.2723-0.064-0.01280.1753-0.03040.3631.64093.87735.2929
46.02620.05895.15773.0361-2.76677.02270.3270.608-0.2084-0.72230.0283-0.3341-0.61820.9711-0.35561.031-0.18560.24780.6127-0.10280.404837.59357.8716-12.7585
51.1647-0.18010.53742.76931.25195.3579-0.0897-0.0652-0.004-0.3813-0.07680.2642-0.2362-0.92580.16320.27720.0119-0.04810.33340.05040.384525.40549.13112.5559
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 237 through 280 )
2X-RAY DIFFRACTION2chain 'A' and (resid 281 through 328 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 160 )
5X-RAY DIFFRACTION5chain 'A' and (resid 161 through 236 )

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