PDB-8q6q: Structure of human immunity related GTPase Q in complex with GABA...

ID or keywords:

Entry

Database: PDB / ID: 8q6q

Title

Structure of human immunity related GTPase Q in complex with GABARAPL2.

Components

Gamma-aminobutyric acid receptor-associated protein-like 2
Immunity-related GTPase family Q protein

Keywords

IMMUNE SYSTEM / Complex / Autophagy / Cell autonomous immunity

Function / homology

Function and homology information

negative regulation of proteasomal protein catabolic process / protein localization to endoplasmic reticulum / GABA receptor binding / intra-Golgi vesicle-mediated transport / phosphatidylethanolamine binding / positive regulation of ATP-dependent activity / TBC/RABGAPs / cellular response to nitrogen starvation / autophagy of mitochondrion / Macroautophagy ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Bailey, H.J. / Misra, M. / Pomirska, J. / Dikic, I.

Funding support

Germany, 1items

Citation

Journal: To Be Published
Title: Structure of human immunity related GTPase Q in complex with GABARAPL2.
Authors: Bailey, H.J. / Misra, M. / Pomirska, J. / Dikic, I.

History

Deposition	Aug 14, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 28, 2024	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8q6q.cif.gz	238 KB	Display	PDBx/mmCIF format
PDB format	pdb8q6q.ent.gz	192 KB	Display	PDB format
PDBx/mmJSON format	8q6q.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8q6q_validation.pdf.gz	468.4 KB	Display	wwPDB validaton report
Full document	8q6q_full_validation.pdf.gz	475.2 KB	Display
Data in XML	8q6q_validation.xml.gz	27 KB	Display
Data in CIF	8q6q_validation.cif.gz	38.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q6/8q6q ftp://data.pdbj.org/pub/pdb/validation_reports/q6/8q6q	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
Related items in Molecule of the Month	#203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (3) #252 - Dec 2020 Hepatitis C Virus Protease/Helicase similarity (1) #115 - Jul 2009 beta-Secretase similarity (1)

Deposited unit

A: Gamma-aminobutyric acid receptor-associated protein-like 2

C: Immunity-related GTPase family Q protein

B: Gamma-aminobutyric acid receptor-associated protein-like 2

D: Immunity-related GTPase family Q protein

hetero molecules

66.6 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Gamma-aminobutyric acid receptor-associated protein-like 2

C: Immunity-related GTPase family Q protein

hetero molecules

defined by author&software
Evidence: mass spectrometry
33.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Gamma-aminobutyric acid receptor-associated protein-like 2

hetero molecules

D: Immunity-related GTPase family Q protein

hetero molecules

defined by author&software
33.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	56.100, 64.365, 64.467
Angle α, β, γ (deg.)	60.56, 80.88, 84.77
Int Tables number	1
Space group name H-M	P1

#1: Protein	Gamma-aminobutyric acid receptor-associated protein-like 2 / GABA(A) receptor-associated protein-like 2 / Ganglioside expression factor 2 / GEF-2 / General ...GABA(A) receptor-associated protein-like 2 / Ganglioside expression factor 2 / GEF-2 / General protein transport factor p16 / Golgi-associated ATPase enhancer of 16 kDa / GATE-16 / MAP1 light chain 3-related protein Mass: 13686.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL2, FLC3A, GEF2 / Production host: Escherichia coli (E. coli) / References: UniProt: P60520
#2: Protein	Immunity-related GTPase family Q protein Mass: 19214.754 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IRGQ / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WZA9
#3: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	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: 3.04 Å³/Da / Density % sol: 59.56 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20 % w/v Polyethylene glycol 3,350, 200 mM di-Ammonium hydrogen citrate; pH 5.0

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Data collection

Diffraction	Mean temperature: 123 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.999 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 29, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.999 Å / Relative weight: 1
Reflection	Resolution: 1.8→42.22 Å / Num. obs: 63781 / % possible obs: 88.8 % / Redundancy: 2 % / B_iso Wilson estimate: 27.4 Å² / CC_1/2: 1 / R_merge(I) obs: 0.034 / Net I/σ(I): 9.7
Reflection shell	Resolution: 1.8→1.84 Å / R_merge(I) obs: 0.479 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3677 / CC_1/2: 0.77 / % possible all: 86.4

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→42.22 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.75 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2223	3179	4.99 %
R_work	0.1873	-	-
obs	0.189	63731	88.7 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.8→42.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4256	0	52	321	4629

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015
X-RAY DIFFRACTION	f_angle_d	1.351
X-RAY DIFFRACTION	f_dihedral_angle_d	15.244	633
X-RAY DIFFRACTION	f_chiral_restr	0.089	680
X-RAY DIFFRACTION	f_plane_restr	0.013	802

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 (%)
1.8-1.83	0.3512	146	0.3018	2510	X-RAY DIFFRACTION	86
1.83-1.86	0.3378	129	0.2983	2575	X-RAY DIFFRACTION	85
1.86-1.89	0.2991	115	0.2841	2462	X-RAY DIFFRACTION	83
1.89-1.92	0.3384	118	0.2664	2406	X-RAY DIFFRACTION	81
1.92-1.95	0.2575	101	0.2503	2135	X-RAY DIFFRACTION	72
1.95-1.99	0.2728	120	0.2245	2274	X-RAY DIFFRACTION	78
1.99-2.03	0.2613	161	0.2097	2768	X-RAY DIFFRACTION	92
2.03-2.08	0.2644	148	0.2105	2784	X-RAY DIFFRACTION	93
2.08-2.12	0.2773	183	0.1995	2662	X-RAY DIFFRACTION	93
2.12-2.18	0.2411	174	0.1911	2690	X-RAY DIFFRACTION	92
2.18-2.24	0.2468	151	0.1971	2789	X-RAY DIFFRACTION	93
2.24-2.3	0.267	132	0.1956	2750	X-RAY DIFFRACTION	92
2.3-2.38	0.2779	142	0.2033	2737	X-RAY DIFFRACTION	93
2.38-2.46	0.2599	134	0.1989	2744	X-RAY DIFFRACTION	92
2.46-2.56	0.2597	130	0.2069	2743	X-RAY DIFFRACTION	92
2.56-2.68	0.2774	142	0.2158	2708	X-RAY DIFFRACTION	91
2.68-2.82	0.253	145	0.2098	2705	X-RAY DIFFRACTION	91
2.82-2.99	0.28	92	0.2145	2693	X-RAY DIFFRACTION	90
2.99-3.22	0.2528	122	0.2082	2637	X-RAY DIFFRACTION	88
3.22-3.55	0.2114	88	0.1858	2406	X-RAY DIFFRACTION	80
3.55-4.06	0.1675	135	0.1576	2594	X-RAY DIFFRACTION	87
4.06-5.12	0.1721	208	0.1395	2862	X-RAY DIFFRACTION	99
5.12-42.22	0.1852	163	0.1657	2918	X-RAY DIFFRACTION	99

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	1.5136	-1.0556	0.4979	2.3288	2.2018	5.5499	-0.0592	0.1811	0.0245	-0.065	-0.1835	0.1866	-0.3794	-0.4076	0.2296	0.3034	0.0431	-0.005	0.3651	-0.0696	0.275	-35.1992	19.2408	-25.7745
2	2.8648	0.7541	-0.8748	4.3362	-6.4285	9.6826	-0.2046	-0.0959	0.3293	-0.3608	0.281	0.5057	-0.0152	-0.8599	-0.124	0.3152	0.0891	-0.0662	0.577	-0.1551	0.4121	-41.9714	13.3466	-37.5504
3	1.6757	-0.4728	-1.4557	2.79	1.4145	4.2666	-0.0374	0.0311	0.0822	-0.0124	-0.068	0.0617	-0.0374	-0.1072	0.095	0.258	0.0207	0.0094	0.3601	-0.0529	0.2413	-31.8814	12.0258	-34.4916
4	3.3509	-1.098	-0.0054	5.3041	-1.2877	3.7851	0.1116	0.1752	-0.269	-0.0302	-0.1137	0.2575	0.2877	-0.269	-0.0245	0.2186	-0.0503	0.0321	0.2255	-0.0093	0.2486	-34.3395	17.2202	-0.593
5	6.055	6.5465	-4.8221	7.559	-4.5289	4.8481	-0.1957	-1.2421	-0.8694	0.7129	-0.1908	0.6516	0.2	0.3325	0.4188	0.3325	-0.0082	0.0398	0.5083	-0.0266	0.8043	-43.9164	13.0955	-3.3737
6	3.3179	-0.7627	-0.8682	2.4414	0.6058	1.0044	0.1293	0.0689	-0.3332	0.0609	-0.2479	0.1736	0.002	0.015	0.0963	0.2153	-0.0182	-0.0089	0.2453	0.0043	0.2037	-29.1657	21.8944	-3.4974
7	2.2537	-1.646	-0.9639	7.0895	1.92	7.4745	-0.3281	-0.6345	-0.3758	0.2367	-0.0261	-1.3804	0.8406	0.0766	0.3324	0.3812	-0.0338	-0.002	0.3221	0.0338	0.4309	-18.2521	20.5084	10.4559
8	5.2003	-0.6879	-0.3595	2.1176	0.6842	3.5254	0.0791	-0.0021	0.0502	0.0479	-0.26	0.2311	-0.1539	0.0881	0.1836	0.2121	-0.0275	-0.0063	0.2034	-0.004	0.2502	-28.3689	28.9178	2.3887
9	2.2148	-0.1264	0.9743	0.6505	-0.4003	0.8315	0.6021	0.1263	-0.8138	-0.267	-0.2084	-1.148	1.26	1.0516	-0.2235	0.8364	0.0859	0.1315	0.4683	0.2493	0.8889	-26.1571	13.0562	17.8719
10	5.2731	1.1985	0.4654	4.435	0.0467	3.7098	-0.0132	-0.8156	-0.1801	0.4781	-0.0864	0.1876	0.3116	-0.2552	0.1046	0.2975	-0.0321	0.0727	0.3669	-0.0061	0.2427	-30.0525	24.1945	14.4608
11	3.0961	-2.0783	1.7096	6.5835	-4.466	7.4402	-0.0886	-0.3216	-0.302	0.5162	0.0347	0.6867	-0.3707	-0.5234	-0.0835	0.2473	-0.0182	0.0606	0.3505	-0.0417	0.3414	-43.5146	24.4942	3.062
12	1.0988	0.6315	0.566	7.6176	6.5152	7.8535	0.0068	0.1224	0.0992	0.1744	-0.4731	0.5441	-0.7895	-0.2709	0.4637	0.5956	0.1048	0.0228	0.5229	-0.1418	0.4093	-43.8363	23.4403	-20.4889
13	6.1524	-0.606	0.386	3.4773	0.8398	7.8635	0.1192	0.9834	0.6776	-1.3396	-0.0383	1.2263	0.0352	-0.3284	-0.143	0.3452	0.0012	-0.0787	0.3581	0.0615	0.46	-16.082	-5.1693	-6.6822
14	1.6386	-0.9122	-0.2235	3.4254	-0.3421	1.0375	0.0439	0.0884	0.1259	-0.2538	-0.0721	-0.449	0.1376	0.0471	0.0551	0.2765	0.0187	0.0354	0.2425	0.0193	0.3904	-5.8264	-1.6663	-1.9938
15	4.3626	0.7111	0.804	3.783	-2.8144	2.5389	0.089	0.4514	0.206	-0.2861	-0.1967	-0.6619	-0.0621	0.2644	0.1383	0.3723	0.0414	0.1131	0.3163	0.0732	0.4712	-2.2561	11.0937	-4.7769
16	3.8119	-0.9682	0.2236	2.5186	0.2664	3.5676	0.1111	0.3396	0.3148	-0.1214	0.0761	-0.1982	-0.2802	-0.0502	-0.2203	0.3124	0.0125	0.0389	0.2253	0.0672	0.371	-10.1955	13.0594	-1.4627
17	3.5416	3.7496	1.0299	6.2274	2.1284	3.004	0.0419	0.0687	-0.0048	0.5557	0.0096	0.4234	-0.0547	-0.039	-0.0379	0.3205	0.0502	-0.0054	0.2283	0.0435	0.3994	-9.9512	-0.2221	6.9479
18	3.9054	-1.5244	0.736	4.1887	-0.8387	2.636	0.1334	0.2911	0.1137	-0.4827	-0.0488	0.4533	-0.2433	-0.4193	-0.102	0.3893	0.0303	0.0527	0.3201	0.0146	0.3903	-16.0385	10.5857	-6.0339
19	1.9273	0.1498	-0.1499	3.2777	-0.5209	3.9321	0.0596	-0.2929	0.1784	0.1042	-0.0321	-0.3034	0.01	0.3082	-0.023	0.2821	0.0253	-0.0364	0.2968	-0.049	0.2451	-9.0473	9.9357	-45.3643
20	4.7923	5.4548	-0.51	6.333	-0.05	3.1873	0.2738	-1.1565	1.0771	0.3401	-0.035	-0.3139	0.0254	0.8532	-0.1722	0.3133	-0.0292	-0.0217	0.4194	-0.0821	0.3495	-6.8164	14.0855	-45.8424
21	3.3786	-0.4543	-0.9497	2.9536	0.3638	1.0831	-0.0034	-0.0614	-0.0293	0.1227	-0.0244	0.0585	0.0045	-0.1146	0.0499	0.2082	-0.0173	-0.0354	0.2346	-0.0159	0.182	-18.2999	3.3267	-49.7391
22	1.1974	0.254	1.3362	0.0831	0.2218	2.5187	-0.2626	-1.5937	0.4665	1.5257	0.4535	0.7514	-0.7855	-1.5254	-0.1189	0.6817	0.1016	-0.0148	0.8999	-0.0332	0.3815	-15.4277	-5.1585	-31.8121
23	5.5989	0.4078	0.0421	4.0174	-0.575	4.0142	0.056	-0.4581	-0.3745	0.2539	-0.054	-0.2374	0.1519	0.2511	-0.016	0.2855	0.035	-0.024	0.2526	0.0182	0.2691	-12.0391	-6.5792	-43.3758
24	2.3952	-0.8363	-1.3393	4.2717	-0.39	1.5429	0.1187	-0.062	0.2948	-0.3289	-0.2579	-0.6175	-0.1312	0.2045	0.1628	0.2106	-0.0227	-0.0133	0.2578	-0.0499	0.2973	-1.1422	11.5406	-53.7533

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 56 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 57 through 67 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 68 through 117 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 5 through 28 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 29 through 55 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 56 through 82 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 83 through 93 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 94 through 115 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 116 through 123 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 124 through 158 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 159 through 178 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 179 through 189 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 1 through 10 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 11 through 56 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 57 through 68 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 69 through 90 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 91 through 104 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 105 through 117 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 4 through 28 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 29 through 62 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 63 through 115 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 116 through 123 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 124 through 158 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 159 through 190 )

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