PDB-9kpg: Crystal structure of human CASTOR2-arginine

ID or keywords:

Entry

Database: PDB / ID: 9kpg

Title

Crystal structure of human CASTOR2-arginine

Components

Cytosolic arginine sensor for mTORC1 subunit 2

Keywords

SIGNALING 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

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Liu, C. / Ding, J. / Zhang, T.

Funding support

China, 2items

Citation

Journal: 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

Deposition	Nov 22, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Mar 25, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9kpg.cif.gz	277.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9kpg.ent.gz	222.4 KB	Display	PDB format
PDBx/mmJSON format	9kpg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kp/9kpg ftp://data.pdbj.org/pub/pdb/validation_reports/kp/9kpg	HTTPS FTP

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Related structure data

Related structure data	9kp4C 9kpbC 5gs9S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#133 - Jan 2011 Nitric Oxide Synthase similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1)

Deposited unit

A: Cytosolic arginine sensor for mTORC1 subunit 2

C: Cytosolic arginine sensor for mTORC1 subunit 2

hetero molecules

74.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	74.338, 48.391, 94.336
Angle α, β, γ (deg.)	90.00, 106.06, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#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.: 2 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: Chemical	ChemComp-ARG / ARGININE Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₅N₄O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: K
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 749 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.94 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, 0.1 M KCl, and 15% PEG5000 MME

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 15, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.85→45.33 Å / Num. obs: 55304 / % possible obs: 97.6 % / Redundancy: 4.9 % / CC_1/2: 0.99 / R_merge(I) obs: 0.113 / Net I/σ(I): 7.4
Reflection shell	Resolution: 1.85→1.89 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.629 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4569 / CC_1/2: 0.854 / % possible all: 84

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Processing

Software

Name	Version	Classification
PHENIX	(1.20.1_4487: ???)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5GS9

5gs9

Resolution: 1.85→45.33 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.04 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2302	3859	3.7 %	0
R_work	0.1852	-	-	-
obs	0.1869	53971	96.56 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.85→45.33 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4842	0	31	749	5622

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	5084
X-RAY DIFFRACTION	f_angle_d	0.851	6930
X-RAY DIFFRACTION	f_dihedral_angle_d	13.444	1826
X-RAY DIFFRACTION	f_chiral_restr	0.056	820
X-RAY DIFFRACTION	f_plane_restr	0.006	879

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.85-1.87	0.3344	110	0.2944	2830	X-RAY DIFFRACTION	76
1.87-1.9	0.3258	117	0.2692	3122	X-RAY DIFFRACTION	85
1.9-1.92	0.2839	126	0.2614	3293	X-RAY DIFFRACTION	89
1.92-1.95	0.2709	131	0.2377	3407	X-RAY DIFFRACTION	92
1.95-1.98	0.271	134	0.2365	3431	X-RAY DIFFRACTION	94
1.98-2	0.2702	141	0.228	3642	X-RAY DIFFRACTION	97
2-2.04	0.2366	136	0.2281	3548	X-RAY DIFFRACTION	97
2.04-2.07	0.2655	144	0.2211	3650	X-RAY DIFFRACTION	98
2.07-2.11	0.2844	140	0.2098	3707	X-RAY DIFFRACTION	98
2.11-2.14	0.2487	134	0.2135	3494	X-RAY DIFFRACTION	96
2.14-2.18	0.2606	143	0.209	3670	X-RAY DIFFRACTION	99
2.18-2.23	0.231	141	0.1904	3626	X-RAY DIFFRACTION	99
2.23-2.28	0.2608	143	0.199	3719	X-RAY DIFFRACTION	100
2.28-2.33	0.2488	142	0.1875	3714	X-RAY DIFFRACTION	100
2.33-2.39	0.2635	141	0.193	3696	X-RAY DIFFRACTION	100
2.39-2.45	0.2317	143	0.1973	3674	X-RAY DIFFRACTION	100
2.45-2.53	0.2939	142	0.1996	3701	X-RAY DIFFRACTION	99
2.53-2.61	0.2708	139	0.1953	3678	X-RAY DIFFRACTION	99
2.61-2.7	0.2587	148	0.1914	3724	X-RAY DIFFRACTION	99
2.7-2.81	0.2415	136	0.1887	3589	X-RAY DIFFRACTION	98
2.81-2.94	0.246	144	0.1832	3709	X-RAY DIFFRACTION	99
2.94-3.09	0.1953	143	0.1752	3687	X-RAY DIFFRACTION	100
3.09-3.28	0.2133	144	0.165	3694	X-RAY DIFFRACTION	99
3.28-3.54	0.182	142	0.1504	3695	X-RAY DIFFRACTION	99
3.54-3.89	0.2033	141	0.1438	3665	X-RAY DIFFRACTION	99
3.89-4.46	0.1465	136	0.1384	3629	X-RAY DIFFRACTION	98
4.46-5.61	0.1832	143	0.151	3670	X-RAY DIFFRACTION	99
5.61-10	0.2392	135	0.2023	3648	X-RAY DIFFRACTION	98

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.5387	0.046	1.1103	1.0038	-0.3754	3.9939	-0.121	0.1868	0.1449	-0.1456	-0.0136	-0.0779	-0.3036	0.2429	0.1258	0.1426	-0.0251	0.0071	0.0659	0.0133	0.1078	25.918	-2.624	14.475
2	1.9476	1.8736	3.2517	1.9637	-3.064	0.8027	0.2189	0.2407	-0.321	-0.5213	-0.3984	-0.9928	0.4316	0.5725	0.2088	0.2601	0.127	0.0207	0.2303	0.09	0.4135	33.99	-23.27	32.529
3	2.6857	0.1019	1.2876	1.7515	0.5237	3.2554	-0.0203	0.0269	-0.0012	0.0694	0.0188	-0.3747	0.0029	0.3921	-0.0039	0.0853	-0.0106	0.006	0.1094	0.0178	0.1434	33.083	-5.987	32.841
4	0.948	0.0594	-0.2084	0.6591	0.479	2.6816	-0.0451	0.0576	0.0375	-0.0344	-0.0356	-0.0443	0.0443	-0.1351	0.0901	0.1167	0.0082	-0.0052	0.074	0.0165	0.1112	15.59	-8.104	19.687
5	2.8096	0.8449	-0.4282	0.4833	-1.0452	3.2019	-0.0994	0.4691	-0.551	-0.1622	-0.0704	-0.0424	0.7484	-0.5286	0.1461	0.2329	-0.0666	0.0213	0.1788	-0.0667	0.1743	12.066	-17.527	18.792
6	2.4718	0.5559	-0.9386	1.454	-0.7586	2.678	-0.0017	-0.1507	0.1363	0.0848	-0.0164	-0.0196	-0.2141	-0.0915	0.0166	0.0849	0.0208	-0.0275	0.0778	-0.0092	0.0719	14.683	-4.907	36.054
7	2.0003	2.0008	1.9994	2.0005	2.0003	2.0003	0.0007	-0.0232	-0.0368	0.0347	0.2731	-0.0886	-0.3687	-0.3145	-0.2006	0.2338	0.0284	0.0087	-0.0715	-0.0516	0.0854	21.33	1.095	30.445
8	1.8462	0.0516	1.4129	2.8091	-0.5276	4.5337	-0.0156	-0.0151	0.0667	0.0909	0.0207	0.1282	-0.1869	-0.2187	-0.0018	0.0891	0.0271	0.011	0.1288	-0.0182	0.0811	11.419	-1.163	-12.01
9	1.3889	0.6142	0.4428	0.8301	-0.6161	1.4934	0.0823	0.1699	-0.1992	-0.4227	-0.0626	0.0225	0.3594	-0.1996	-0.0091	0.1998	0.0431	-0.0029	0.2128	-0.0438	0.1848	7.894	-9.86	-31.549
10	1.601	-1.5308	1.2804	3.996	-1.762	4.1282	0.1966	-0.1745	-0.0747	-0.2242	0.1606	0.3688	0.4442	-0.939	-0.3164	0.1455	-0.0251	-0.0258	0.298	0.0146	0.1861	-0.717	-1.744	-31.248
11	3.5665	-0.5098	-0.0312	0.3427	0.5619	0.5638	0.1391	0.2854	0.2468	-0.018	-0.2571	-0.0625	0.1231	0.2991	0.1099	0.1608	0.034	0.0205	0.1309	-0.0623	0.1157	19.917	-6.031	-28.629
12	2.2211	-0.4747	-0.3123	2.9192	0.28	3.1553	-0.0107	0.0776	-0.4069	0.0248	-0.067	-0.2188	0.773	0.4271	0.0688	0.3102	0.0775	0.0179	0.2063	-0.0102	0.1672	21.099	-16.213	-12.488
13	2.2345	-0.6651	-1.5706	0.4028	1.1277	2.4839	0.1375	0.146	0.0934	-0.1549	-0.0804	-0.0665	-0.1249	0.0049	-0.0576	0.1424	0.0683	0.0136	0.1717	0.0095	0.1261	23.228	-6.091	-33.901
14	2	6.8989	2.0001	8.0741	1.9997	2	0.0729	0.3488	-0.0392	-0.0405	0.0732	0.1464	-0.1932	0.3179	-0.1743	0.0945	0.1248	0.0368	0.1213	0.0103	0.1236	16.364	1.266	-29.021

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 1:82 )	A	1 - 82
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 83:96 )	A	83 - 96
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 97:165 )	A	97 - 165
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 166:236 )	A	166 - 236
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 237:269 )	A	237 - 269
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 270:334 )	A	270 - 334
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 401:401 )	A	401
8	X-RAY DIFFRACTION	8	( CHAIN C AND RESID 1:75 )	C	1 - 75
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 76:122 )	C	76 - 122
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 123:165 )	C	123 - 165
11	X-RAY DIFFRACTION	11	( CHAIN C AND RESID 166:192 )	C	166 - 192
12	X-RAY DIFFRACTION	12	( CHAIN C AND RESID 193:263 )	C	193 - 263
13	X-RAY DIFFRACTION	13	( CHAIN C AND RESID 264:335 )	C	264 - 335
14	X-RAY DIFFRACTION	14	( CHAIN C AND RESID 401:401 )	C	401

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