PDB-5xv3: Crystal structure of ATG101-ATG13HORMA

ID or keywords:

Entry

Database: PDB / ID: 5xv3

Title

Crystal structure of ATG101-ATG13HORMA

Components

Autophagy-related protein 101
Autophagy-related protein 13

Keywords

PROTEIN BINDING /

AUTOPHAGY /

ATG101 /

ATG13 /

HORMA

Function / homology

Function and homology information

regulation of protein lipidation / Atg1/ULK1 kinase complex / response to mitochondrial depolarisation / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / protein kinase regulator activity / phagophore assembly site / positive regulation of protein targeting to mitochondrion /

Macroautophagy ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.57 Å

Authors

Kim, B.-W. / Song, H.K.

Citation

Journal: Autophagy / Year: 2018
Title: The C-terminal region of ATG101 bridges ULK1 and PtdIns3K complex in autophagy initiation.
Authors: Kim, B.-W. / Jin, Y. / Kim, J. / Kim, J.H. / Jung, J. / Kang, S. / Kim, I.Y. / Kim, J. / Cheong, H. / Song, H.K.

History

Deposition	Jun 26, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 4, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 16, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 22, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5xv3.cif.gz	316.2 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xv/5xv3 ftp://data.pdbj.org/pub/pdb/validation_reports/xv/5xv3	HTTPS FTP

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Related structure data

Related structure data	5xuySC 5xv4C 5xv6C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5xv4-2 5xv4-5 5xv4-1 5xv4-3 5xuy-1 5xv4-6 5xv6-d 6fl3-1 4f48-d 5xv4-8 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
Related items in Molecule of the Month	#203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (5)

Deposited unit

A: Autophagy-related protein 13

B: Autophagy-related protein 101

C: Autophagy-related protein 13

D: Autophagy-related protein 101

hetero molecules

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

1

A: Autophagy-related protein 13

B: Autophagy-related protein 101

defined by author&software
Evidence: gel filtration, 1:1 heterodimer, SAXS, 1:1 heterodimer
46.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Autophagy-related protein 13

D: Autophagy-related protein 101

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.775, 101.116, 125.260
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	Autophagy-related protein 13 / Mass: 21319.652 Da / Num. of mol.: 2 / Fragment: UNP residues 1-190 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATG13, KIAA0652 / Production host: Escherichia coli (E. coli) / References: UniProt: O75143
#2: Protein	Autophagy-related protein 101 / Mass: 24862.424 Da / Num. of mol.: 2 / Mutation: K40A/K41A/E42A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ATG101, C12orf44, PP894 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BSB4
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.96 Å³/Da / Density % sol: 58.5 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1M HEPES (pH7.5), 0.2M MgCl2, 6-8% (w/v) PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SPring-8

/ Beamline: BL26B2 / Wavelength: 1 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Jan 15, 2015

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.57→50 Å / Num. obs: 36347 / % possible obs: 100 % / Redundancy: 8.2 % / B_iso Wilson estimate: 54.38 Å² / R_merge(I) obs: 0.092 / R_pim(I) all: 0.034 / R_rim(I) all: 0.098 / Χ²: 1.058 / Net I/av σ(I): 26.647 / Net I/σ(I): 7.5 / Num. measured all: 299829

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.57-2.61	8.2	0.889	1777	0.939	0.327	0.948	0.727	100
2.61-2.66	8.3	0.879	1794	0.95	0.323	0.937	0.752	100
2.66-2.71	8.4	0.782	1769	0.938	0.286	0.833	0.829	100
2.71-2.77	8.4	0.709	1799	0.971	0.258	0.755	0.771	100
2.77-2.83	8.4	0.552	1800	0.968	0.202	0.588	0.744	100
2.83-2.89	8.4	0.513	1785	0.973	0.187	0.546	0.763	100
2.89-2.97	8.4	0.373	1794	0.988	0.136	0.397	0.772	100
2.97-3.05	8.3	0.302	1798	0.992	0.111	0.322	0.799	100
3.05-3.14	8.4	0.254	1804	0.992	0.093	0.27	0.799	100
3.14-3.24	8.4	0.191	1802	0.994	0.07	0.204	0.813	100
3.24-3.35	8.4	0.146	1808	0.997	0.053	0.155	0.866	100
3.35-3.49	8.3	0.132	1809	0.997	0.049	0.141	1.05	100
3.49-3.65	8.3	0.115	1812	0.997	0.043	0.123	1.236	100
3.65-3.84	8.3	0.101	1807	0.997	0.038	0.108	1.509	100
3.84-4.08	8.2	0.09	1825	0.996	0.034	0.096	1.734	100
4.08-4.39	8.2	0.077	1834	0.998	0.029	0.083	1.932	100
4.39-4.84	8.2	0.059	1838	0.999	0.022	0.063	1.593	100
4.84-5.53	8.2	0.046	1850	0.999	0.017	0.049	1.133	100
5.53-6.97	8.1	0.041	1874	0.999	0.016	0.044	1.045	100
6.97-50	7.6	0.031	1968	0.999	0.012	0.034	1.299	99.1

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Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX	1.10.1_2155	refinement
PDB_EXTRACT	3.2	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5XUY

5xuy

Resolution: 2.57→38.593 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.63

	R_factor	Num. reflection	% reflection
R_free	0.2826	1995	5.51 %
R_work	0.2321	-	-
obs	0.2348	36175	98.76 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 198.17 Å² / B_iso mean: 82.9842 Å² / B_iso min: 30 Å²

Refinement step

Cycle: final / Resolution: 2.57→38.593 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5823	0	7	70	5900
B_iso mean	-	-	85.15	72.37	-
Num. residues	-	-	-	-	774

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	5928
X-RAY DIFFRACTION	f_angle_d	0.766	8046
X-RAY DIFFRACTION	f_chiral_restr	0.045	956
X-RAY DIFFRACTION	f_plane_restr	0.004	1017
X-RAY DIFFRACTION	f_dihedral_angle_d	16.343	3532

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.5501-2.6138	0.3091	125	0.3129	2135	2260	87
2.6138-2.6845	0.3789	140	0.3196	2395	2535	99
2.6845-2.7635	0.4121	142	0.3096	2422	2564	99
2.7635-2.8526	0.3589	142	0.2907	2439	2581	100
2.8526-2.9546	0.3649	142	0.274	2424	2566	100
2.9546-3.0728	0.3391	142	0.2819	2433	2575	100
3.0728-3.2126	0.3004	144	0.2777	2461	2605	100
3.2126-3.3819	0.3195	143	0.2564	2451	2594	100
3.3819-3.5936	0.3311	143	0.2448	2452	2595	100
3.5936-3.8709	0.2733	143	0.2222	2453	2596	100
3.8709-4.2599	0.305	144	0.208	2471	2615	100
4.2599-4.8753	0.2335	145	0.1869	2497	2642	100
4.8753-6.1384	0.2762	148	0.2167	2523	2671	100
6.1384-38.597	0.2154	152	0.2054	2624	2776	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	7.6583	2.0875	-0.1184	8.745	-1.1919	5.4619	0.0908	-0.1742	0.2736	-0.7451	-0.0074	0.8523	-0.6262	0.559	-0.0834	0.6015	0.0284	-0.1502	0.3909	-0.0399	0.3902	-16.6396	21.101	-11.5359
2	9.4309	1.8321	-1.397	2	-2.9223	4.692	0.2263	-0.5448	-0.195	1.357	0.3398	1.1033	0.3384	-1.1756	-0.5661	0.611	0.0501	0.1203	0.561	0.1541	0.647	-34.2788	11.0742	-8.5819
3	2	-0.4502	4.4842	2	-3.2984	9.9473	-0.6431	0.0099	0.6511	0.5588	0.5644	1.5135	-1.8423	-0.8433	0.0787	0.7681	0.1185	0.0616	0.5374	-0.0119	0.4293	-26.5459	19.2923	-20.7317
4	6.1602	2.9592	2.8085	6.8254	1.1917	8.4824	0.038	-0.836	0.9887	0.169	-0.0115	1.5473	-1.4379	-0.9193	-0.0265	1.2992	0.1907	0.106	0.5226	-0.0194	0.6088	-25.804	23.3651	-4.5606
5	6.8844	2.7062	-2.498	7.6225	-4.3175	2	0.244	-1.0425	-0.3701	-0.2066	0.1349	2.2074	0.1292	0.0929	-0.379	1.3721	0.0444	-0.1293	0.6906	-0.0389	0.5796	-18.1291	17.8201	4.6392
6	6.007	1.5825	2.9807	9.9192	0.4064	1.4942	0.4621	-0.8004	-0.1449	-0.1985	-0.1173	2.1832	0.4716	0.6615	-0.3448	1.2344	0.0873	-0.2644	0.6684	-0.0012	0.5333	-16.6519	11.6048	3.3921
7	2.8596	0.6342	-1.5948	2.2182	1.7628	3.0456	-1.1759	0.7079	1.6021	1.018	0.9991	-0.4305	-0.6079	0.3629	0.1767	1.0786	-0.2197	-0.4129	1.1969	0.1096	1.3866	-3.1725	14.8813	-16.8228
8	8.5616	1.9833	-1.3866	7.037	-3.3536	2	-0.1976	0.025	-0.2319	-0.4999	0.5036	0.7056	-0.1116	0.5122	-0.306	0.5199	0.1113	-0.0979	0.5146	-0.0813	0.3739	-18.8789	10.4312	-13.8136
9	3.1605	0.7082	3.7832	9.5372	2.8981	4.9768	0.2178	-0.8171	0.1009	0.9299	0.2568	2.4786	-0.9604	-0.2539	-0.4746	1.5879	0.1127	0.1705	0.7959	0.0789	0.5644	-27.7096	11.0774	4.8652
10	0.793	0.7666	-1.9408	0.741	-1.8761	4.7499	0.6784	-0.0034	-0.1445	-0.9683	-1.2135	1.3487	0.4836	1.7199	0.5351	2.0692	-0.093	-0.2849	1.3174	0.2045	0.7994	-13.7525	8.1426	10.782
11	0.8899	-0.4062	-0.7411	3.8265	1.5601	1.0271	0.1654	-0.7705	-0.4803	-0.8575	-0.5234	0.9636	0.1288	0.8628	0.358	0.9163	0.0667	-0.3952	0.6608	0.0236	0.7241	-12.2392	8.7231	-4.6737
12	1.8371	0.4197	-0.518	9.6129	-5.7372	7.0876	0.0585	-0.0588	-0.1582	0.9304	0.5511	-0.2755	0.6109	-0.3596	-0.6096	0.5156	0.0218	-0.1454	0.5134	0.0367	0.4002	-28.0185	0.1173	-16.589
13	2.4076	1.5619	-1.5191	2	-2.0997	3.083	-0.0983	-0.4473	-0.757	1.8647	0.911	-0.7098	1.3424	-1.232	-0.8127	1.0764	-0.2576	-0.2624	0.7059	0.2491	0.852	-36.3559	-10.9612	-19.9059
14	4.9698	-0.828	0.5796	1.2066	2.3838	5.8245	0.2125	0.3082	-0.1775	-0.3312	0.239	-0.8403	0.0767	0.088	-0.4515	1.2581	0.0154	0.0046	0.4715	-0.0712	0.5448	-20.8697	-11.2328	-31.2573
15	3.4071	0.9315	-1.2293	5.5517	-0.9701	7.077	0.1799	-0.3686	-0.616	0.1278	0.2326	-0.0485	0.8652	-0.0751	-0.4126	0.8254	0.1057	-0.2268	0.5323	0.1004	0.5566	-25.1727	-9.6049	-8.7734
16	3.7739	0.6608	-0.867	6.6751	-2.7799	8.1451	0.1205	0.2748	-0.0436	-0.3553	0.3243	-2.2794	0.7439	-0.0303	-0.4448	1.2626	-0.0133	-0.003	0.6655	-0.0908	0.4545	-22.2806	0.9134	-28.7622
17	4.1864	0.6142	0.3624	3.1248	2.3675	3.1192	-0.6974	1.8282	1.0587	0.5613	0.3222	0.4332	0.4663	1.2106	0.3752	1.7345	-0.0718	0.0067	1.0262	0.2175	0.8118	-15.4862	-28.6932	-9.1623
18	3.1445	-1.0851	-0.4913	7.5456	-1.7613	8.5868	0.188	-0.2044	-0.0445	-0.2349	-0.0834	-0.1364	1.2309	0.3711	-0.1046	0.5057	0.0197	0.0311	0.3278	0.0075	0.3835	-23.2274	23.3743	-49.5491
19	4.3357	-0.3972	-2.8605	6.9834	-1.1415	5.9652	0.2536	0.2972	-0.3088	-0.2347	-0.159	-1.4155	1.2936	0.086	-0.0946	0.8878	0.1014	0.0356	0.4977	-0.0033	0.5381	-20.3869	23.7426	-63.8716
20	8.4448	-3.5197	7.4885	8.3845	-5.8905	2	-1.8141	-1.7294	0.9413	-0.9726	0.3224	1.4584	-1.2692	0.1238	1.4917	1.1242	0.2374	-0.2753	1.4404	0.0325	1.3061	-1.9741	27.6698	-45.8293
21	5.1499	-1.8168	-0.1666	8.3357	-1.0439	6.4679	0.299	-0.032	0.113	-0.1694	-0.0532	-0.6477	0.0806	0.5662	-0.2458	0.307	-0.0682	0.1233	0.4152	0.017	0.3888	-23.3074	33.0645	-54.7235
22	3.1934	0.1928	-3.1358	9.6389	0.7831	6.6461	0.612	1.0784	-0.5517	0.2128	-0.4099	-2.5024	0.962	0.2511	-0.2021	1.3258	0.1253	-0.0271	0.6286	-0.1055	0.458	-23.8237	24.7374	-68.7807
23	2.3235	2.2662	2.1731	4.4634	-2.7641	2	0.5446	2.0383	-0.1976	-1.6044	-1.4254	-2.8221	1.1525	1.0643	0.8808	1.1125	0.3457	0.2575	1.2677	0.1193	0.8075	-13.2897	32.7581	-72.8189
24	5.685	-1.6241	1.9479	3.6071	-1.7815	6.5079	0.2631	0.3722	0.4033	-0.432	-0.261	-0.2534	-0.2259	1.3636	-0.0021	0.5352	0.0674	0.3177	0.8867	0.0424	0.7236	-12.4237	33.1443	-58.3331
25	1.8945	-1.5656	0.6623	8.4054	-4.2713	7.2351	0.0788	-0.0698	0.2305	0.5136	0.3714	0.6525	-1.071	-0.2514	-0.4502	0.3852	0.0751	0.1806	0.422	-0.0045	0.468	-27.9023	41.6192	-45.7944
26	2.242	-0.0589	-0.0102	4.8673	2.5529	1.3392	-0.0565	0.2597	0.5359	1.2605	0.6054	0.9958	-1.4363	-1.138	-0.5489	1.2198	0.3808	0.3033	0.7097	0.1554	0.7522	-35.8292	52.813	-42.2254
27	3.1906	1.3183	-0.9819	0.9197	1.2694	7.7839	0.1265	-0.4263	0.434	-0.186	-0.1393	1.0035	-1.392	0.1628	0.0128	1.382	-0.108	0.0158	0.6025	-0.1114	0.6044	-20.7953	53.0459	-31.4484
28	4.316	-0.4747	1.4466	2.4862	-1.1439	8.5564	0.0298	0.4624	0.1763	-0.088	0.1475	0.5519	-1.8627	0.4268	-0.1773	0.9896	-0.0915	0.1394	0.442	-0.0824	0.696	-23.1217	54.6014	-45.5625
29	6.5313	-2.4496	3.056	2	-3.9924	2	0.2185	0.6467	0.4325	-0.1579	-0.1987	-0.6729	-0.9842	0.3807	-0.0198	0.5045	-0.0308	0.1763	0.4672	0.0438	0.4516	-25.6136	48.9178	-59.0123
30	3.5302	-1.5069	0.8924	2	-2.9895	7.6424	-0.1538	-0.3865	0.1713	-0.4504	0.137	2.5258	-1.0376	0.3288	0.0167	1.0895	-0.049	-0.0034	0.5753	-0.0977	0.4568	-22.2364	41.3242	-33.816
31	9.7725	4.7327	-3.8151	2	-3.7343	9.556	-0.1203	-1.6583	-2.3601	-0.759	-0.8982	1.62	1.0571	1.1278	1.0185	1.3541	0.0486	-0.042	0.711	0.1343	0.7801	-14.9639	70.9874	-54.662

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 31 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 32 through 41 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 42 through 52 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 53 through 69 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 70 through 92 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 93 through 104 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 105 through 114 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 115 through 133 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 134 through 157 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 158 through 168 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 169 through 190 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 3 through 69 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 70 through 89 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 90 through 114 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 115 through 161 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 162 through 196 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 197 through 207 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 6 through 52 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 53 through 104 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 105 through 113 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 114 through 147 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 148 through 157 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 158 through 168 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 169 through 190 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 3 through 69 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 70 through 89 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 90 through 114 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 115 through 133 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 134 through 161 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 162 through 196 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 197 through 207 )

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