PDB-6vih: The ligand-free structure of mouse RABL3

ID or keywords:

Entry

Database: PDB / ID: 6vih

Title

The ligand-free structure of mouse RABL3

Components

Rab-like protein 3

Keywords

IMMUNE SYSTEM /

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: 2.993 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 / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6vih.cif.gz	167 KB	Display	PDBx/mmCIF format
PDB format	pdb6vih.ent.gz	132 KB	Display	PDB format
PDBx/mmJSON format	6vih.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/vi/6vih ftp://data.pdbj.org/pub/pdb/validation_reports/vi/6vih	HTTPS FTP

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Related structure data

Related structure data	6viiC 6vijC 6vikC C: citing same article (ref.)
Similar structure data	3dge-3 4q46-d 2okc-2 4emu-d 6vii-d 5xw5-1 2okc-1 3f5n-2 4yy8-2 6qqw-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Deposited unit

B: Rab-like protein 3

A: Rab-like protein 3

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

2

B: Rab-like protein 3

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

3

A: Rab-like protein 3

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

Unit cell

Length a, b, c (Å)	58.998, 79.200, 111.473
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	(chain A and (resid 2 through 33 or resid 39 through 208))
2	1	(chain B and (resid 2 through 33 or resid 39 through 116 or resid 131 or resid 134 through 208))

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ALA	ALA	GLY	GLY	(chain A and (resid 2 through 33 or resid 39 through 208))	A	B	2 - 33	31 - 62
1	2	VAL	VAL	TYR	TYR	(chain A and (resid 2 through 33 or resid 39 through 208))	A	B	39 - 208	68 - 237
2	1	ALA	ALA	GLY	GLY	(chain B and (resid 2 through 33 or resid 39 through 116 or resid 131 or resid 134 through 208))	B	A	2 - 33	31 - 62
2	2	VAL	VAL	ARG	ARG	(chain B and (resid 2 through 33 or resid 39 through 116 or resid 131 or resid 134 through 208))	B	A	39 - 116	68 - 145
2	3	ASP	ASP	ASP	ASP	(chain B and (resid 2 through 33 or resid 39 through 116 or resid 131 or resid 134 through 208))	B	A	131	160
2	4	GLN	GLN	TYR	TYR	(chain B and (resid 2 through 33 or resid 39 through 116 or resid 131 or resid 134 through 208))	B	A	134 - 208	163 - 237

#1: Protein	Rab-like protein 3 Mass: 27726.961 Da / Num. of mol.: 2 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

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.62 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.5 M Ammonium phosphate monobasic

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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

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

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.95→50 Å / Num. obs: 11507 / % possible obs: 99.9 % / Redundancy: 17.8 % / R_merge(I) obs: 0.095 / R_pim(I) all: 0.024 / R_rim(I) all: 0.098 / Χ²: 0.947 / Net I/σ(I): 7.7 / Num. measured all: 205296

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
2.95-3	18.7	3.711	546	0.517	0.877	3.815	0.939	100
3-3.06	18.8	3.071	561	0.68	0.722	3.157	0.951	100
3.06-3.11	18.4	2.329	572	0.706	0.553	2.395	0.949	100
3.11-3.18	18.7	1.632	573	0.86	0.384	1.677	0.942	100
3.18-3.25	18.5	1.216	549	0.878	0.288	1.25	0.956	100
3.25-3.32	18.1	0.897	576	0.946	0.215	0.922	0.95	100
3.32-3.41	18.4	0.72	558	0.946	0.171	0.74	0.956	100
3.41-3.5	17.7	0.52	569	0.973	0.126	0.536	1.039	99.8
3.5-3.6	16.7	0.399	569	0.979	0.099	0.411	0.994	100
3.6-3.72	15.7	0.275	560	0.991	0.071	0.284	1.038	100
3.72-3.85	18.9	0.208	563	0.994	0.049	0.214	0.965	100
3.85-4	18.9	0.15	567	0.996	0.035	0.154	1.022	100
4-4.19	18.8	0.099	583	0.998	0.023	0.102	0.942	100
4.19-4.41	18.5	0.078	574	0.997	0.019	0.08	0.902	99.8
4.41-4.68	18.3	0.064	574	0.999	0.015	0.066	0.87	99.8
4.68-5.04	17.5	0.059	575	0.998	0.014	0.06	0.805	99.8
5.04-5.55	15.4	0.055	583	0.998	0.014	0.057	0.762	99.8
5.55-6.35	18.3	0.053	587	0.998	0.013	0.055	0.708	99.8
6.35-8	17.7	0.047	613	0.999	0.011	0.049	0.687	100
8-50	15.1	0.075	655	0.996	0.019	0.077	1.603	99.5

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 2.993→47.313 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.275	950	10.01 %
R_work	0.2265	8541	-
obs	0.2313	9491	86.03 %

Solvent computation

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

Displacement parameters

B_iso max: 149.63 Å² / B_iso mean: 58.6165 Å² / B_iso min: 6.78 Å²

Refinement step

Cycle: final / Resolution: 2.993→47.313 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2976	0	0	0	2976
Num. residues	-	-	-	-	378

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	1744	X-RAY DIFFRACTION	9.414	TORSIONAL
1	2	B	1744	X-RAY DIFFRACTION	9.414	TORSIONAL

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 (%)
2.993-3.1506	0.3444	30	0.2906	269	19
3.1506-3.348	0.3035	125	0.2647	1123	81
3.348-3.6064	0.2998	156	0.2583	1402	100
3.6064-3.9691	0.2888	155	0.227	1400	100
3.9691-4.5431	0.2328	157	0.1906	1409	100
4.5431-5.7222	0.2175	158	0.1987	1428	100
5.7222-47.313	0.3244	169	0.2416	1510	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	2.9408	0.0605	0.813	4.3148	0.328	0.9655	-0.171	-0.7934	0.0451	0.7284	0.0883	1.2988	-0.1546	-0.5552	0.2867	0.5275	0.3696	0.1503	0.7101	-0.1046	0.4896	-27.7147	-0.5319	-42.274
2	2.2921	0.148	-0.2522	2.2609	0.2772	5.152	0.2893	0.2251	-0.3274	-0.3113	-0.0109	0.6077	0.144	-0.1777	0.0929	0.2121	0.2354	-0.1351	0.2031	0.0032	0.348	-19.0913	-11.5014	-44.0183
3	4.3446	0.521	0.9921	2.8044	1.9127	6.4105	-0.0017	0.6591	0.4258	-0.2866	0.1807	-0.1608	-0.7527	0.3457	-0.198	0.0955	0.0249	0.0181	0.173	-0.1131	0.232	1.8731	1.5645	-28.3774
4	2.5744	-0.4519	0.8446	3.6107	-0.4529	3.8622	-0.2062	0.1092	0.8008	0.1456	0.101	-0.0024	-0.6527	0.2283	-0.1965	0.1141	-0.0696	0.0235	0.3381	0.0198	0.3377	3.3853	4.1721	-31.9882
5	3.3288	-0.5468	1.6866	3.4098	0.8627	4.1242	-0.2248	0.026	-0.2847	-0.003	0.2281	0.1989	0.2386	0.1947	-0.0629	0.2105	-0.0532	-0.0608	0.0707	-0.0102	0.3377	1.955	-4.1198	-29.5962
6	1.9486	0.0663	0.7731	2.5381	1.093	4.3828	0.122	-0.3481	0.2005	0.7493	0.1321	0.0992	0.0435	-0.2762	0.8855	0.4003	-0.0434	0.08	0.0621	-0.0612	0.1071	-2.1785	-3.1181	-16.5122
7	3.2844	-0.7365	0.1237	2.3233	0.8526	3.1768	0.0554	-0.6379	0.0775	1.2563	0.0173	-0.2509	0.1404	0.3254	-0.5845	0.5717	-0.0532	-0.1424	0.1694	-0.0856	0.3397	8.3534	-1.8281	-11.3923
8	2.9441	-1.1031	1.2562	1.5762	0.5529	4.3413	-0.3075	0.2819	0.5442	0.1949	0.1867	-0.6927	-0.8467	0.714	0.0934	0.2594	0.022	-0.0777	0.2206	0.0459	0.4258	13.1628	5.045	-21.0707
9	4.009	-0.659	0.816	3.8945	-0.616	5.5105	0.0472	0.624	-0.5854	-0.0552	0.0492	-0.3078	0.5403	0.4668	-0.8614	0.0432	-0.0276	-0.0273	0.3175	-0.2773	0.2624	12.2011	-7.3209	-28.6279
10	1.7623	-0.4552	-0.662	1.5164	0.4356	1.7136	-0.2037	-0.199	0.0478	0.1535	0.04	0.1944	-0.3417	-0.3699	-0.4844	0.2275	0.2097	0.0298	0.1851	-0.1508	0.0926	-14.7721	-0.7897	-37.2478
11	2.2445	-1.9192	-0.3017	2.7096	0.3485	3.2681	-0.0144	-0.4834	0.3572	0.4398	-0.1159	0.5789	-0.2544	-0.879	0.1719	0.8276	0.0293	0.1003	0.7438	-0.2569	0.5614	-19.0085	5.0059	-29.7758
12	3.7686	-1.8455	1.0752	1.0672	-0.895	5.2539	0.1428	-0.2293	-0.9671	0.0972	-0.1343	0.6858	0.7043	-0.681	0.0177	0.1172	-0.0611	0.0658	0.2539	-0.0829	0.2802	-16.3754	-12.1037	-35.1557
13	5.3181	-1.5029	4.164	1.8955	-0.1712	5.5348	-0.107	0.8968	1.061	-0.7204	-0.4089	-0.3875	-0.8852	0.8827	-0.6506	0.4103	0.1075	0.0568	0.3482	0.1146	0.2912	-9.8368	6.593	-47.8344
14	0.9117	-1.0187	0.5313	1.1379	-0.56	3.5456	0.3608	1.1252	-0.0155	-0.6104	-0.1356	-0.1238	-0.3312	0.4856	-0.144	0.7805	0.1165	0.1121	1.4432	-0.0846	0.5492	-7.6967	-4.2132	-55.166
15	4.6045	-0.8744	-0.1186	4.5617	0.0324	2.4698	0.2418	0.0364	0.659	-0.1884	-0.2075	0.8608	-0.9303	-0.9276	0.6655	0.4115	0.4225	-0.0396	0.5181	-0.1736	0.3842	-28.7078	7.5446	-46.6097
16	3.4818	-0.9624	1.2598	4.0831	0.7024	3.7209	-0.0928	-0.1274	0.1372	-0.2702	-0.1913	0.4318	-0.5774	-0.5712	0.2486	0.8802	0.4402	-0.0952	0.6427	-0.1011	0.3256	-27.4959	5.1602	-56.0115

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 171 through 190 )	A	171 - 190
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 191 through 208 )	A	191 - 208
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 2 through 28 )	B	2 - 28
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 29 through 50 )	B	29 - 50
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 51 through 78 )	B	51 - 78
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 79 through 114 )	B	79 - 114
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 115 through 170 )	B	115 - 170
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 171 through 190 )	B	171 - 190
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 191 through 209 )	B	191 - 209
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 2 through 27 )	A	2 - 27
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 28 through 41 )	A	28 - 41
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 42 through 66 )	A	42 - 66
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 67 through 115 )	A	67 - 115
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 116 through 140 )	A	116 - 140
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 141 through 156 )	A	141 - 156
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 157 through 170 )	A	157 - 170

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