PDB-8yl2: Crystal Structure of Homo Tetrameric RagA-like small GTPase from ...

ID or keywords:

Entry

Database: PDB / ID: 8yl2

Title

Crystal Structure of Homo Tetrameric RagA-like small GTPase from Asgard Lokiarchaeota (LokiRagO) in complex with GTP

Components

GTP-binding protein

Keywords

HYDROLASE / RAGA / Small GTPase / Asgard / homo tetramer / GTP Binding protein

Function / homology

Function and homology information

Gtr1-Gtr2 GTPase complex / positive regulation of TORC1 signaling / negative regulation of autophagy / cellular response to starvation / lysosome / GTPase activity / GTP binding
Similarity search - Function

Biological species

Candidatus Prometheoarchaeum syntrophicum (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Alsheikh, F.B. / Robinson, R.C.

Funding support

Thailand,

United States, 3items

Citation

Journal: To Be Published
Title: Crystal Structure of Homo Tetrameric RagA-like small GTPase from Asgard Lokiarchaeota (LokiRagO) in complex with GTP
Authors: Alsheikh, F.B. / Robinson, R.C.

History

Deposition	Mar 5, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 10, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8yl2.cif.gz	970.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8yl2.ent.gz	805.6 KB	Display	PDB format
PDBx/mmJSON format	8yl2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8yl2_validation.pdf.gz	5.9 MB	Display	wwPDB validaton report
Full document	8yl2_full_validation.pdf.gz	6 MB	Display
Data in XML	8yl2_validation.xml.gz	96.4 KB	Display
Data in CIF	8yl2_validation.cif.gz	120.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yl/8yl2 ftp://data.pdbj.org/pub/pdb/validation_reports/yl/8yl2	HTTPS FTP

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Related structure data

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

Deposited unit

A: GTP-binding protein

B: GTP-binding protein

C: GTP-binding protein

D: GTP-binding protein

E: GTP-binding protein

F: GTP-binding protein

G: GTP-binding protein

H: GTP-binding protein

hetero molecules

324 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: GTP-binding protein

B: GTP-binding protein

C: GTP-binding protein

D: GTP-binding protein

E: GTP-binding protein

F: GTP-binding protein

G: GTP-binding protein

H: GTP-binding protein

hetero molecules

A: GTP-binding protein

B: GTP-binding protein

C: GTP-binding protein

D: GTP-binding protein

E: GTP-binding protein

F: GTP-binding protein

G: GTP-binding protein

H: GTP-binding protein

hetero molecules

defined by author
Evidence: gel filtration, Molecular weight was determined using Gel Filtration by constructing a calibration curve using a set of stander proteins.
647 kDa, 16 polymers

Unit cell

Length a, b, c (Å)	118.756, 97.183, 145.738
Angle α, β, γ (deg.)	90.00, 104.28, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	GTP-binding protein Mass: 39914.559 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Candidatus Prometheoarchaeum syntrophicum (archaea) Gene: DSAG12_02311 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5B9DBS5
#2: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.56 Å³/Da / Density % sol: 51.95 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: Poly Ethylene Glycol (PEG) 6,000 and 2-Methyl-2,4-pentanediol (MPD).

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1.000032 Å
Detector	Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 23, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.000032 Å / Relative weight: 1
Reflection	Resolution: 2.2→27.25 Å / Num. obs: 162816 / % possible obs: 99.9 % / Redundancy: 7 % / CC_1/2: 0.998 / R_merge(I) obs: 0.102 / R_pim(I) all: 0.041 / Net I/σ(I): 12.9
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 5.9 % / R_merge(I) obs: 1.666 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 7967 / CC_1/2: 0.385 / R_pim(I) all: 0.75 / % possible all: 99.6

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1	refinement
Blu-Ice		data collection
DIALS	3.18.0	data reduction
DIALS	3.18.0	data scaling
PHASER	2.8.3	phasing
PDB_EXTRACT	4.2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→27.25 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 24.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2295	8256	5.08 %
R_work	0.202	-	-
obs	0.2035	162671	99.84 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.2→27.25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19048	0	264	373	19685

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	20496
X-RAY DIFFRACTION	f_angle_d	0.519	27680
X-RAY DIFFRACTION	f_dihedral_angle_d	15.631	7840
X-RAY DIFFRACTION	f_chiral_restr	0.043	3080
X-RAY DIFFRACTION	f_plane_restr	0.003	3504

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 (%)
2.2-2.22	0.3123	271	0.3054	5080	X-RAY DIFFRACTION	100
2.23-2.25	0.3291	270	0.2921	5157	X-RAY DIFFRACTION	100
2.25-2.28	0.309	270	0.2792	5121	X-RAY DIFFRACTION	100
2.28-2.31	0.3006	297	0.2634	5104	X-RAY DIFFRACTION	100
2.31-2.34	0.3162	248	0.2557	5148	X-RAY DIFFRACTION	100
2.34-2.37	0.2904	283	0.2503	5134	X-RAY DIFFRACTION	100
2.37-2.4	0.2722	279	0.2364	5097	X-RAY DIFFRACTION	100
2.4-2.44	0.2751	282	0.2298	5129	X-RAY DIFFRACTION	100
2.44-2.48	0.2792	274	0.2274	5138	X-RAY DIFFRACTION	100
2.48-2.52	0.2932	247	0.2247	5109	X-RAY DIFFRACTION	100
2.52-2.56	0.2705	267	0.2199	5191	X-RAY DIFFRACTION	100
2.56-2.61	0.2765	240	0.2157	5128	X-RAY DIFFRACTION	100
2.61-2.66	0.249	273	0.2169	5098	X-RAY DIFFRACTION	100
2.66-2.71	0.2638	285	0.219	5148	X-RAY DIFFRACTION	100
2.71-2.77	0.2594	256	0.2176	5162	X-RAY DIFFRACTION	100
2.77-2.84	0.2557	261	0.2097	5172	X-RAY DIFFRACTION	100
2.84-2.91	0.2649	292	0.2078	5115	X-RAY DIFFRACTION	100
2.91-2.99	0.2509	264	0.2143	5166	X-RAY DIFFRACTION	100
2.99-3.07	0.2718	289	0.2082	5156	X-RAY DIFFRACTION	100
3.07-3.17	0.2471	253	0.2007	5139	X-RAY DIFFRACTION	100
3.17-3.29	0.2344	261	0.1871	5169	X-RAY DIFFRACTION	100
3.29-3.42	0.214	310	0.1814	5118	X-RAY DIFFRACTION	100
3.42-3.57	0.2222	268	0.1971	5198	X-RAY DIFFRACTION	100
3.57-3.76	0.1958	271	0.1825	5140	X-RAY DIFFRACTION	100
3.76-3.99	0.2182	298	0.1855	5149	X-RAY DIFFRACTION	100
3.99-4.3	0.1932	282	0.1849	5171	X-RAY DIFFRACTION	100
4.3-4.73	0.1991	315	0.1731	5152	X-RAY DIFFRACTION	100
4.73-5.41	0.2119	284	0.1916	5195	X-RAY DIFFRACTION	100
5.41-6.8	0.2349	296	0.2381	5178	X-RAY DIFFRACTION	100
6.8-27.25	0.1816	270	0.1745	5253	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	2.5762	-0.0045	-0.5408	1.8463	0.0229	1.6785	-0.0051	-0.404	0.1892	0.2614	0.0297	0.1688	-0.104	0.1352	-0.017	0.1065	0.0226	0.0643	0.0619	0.0708	-0.0129	80.649	-16.808	84.7
2	2.1226	-0.523	-0.4489	1.6186	0.4464	1.7656	0.1527	0.445	-0.0483	-0.1728	-0.1842	0.2948	0.1265	-0.0833	-0.8553	-0.0498	0.0751	-0.1933	0.1172	-0.0043	0.0195	74.973	-34.349	47.718
3	1.8556	0.2008	-0.2578	0.6063	0.3502	1.8111	0.2134	0.2452	0.3036	-0.0926	0.0098	-0.1943	-0.2027	-0.0455	2.6608	0.2403	-0.0062	0.1074	0.009	0.138	0.0913	92.164	-4.229	49.357
4	2.0299	0.5336	-0.4359	1.2355	0.7402	1.9422	0.4021	0.2273	0.31	0.1774	-0.1393	0.516	-0.1591	-0.6255	1.4672	-0.1193	0.3287	-0.0108	0.1206	0.1188	0.2101	54.454	-5.334	64.546
5	2.3667	-0.223	-0.1945	1.1005	0.1408	1.6837	-0.0838	0.5649	0.2427	-0.3851	0.2423	-0.0972	-0.187	-0.1647	1.0005	0.2393	-0.0686	0.1959	0.1702	-0.2146	-0.0911	20.688	-17.77	-13.576
6	1.6034	0.0742	-0.2019	1.2297	0.0637	1.7179	-0.06	-0.3051	-0.0254	0.1855	0.0419	-0.2083	0.1489	0.1165	-0.661	0.0933	0.0433	-0.082	0.2301	0.087	0.1849	25.971	-32.026	24.458
7	1.0703	0.0956	-0.0106	1.5306	-0.0964	1.6226	0.1373	-0.2312	0.0738	0.0091	-0.0347	-0.0713	-0.2339	-0.0232	0.861	0.1774	0.031	0.0755	0.1391	-0.0789	0.106	6.991	-3.396	19.859
8	1.9549	0.1923	-0.3107	1.5963	-0.7396	2.0645	0.1882	-0.2697	0.3261	-0.0637	-0.05	-0.6913	-0.1971	0.4936	0.3013	0.1374	-0.1762	0.111	0.2512	-0.1053	0.3428	45.576	-3.259	6.092

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 41:341 )	A	41 - 341
2	X-RAY DIFFRACTION	2	( CHAIN B AND ( RESID 41:341 OR RESID 401:401 ) )	B	41 - 341
3	X-RAY DIFFRACTION	2	( CHAIN B AND ( RESID 41:341 OR RESID 401:401 ) )	B	401
4	X-RAY DIFFRACTION	3	( CHAIN C AND ( RESID 41:341 OR RESID 401:401 ) )	C	41 - 341
5	X-RAY DIFFRACTION	3	( CHAIN C AND ( RESID 41:341 OR RESID 401:401 ) )	C	401
6	X-RAY DIFFRACTION	4	( CHAIN D AND ( RESID 41:341 OR RESID 401:401 ) )	D	41 - 341
7	X-RAY DIFFRACTION	4	( CHAIN D AND ( RESID 41:341 OR RESID 401:401 ) )	D	401
8	X-RAY DIFFRACTION	5	( CHAIN E AND ( RESID 41:341 OR RESID 401:401 ) )	E	41 - 341
9	X-RAY DIFFRACTION	5	( CHAIN E AND ( RESID 41:341 OR RESID 401:401 ) )	E	401
10	X-RAY DIFFRACTION	6	( CHAIN F AND ( RESID 41:341 OR RESID 401:401 ) )	F	41 - 341
11	X-RAY DIFFRACTION	6	( CHAIN F AND ( RESID 41:341 OR RESID 401:401 ) )	F	401
12	X-RAY DIFFRACTION	7	( CHAIN G AND ( RESID 41:341 OR RESID 401:401 ) )	G	41 - 341
13	X-RAY DIFFRACTION	7	( CHAIN G AND ( RESID 41:341 OR RESID 401:401 ) )	G	401
14	X-RAY DIFFRACTION	8	( CHAIN H AND ( RESID 41:341 OR RESID 401:401 ) )	H	41 - 341
15	X-RAY DIFFRACTION	8	( CHAIN H AND ( RESID 41:341 OR RESID 401:401 ) )	H	401

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