PDB-8jca: Cyrstal structure of SKIP RUN domain in complex with GTP-bound Ar...

ID or keywords:

Entry

Database: PDB / ID: 8jca

Title

Cyrstal structure of SKIP RUN domain in complex with GTP-bound Arl8b(Q75L)

Components

ADP-ribosylation factor-like protein 8B
Pleckstrin homology domain-containing family M member 2

Keywords

PROTEIN BINDING / SKIP / RUN / Arl8b / GTP-bound / GTPase / Arf

Function / homology

Function and homology information

antigen processing and presentation of polysaccharide antigen via MHC class II / antigen processing and presentation following phagocytosis / viral exocytosis / calcium ion regulated lysosome exocytosis / endosome to lysosome transport of low-density lipoprotein particle / cytolytic granule membrane / phagosome-lysosome fusion / late endosome to lysosome transport / autophagosome-lysosome fusion / lysosome localization ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Qiu, X.H. / Pan, L.F.

Funding support

China, 1items

Citation

Journal: J.Mol.Biol. / Year: 2023
Title: Mechanistic Insights into the Interactions of Arl8b with the RUN Domains of PLEKHM1 and SKIP.
Authors: Qiu, X. / Li, Y. / Wang, Y. / Gong, X. / Wang, Y. / Pan, L.

History

Deposition	May 10, 2023	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Mar 27, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8jca.cif.gz	159.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8jca.ent.gz	123.3 KB	Display	PDB format
PDBx/mmJSON format	8jca.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8jca_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	8jca_full_validation.pdf.gz	1.2 MB	Display
Data in XML	8jca_validation.xml.gz	18 KB	Display
Data in CIF	8jca_validation.cif.gz	26.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jc/8jca ftp://data.pdbj.org/pub/pdb/validation_reports/jc/8jca	HTTPS FTP

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Related structure data

Related structure data	8jc5C C: citing same article (ref.)
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	#148 - Apr 2012 Ras Protein similarity (2) #245 - May 2020 Spliceosomes similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1)

Deposited unit

A: ADP-ribosylation factor-like protein 8B

B: Pleckstrin homology domain-containing family M member 2

hetero molecules

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

1

Idetical with deposited unit
defined by author
Evidence: equilibrium centrifugation

Unit cell

Length a, b, c (Å)	178.687, 53.836, 40.512
Angle α, β, γ (deg.)	90.00, 98.13, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-225- HOH

#1: Protein	ADP-ribosylation factor-like protein 8B / ADP-ribosylation factor-like protein 10C / Novel small G protein indispensable for equal chromosome ...ADP-ribosylation factor-like protein 10C / Novel small G protein indispensable for equal chromosome segregation 1 Mass: 19400.438 Da / Num. of mol.: 1 / Mutation: Q75L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARL8B, ARL10C, GIE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NVJ2, small monomeric GTPase
#2: Protein	Pleckstrin homology domain-containing family M member 2 / PH domain-containing family M member 2 / Salmonella-induced filaments A and kinesin-interacting ...PH domain-containing family M member 2 / Salmonella-induced filaments A and kinesin-interacting protein / SifA and kinesin-interacting protein Mass: 19180.037 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLEKHM2, KIAA0842, SKIP / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IWE5
#3: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 296 / 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: 2.5 Å³/Da / Density % sol: 50.8 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 800mM Potassiam phosphate dibasic 1.2 M Sodium phosphate monobasic 0.1M CAPS/Sodium hydroxide 0.2M Lithium sulfate pH10.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 20, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.647→51.504 Å / Num. obs: 41074 / % possible obs: 89.1 % / Redundancy: 2.7 % / CC_1/2: 0.99 / Net I/σ(I): 0.073
Reflection shell	Resolution: 1.65→1.68 Å / R_merge(I) obs: 0.775 / Num. unique obs: 41074 / CC_1/2: 0.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.17.1_3660: ???)	refinement
autoPROC		data reduction
autoPROC		data scaling
PHENIX	(1.17.1_3660: ???)	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.65→32.05 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.206	2010	4.89 %
R_work	0.1746	-	-
obs	0.1761	41074	88.84 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.65→32.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2665	0	33	296	2994

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2749
X-RAY DIFFRACTION	f_angle_d	1.034	3725
X-RAY DIFFRACTION	f_dihedral_angle_d	18.329	372
X-RAY DIFFRACTION	f_chiral_restr	0.063	420
X-RAY DIFFRACTION	f_plane_restr	0.005	468

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 (%)
1.65-1.69	0.2809	158	0.2603	3099	X-RAY DIFFRACTION	98
1.69-1.73	0.2588	169	0.2457	3043	X-RAY DIFFRACTION	99
1.73-1.79	0.2807	160	0.2311	3038	X-RAY DIFFRACTION	98
1.79-1.84	0.251	175	0.2251	3097	X-RAY DIFFRACTION	99
1.84-1.91	0.2322	76	0.223	1732	X-RAY DIFFRACTION	55
1.91-1.99	0.2506	96	0.2139	1903	X-RAY DIFFRACTION	60
1.99-2.08	0.2408	161	0.1916	3028	X-RAY DIFFRACTION	98
2.08-2.18	0.2425	152	0.1766	3119	X-RAY DIFFRACTION	99
2.18-2.32	0.2553	141	0.1831	3107	X-RAY DIFFRACTION	98
2.32-2.5	0.2153	173	0.1756	3120	X-RAY DIFFRACTION	99
2.5-2.75	0.1693	66	0.172	1553	X-RAY DIFFRACTION	49
2.75-3.15	0.1847	172	0.1712	3100	X-RAY DIFFRACTION	98
3.15-3.97	0.1845	155	0.1451	3073	X-RAY DIFFRACTION	97
3.97-32.05	0.1728	156	0.1566	3052	X-RAY DIFFRACTION	94

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	5.2477	-3.686	-3.0768	7.0904	6.2277	7.4204	-0.14	-0.0496	-0.4271	0.1893	-0.2127	0.5616	0.3598	-0.5072	0.4059	0.1715	-0.0324	0.0405	0.2321	0.0409	0.2502	8.5584	2.2524	15.7746
2	3.5596	1.1999	-2.8671	1.9089	-1.2625	4.1598	0.07	-0.1771	0.2017	0.0439	-0.0532	0.2245	-0.0633	-0.1079	-0.0191	0.109	-0.0051	-0.0266	0.2146	-0.009	0.1878	8.7223	18.5626	17.8717
3	4.7666	2.496	2.383	7.8617	2.4312	8.7037	-0.5606	0.9145	0.7507	-0.6534	0.182	0.3903	-0.6026	-0.1015	0.274	0.2085	-0.0033	-0.0772	0.2811	0.0407	0.2397	9.9369	19.4918	3.4493
4	2.2269	0.4386	0.6864	3.2928	1.6261	5.7452	0.0017	-0.0297	-0.0767	-0.0092	0.0088	-0.0815	0.0053	0.1736	-0.0318	0.1169	-0.0202	0.0201	0.1539	0.042	0.1627	15.4074	12.7877	13.9262
5	3.9862	0.4805	3.9062	6.891	1.3371	3.9514	0.1448	-0.622	0.6243	0.232	-0.1388	-0.1977	-0.1166	-0.0242	0.1003	0.2887	-0.0113	0.0052	0.262	-0.0396	0.203	13.5203	21.9785	25.9067
6	7.3246	-5.7537	-0.2782	8.9492	1.7906	2.655	-0.383	-0.6779	-0.1018	0.6603	0.2578	-0.1654	0.0687	0.083	0.0792	0.2133	-0.0513	-0.0013	0.2951	0.0647	0.1849	15.2679	9.3845	27.0156
7	5.6329	-5.9146	4.6564	6.8746	-5.3291	4.2573	-0.3434	0.305	0.4162	-0.1532	0.0743	-0.2911	-0.004	-0.0074	0.1131	0.2648	-0.0377	-0.0265	0.2366	-0.0071	0.266	17.6628	5.1901	5.6588
8	7.8494	4.6006	-7.6849	8.8723	-3.0203	9.2866	-0.3879	1.3505	-0.1446	-0.2606	0.4233	0.0794	0.2767	-1.1644	-0.057	0.2209	-0.0656	-0.0412	0.3928	-0.0144	0.2471	-1.0658	8.5869	10.228
9	9.1955	-6.4136	-4.6368	5.4904	5.2244	7.1909	0.0943	-0.0313	0.4959	-0.3708	-0.0187	0.2049	-0.7059	-0.3412	0.059	0.2251	0.0128	0.0118	0.1762	0.0354	0.2967	27.3841	30.7315	11.8457
10	5.1832	-0.8464	-0.4976	5.0958	0.7278	4.423	0.0615	-0.4323	0.1476	0.5653	0.0117	-0.1362	0.0891	0.0024	-0.093	0.1417	-0.0142	-0.0103	0.1305	0.0026	0.0941	36.7059	21.433	22.4143
11	5.5415	-0.2243	0.3738	3.5519	4.9909	7.4191	-0.1157	-0.2631	0.4011	0.5069	0.0695	0.1875	-0.5359	0.0023	0.1255	0.2906	-0.0016	0.0393	0.2147	0.0001	0.1959	26.0095	27.0348	18.7654
12	4.1457	-2.2071	0.8297	4.8137	-0.5885	1.1163	-0.0059	0.077	0.0492	-0.0237	0.0525	0.1698	0.0698	0.0015	-0.0432	0.1192	-0.0202	0.0101	0.1148	0.005	0.0903	32.2704	21.7965	10.4967
13	3.6467	-1.9956	5.414	2.5638	-2.254	8.4574	0.0419	0.4951	0.133	-0.2129	-0.0313	-0.5661	0.367	0.5378	-0.0488	0.2374	0.0328	0.0225	0.2494	-0.0247	0.2092	45.0634	17.5823	5.1298
14	9.1211	1.583	5.1524	2.9475	1.4612	3.0612	-0.1675	0.5761	0.2159	-0.3996	0.049	0.0891	-0.0423	0.186	0.0525	0.1901	-0.0263	0.0252	0.1973	0.0276	0.0844	35.6082	25.8652	2.3243
15	4.7453	1.3441	-0.3836	3.3022	-0.7152	2.0981	-0.1638	0.4093	0.095	-0.095	0.024	-0.388	-0.1722	0.5353	0.1039	0.1887	-0.0074	0.0055	0.2428	0.021	0.272	52.3402	26.6517	12.8996
16	6.5442	-5.7888	5.3269	5.1323	-4.7139	4.3196	0.4622	1.1815	-0.4076	-0.2896	-0.529	0.1588	-0.2008	0.9529	-0.0858	0.3451	-0.0125	-0.0322	0.4112	-0.0504	0.2382	43.058	28.4657	-1.6686
17	2.8241	1.5474	0.5623	4.3242	-0.5329	8.3353	0.063	0.1242	-0.0191	0.0855	0.1076	-0.1637	-0.3293	0.2202	-0.0691	0.1361	-0.0072	-0.0017	0.1312	-0.0117	0.1921	44.3869	31.6444	17.0329
18	9.0458	-1.1756	5.5379	6.0531	-0.4024	3.4172	0.1137	0.1174	0.2173	-0.2755	-0.1814	0.4315	-0.1755	-0.0749	0.1242	0.2437	0.0011	-0.0257	0.1588	0.0046	0.2368	35.6618	37.4375	12.3951
19	8.2951	-4.5814	-5.3537	6.4152	4.3543	4.1343	-0.3877	-0.5753	-0.5651	0.6895	0.1195	0.3388	0.8689	0.1758	0.2866	0.2425	-0.0076	0.0234	0.2313	0.0925	0.2702	12.7296	-2.1779	22.454
20	5.9933	-3.4359	0.0836	2.3683	1.6528	7.4024	0.4616	0.5977	-0.5681	-0.6817	-0.3902	-0.0608	0.991	0.2591	-0.083	0.4029	0.0397	0.0691	0.2683	-0.0479	0.388	17.8621	-4.0862	1.6868

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 40 through 54 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 55 through 73 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 74 through 88 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 89 through 114 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 115 through 123 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 124 through 146 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 147 through 157 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 158 through 165 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 18 through 27 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 28 through 54 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 55 through 62 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 63 through 100 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 101 through 115 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 116 through 130 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 131 through 146 )
16	X-RAY DIFFRACTION	16	chain 'A' and (resid 147 through 156 )
17	X-RAY DIFFRACTION	17	chain 'A' and (resid 157 through 169 )
18	X-RAY DIFFRACTION	18	chain 'A' and (resid 170 through 181 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 1 through 27 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 28 through 39 )

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