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- PDB-9kp4: Crystal structure of human CASTOR1 in apo form -

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Basic information

Entry
Database: PDB / ID: 9kp4
TitleCrystal structure of human CASTOR1 in apo form
ComponentsMaltose/maltodextrin-binding periplasmic protein,Cytosolic arginine sensor for mTORC1 subunit 1
KeywordsSIGNALING PROTEIN / CASTOR1 / mTORC1 / arginine sensor
Function / homology
Function and homology information


cellular response to L-arginine / molecular sensor activity / Amino acids regulate mTORC1 / arginine binding / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport ...cellular response to L-arginine / molecular sensor activity / Amino acids regulate mTORC1 / arginine binding / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of TORC1 signaling / positive regulation of TORC1 signaling / ATP-binding cassette (ABC) transporter complex / cellular response to amino acid starvation / cell chemotaxis / protein sequestering activity / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane / 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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...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 / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltose / ACETIC ACID / AMMONIUM ION / Maltose/maltodextrin-binding periplasmic protein / Cytosolic arginine sensor for mTORC1 subunit 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 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

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Cytosolic arginine sensor for mTORC1 subunit 1
B: Maltose/maltodextrin-binding periplasmic protein,Cytosolic arginine sensor for mTORC1 subunit 1
C: Maltose/maltodextrin-binding periplasmic protein,Cytosolic arginine sensor for mTORC1 subunit 1
D: Maltose/maltodextrin-binding periplasmic protein,Cytosolic arginine sensor for mTORC1 subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,55517
Polymers307,8134
Non-polymers1,74213
Water00
1
A: Maltose/maltodextrin-binding periplasmic protein,Cytosolic arginine sensor for mTORC1 subunit 1
B: Maltose/maltodextrin-binding periplasmic protein,Cytosolic arginine sensor for mTORC1 subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,6877
Polymers153,9062
Non-polymers7815
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint1 kcal/mol
Surface area53070 Å2
MethodPISA
2
C: Maltose/maltodextrin-binding periplasmic protein,Cytosolic arginine sensor for mTORC1 subunit 1
D: Maltose/maltodextrin-binding periplasmic protein,Cytosolic arginine sensor for mTORC1 subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,86710
Polymers153,9062
Non-polymers9618
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint4 kcal/mol
Surface area51780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.768, 168.780, 98.761
Angle α, β, γ (deg.)90.00, 104.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Maltose/maltodextrin-binding periplasmic protein,Cytosolic arginine sensor for mTORC1 subunit 1 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Cellular arginine sensor for ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / Cellular arginine sensor for mTORC1 protein 1 / GATS-like protein 3


Mass: 76953.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, CASTOR1, GATSL3 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: Q8WTX7
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H4N
#4: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H4O2
Has ligand of interestN
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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Barium chloride, 30% v/v ethanol, 0.2 M NH4Ac, 0.1 M Tris pH 8.5, and 25% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.07→48.49 Å / Num. obs: 47329 / % possible obs: 97.9 % / Redundancy: 3.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.112 / Net I/σ(I): 10.9
Reflection shellResolution: 3.07→3.16 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2 / Num. unique obs: 3323 / CC1/2: 0.695 / % possible all: 62.3

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Processing

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

5gs9


Resolution: 3.08→48.49 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 1999 4.23 %0
Rwork0.225 ---
obs0.2266 47255 96.24 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.08→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18664 0 116 0 18780
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.503
X-RAY DIFFRACTIONf_dihedral_angle_d12.7696700
X-RAY DIFFRACTIONf_chiral_restr0.0413048
X-RAY DIFFRACTIONf_plane_restr0.0043350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.08-3.160.3695910.32292075X-RAY DIFFRACTION63
3.16-3.240.31441320.28772982X-RAY DIFFRACTION89
3.24-3.340.32921450.28283281X-RAY DIFFRACTION99
3.34-3.450.3111480.27313355X-RAY DIFFRACTION100
3.45-3.570.2881470.26563323X-RAY DIFFRACTION100
3.57-3.710.28631490.24123370X-RAY DIFFRACTION100
3.71-3.880.27281480.22753347X-RAY DIFFRACTION100
3.88-4.080.30441480.21853357X-RAY DIFFRACTION100
4.08-4.340.23931480.21243345X-RAY DIFFRACTION100
4.34-4.680.22541480.17753372X-RAY DIFFRACTION100
4.68-5.150.20991480.18493346X-RAY DIFFRACTION100
5.15-5.890.26341490.21883369X-RAY DIFFRACTION100
5.89-7.410.26021480.22733373X-RAY DIFFRACTION100
7.42-9.990.22271500.20593361X-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)
11.9519-0.6578-0.16062.4245-0.53281.3476-0.01680.15380.24390.02530.21280.1219-0.1487-0.2695-0.14910.18630.06440.08260.54970.08190.2839170.82316.6724171.4416
21.31070.39321.73750.32310.20843.94-0.0585-0.00960.1306-0.1471-0.0952-0.05310.0451-0.36810.15270.31010.02560.03480.6562-0.01340.2919141.2629-11.8515139.7507
32.6389-0.51940.70392.63541.34084.44240.1044-0.2122-0.2790.3611-0.0736-0.24690.69610.6192-0.0360.35390.0841-0.03570.68580.10040.3709144.7189-18.5501144.6055
41.3935-0.19940.0493.3399-0.99092.77610.1250.01530.0870.4039-0.2512-0.35580.0616-0.00180.12190.38460.0291-0.07150.4401-0.04890.316146.68-60.946366.347
52.25610.02471.21212.39580.13684.3350.19110.1817-0.0237-0.05870.00580.19920.483-0.2383-0.19860.47690.0632-0.0240.74240.0230.2463134.1972-23.297396.8111
62.96131.13920.39354.17042.122.1120.5180.11590.2370.3228-0.45120.59060.529-0.4361-0.10960.6579-0.16820.02870.89850.07650.4349169.0202-64.6912168.3253
72.04890.0913-0.22882.7705-1.21052.0416-0.1264-0.0417-0.20260.0907-0.0245-0.19240.5178-0.10950.10110.49170.00360.00790.5949-0.07710.2575186.8549-32.3749142.9967
81.97790.74070.30892.2393-0.53093.0481-0.0920.2864-0.27770.4884-0.12350.2591-0.3974-0.94930.30080.45410.0934-0.00330.8395-0.21670.3564180.0173-18.7157145.7853
92.5801-0.0174-0.72082.37381.04041.44820.0860.07150.3811-0.12170.1894-0.1714-0.16450.2716-0.1870.1891-0.06820.0650.4842-0.05440.2483145.882215.104569.4396
102.3761-0.63320.95011.8939-1.55543.9934-0.0614-0.1874-0.0021-0.2884-0.08450.0910.2419-0.29470.13040.3106-0.0529-0.03820.7491-0.14010.2934174.6644-17.714598.9476
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -371 through -22 )
2X-RAY DIFFRACTION2chain 'A' and (resid -21 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 325 )
4X-RAY DIFFRACTION4chain 'B' and (resid -373 through -5 )
5X-RAY DIFFRACTION5chain 'B' and (resid -4 through 328 )
6X-RAY DIFFRACTION6chain 'C' and (resid -372 through -24 )
7X-RAY DIFFRACTION7chain 'C' and (resid -23 through 155 )
8X-RAY DIFFRACTION8chain 'C' and (resid 172 through 328 )
9X-RAY DIFFRACTION9chain 'D' and (resid -369 through -2 )
10X-RAY DIFFRACTION10chain 'D' and (resid -1 through 323 )

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