PDB-6vik: Crystal structure of mouse xm RABL3 in complex with GTPgammsS

ID or keywords:

Entry

Database: PDB / ID: 6vik

Title

Crystal structure of mouse xm RABL3 in complex with GTPgammsS

Components

Rab-like protein 3

Keywords

IMMUNE SYSTEM /

small GTPase

Function / homology

Function and homology information

regulation of protein lipidation / regulation of Ras protein signal transduction / natural killer cell differentiation /

endomembrane system / B cell differentiation /

intracellular protein transport / T cell differentiation in thymus / protein stabilization /

GTPase activity / GTP binding / protein homodimerization activity
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Su, L. / Tomchick, D.R. / Beutler, B.

Funding support

1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Genetic and structural studies of RABL3 reveal an essential role in lymphoid development and function.
Authors: Zhong, X. / Su, L. / Yang, Y. / Nair-Gill, E. / Tang, M. / Anderton, P. / Li, X. / Wang, J. / Zhan, X. / Tomchick, D.R. / Brautigam, C.A. / Moresco, E.M.Y. / Choi, J.H. / Beutler, B.

History

Deposition	Jan 13, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2020	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6vik.cif.gz	90 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vi/6vik ftp://data.pdbj.org/pub/pdb/validation_reports/vi/6vik	HTTPS FTP

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Related structure data

Related structure data	6vihC 6viiC 6vijC C: citing same article (ref.)
Similar structure data	4jet-2 4al2-3 3ldy-d 6v8s-16 3ie5-2 3a2y-d 6zqq-4 3erv-d 4w6l-d 1xem-d Search similar-shape structures by Omokage search (details) 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	#251 - Nov 2020 Adenylyl Cyclase similarity (1) #58 - Oct 2004 G Proteins similarity (1)

Deposited unit

B: Rab-like protein 3

hetero molecules

27.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	61.117, 61.117, 224.311
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	B-476- HOH

#1: Protein	Rab-like protein 3 Mass: 27242.393 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rabl3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9D4V7
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃S / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.18 Å³/Da / Density % sol: 43.6 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 16% EG 1000

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.979 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 1.7→50 Å / Num. obs: 28484 / % possible obs: 100 % / Redundancy: 33.7 % / R_merge(I) obs: 0.126 / R_pim(I) all: 0.022 / R_rim(I) all: 0.128 / Χ²: 0.985 / Net I/σ(I): 6.3 / Num. measured all: 960436

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.7-1.73	23.4	5.362	1357	0.568	1.13	5.483	0.901	99.9
1.73-1.76	26.3	5.157	1396	0.703	1.015	5.258	0.891	100
1.76-1.79	28.1	3.658	1393	0.824	0.696	3.725	0.905	100
1.79-1.83	28.6	3.76	1362	0.849	0.707	3.827	0.898	100
1.83-1.87	34.6	3.065	1380	0.914	0.524	3.11	0.898	100
1.87-1.91	35.7	2.483	1413	0.932	0.418	2.519	0.952	100
1.91-1.96	36.6	1.755	1388	0.966	0.291	1.78	0.988	100
1.96-2.02	36.5	1.33	1378	0.975	0.22	1.349	0.937	100
2.02-2.07	35.9	0.906	1403	0.986	0.152	0.919	0.985	100
2.07-2.14	34.9	0.708	1386	0.988	0.12	0.718	0.98	100
2.14-2.22	33	0.448	1417	0.995	0.078	0.455	0.989	100
2.22-2.31	37.6	0.354	1402	0.996	0.058	0.359	1.066	100
2.31-2.41	37.1	0.264	1431	0.997	0.044	0.268	0.988	100
2.41-2.54	37	0.194	1417	0.998	0.032	0.196	0.985	99.9
2.54-2.7	36.2	0.144	1419	0.999	0.024	0.146	1.042	100
2.7-2.91	33.6	0.112	1447	0.998	0.019	0.113	1.065	100
2.91-3.2	37.5	0.081	1447	0.999	0.013	0.082	1.105	100
3.2-3.66	36.3	0.065	1470	0.999	0.011	0.066	1.177	100
3.66-4.61	33.1	0.052	1513	0.999	0.009	0.053	1.123	100
4.61-50	31.9	0.041	1665	0.998	0.007	0.041	0.721	99.7

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Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.7→47.866 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2348	1998	7.72 %
R_work	0.2073	23880	-
obs	0.2094	25878	91.16 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 111.03 Å² / B_iso mean: 26.276 Å² / B_iso min: 4.73 Å²

Refinement step

Cycle: final / Resolution: 1.7→47.866 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1364	0	33	97	1494
B_iso mean	-	-	32.06	34.07	-
Num. residues	-	-	-	-	173

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.7004-1.7429	0.3338	57	0.2994	676	38
1.7429-1.79	0.282	81	0.2643	981	54
1.79-1.8427	0.2835	125	0.2581	1483	82
1.8427-1.9022	0.2945	152	0.2311	1818	99
1.9022-1.9701	0.2353	154	0.2265	1843	100
1.9701-2.049	0.2569	154	0.2201	1833	100
2.049-2.1423	0.2487	152	0.2185	1816	100
2.1423-2.2552	0.2509	154	0.2038	1868	100
2.2552-2.3965	0.222	156	0.2044	1850	100
2.3965-2.5815	0.2118	156	0.2116	1879	100
2.5815-2.8413	0.2331	158	0.2153	1876	100
2.8413-3.2524	0.2565	159	0.2043	1904	100
3.2524-4.0973	0.2294	164	0.1867	1951	100
4.0973-47.866	0.1958	176	0.1864	2102	100

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	0.223	-0.1869	-0.3063	0.2912	0.1218	0.5572	0.0339	-0.0199	0.0354	0.1095	-0.0334	-0.0057	-0.094	-0.0216	-0.0596	0.0592	-0.0088	-0.0286	0.0972	-0.0793	0.0761	21.3342	-16.4437	10.191
2	0.0981	0.1176	-0.014	0.4992	0.2568	0.6207	0.0108	0.0343	-0.0345	-0.0311	0.019	-0.0225	-0.0018	0.0123	0.0502	0.0278	0.0057	-0.0238	0.0682	-0.0903	0.0703	27.5199	-21.2879	12.1345
3	1.8319	0.6908	-0.9108	1.7713	-1.1216	3.3112	0.0008	0.3098	0.0963	-0.3024	0.0186	-0.0681	-0.1917	0.0164	-0.0596	0.1851	0.0392	-0.0019	0.1363	-0.0391	0.0417	27.4913	-11.0047	3.0308
4	0.0876	0.0022	-0.0074	0.0953	-0.0202	0.0138	0.1971	-0.5465	0.0669	0.5493	-0.1939	0.5539	0.1947	-0.4502	-0.0035	0.2221	-0.0477	0.0213	0.3544	-0.0812	0.3015	10.6917	-25.2904	20.9628
5	0.1655	0.3288	-0.5873	0.9016	-1.3627	2.237	0.0288	-0.0426	0.0665	0.0988	0.0289	0.0843	-0.1513	-0.0399	-0.0603	0.1169	0.083	-0.0261	0.1905	-0.0962	0.1428	14.3188	-14.0667	16.5526
6	1.0939	-0.1541	0.2564	2.5407	0.9257	0.8207	0.0457	0.0592	-0.1529	0.0898	-0.1123	0.0883	0.0936	-0.1119	0.0418	0.0603	-0.0197	-0.0012	0.1891	-0.1314	0.1615	15.02	-30.2404	6.9567
7	2.3611	-1.3169	0.2295	2.6962	0.8892	1.6367	0.0452	-0.0126	-0.1424	-0.0044	-0.1398	0.2345	0.0953	-0.2179	0.0756	0.0841	-0.057	-0.008	0.3409	-0.1795	0.2361	6.7512	-28.5854	10.0855
8	1.8806	0.1868	0.3179	1.4285	0.5093	2.0145	0.0321	0.0972	-0.1127	-0.0774	-0.1274	0.1398	0.0194	-0.0907	0.0621	0.044	0.0111	-0.0223	0.2151	-0.1521	0.1674	16.3242	-28.5785	3.6788
9	1.9148	-0.1485	0.0754	1.5717	0.4591	1.9786	0.0012	0.1837	-0.2977	-0.0867	0.0645	-0.0228	0.227	0.1425	-0.112	0.1782	0.0145	-0.0756	0.3245	-0.2212	0.3024	11.8613	-35.5553	-3.619
10	5.454	-3.1077	1.1443	2.6719	-0.0615	0.8109	0.0768	0.1574	0.0351	-0.0908	-0.1099	-0.0114	0.0081	-0.0043	0.0206	0.0691	0.0188	-0.0275	0.1957	-0.1376	0.2073	20.8709	-29.3649	0.8542
11	1.5967	1.1717	-0.6361	3.5096	-1.9523	5.2508	0.047	0.0658	-0.0346	-0.0708	-0.0241	-0.0832	0.0763	0.0945	-0.0201	0.1338	0.0025	0.0528	0.2516	-0.1431	0.2527	31.706	-28.3887	-1.3005
12	1.5046	-0.3462	0.1105	3.5717	1.2443	3.2078	0.0379	0.0747	0.0516	-0.2121	-0.149	0.1657	-0.2898	-0.2589	0.1008	0.2389	0.0623	-0.0629	0.2106	-0.0677	0.0635	20.7636	-15.951	-1.226

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 1 through 18 )	B	1 - 18
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 19 through 50 )	B	19 - 50
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 51 through 66 )	B	51 - 66
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 67 through 81 )	B	67 - 81
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 82 through 89 )	B	82 - 89
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 90 through 99 )	B	90 - 99
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 100 through 112 )	B	100 - 112
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 113 through 153 )	B	113 - 153
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 154 through 171 )	B	154 - 171
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 172 through 182 )	B	172 - 182
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 183 through 190 )	B	183 - 190
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 191 through 207 )	B	191 - 207

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