PDB-5xv1: Crystal structure of ATG101-ATG13HORMA

ID or keywords:

Entry

Database: PDB / ID: 5xv1

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

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 / : / Macroautophagy / autophagosome assembly ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.508 Å

Authors

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

Citation

Journal: To Be Published
Title: Crystal structure of ATG101-ATG13HORMA
Authors: Kim, B.-W. / 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	Jul 24, 2019	Group: Data collection / Database references / Category: citation / Item: _citation.unpublished_flag
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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Download

PDBx/mmCIF format	5xv1.cif.gz	323.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5xv1.ent.gz	266.8 KB	Display	PDB format
PDBx/mmJSON format	5xv1.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/xv/5xv1 ftp://data.pdbj.org/pub/pdb/validation_reports/xv/5xv1	HTTPS FTP

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Related structure data

Related structure data	5xyuS S: Starting model for refinement
Similar structure data	5xv4-6 5xv4-4 5xv3-2 5xv4-5 5xv4-7 5xv3-1 5xuy-2 5xv4-2 5xv4-3 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 (3)

Deposited unit

A: Autophagy-related protein 13

B: Autophagy-related protein 101

C: Autophagy-related protein 13

D: Autophagy-related protein 101

92.4 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

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

Unit cell

Length a, b, c (Å)	88.483, 125.505, 101.038
Angle α, β, γ (deg.)	90.000, 101.660, 90.000
Int Tables number	5
Space group name H-M	C121

#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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 32 / 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: 58.49 %
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: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5084→50 Å / Num. obs: 36707 / % possible obs: 97.8 % / Redundancy: 3.5 % / R_merge(I) obs: 0.055 / R_pim(I) all: 0.037 / R_rim(I) all: 0.062 / Χ²: 0.755 / Net I/av σ(I): 15.541 / Net I/σ(I): 6 / Num. measured all: 229055

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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: 5XYU

5xyu

Resolution: 2.508→32.984 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.85

	R_factor	Num. reflection	% reflection
R_free	0.2512	1998	5.45 %
R_work	0.2105	-	-
obs	0.2128	36673	99.09 %

Solvent computation

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

Displacement parameters

B_iso max: 224.9 Å² / B_iso mean: 78.872 Å² / B_iso min: 30.25 Å²

Refinement step

Cycle: final / Resolution: 2.508→32.984 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6063	0	0	32	6095
B_iso mean	-	-	-	60.22	-
Num. residues	-	-	-	-	793

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6165
X-RAY DIFFRACTION	f_angle_d	0.926	8356
X-RAY DIFFRACTION	f_chiral_restr	0.051	982
X-RAY DIFFRACTION	f_plane_restr	0.005	1060
X-RAY DIFFRACTION	f_dihedral_angle_d	15.582	3696

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 (%)
2.5084-2.5711	0.3085	128	0.2934	2233	2361	89
2.5711-2.6406	0.3586	144	0.2731	2484	2628	100
2.6406-2.7183	0.3224	143	0.2749	2472	2615	100
2.7183-2.806	0.3535	143	0.2743	2479	2622	100
2.806-2.9062	0.307	143	0.266	2493	2636	100
2.9062-3.0225	0.3287	142	0.2498	2480	2622	100
3.0225-3.1599	0.3116	144	0.2445	2507	2651	100
3.1599-3.3264	0.2603	144	0.2444	2492	2636	100
3.3264-3.5346	0.2999	143	0.2341	2481	2624	100
3.5346-3.8071	0.2432	143	0.2075	2496	2639	100
3.8071-4.1896	0.2201	145	0.1919	2498	2643	100
4.1896-4.7942	0.2091	145	0.1725	2515	2660	100
4.7942-6.0342	0.2212	144	0.1917	2501	2645	100
6.0342-32.9873	0.2138	147	0.1773	2544	2691	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	2.8666	0.5768	0.8012	4.2302	-0.3349	5.7917	-0.0377	-0.003	0.3367	-0.9352	-0.3085	-0.0612	0.7526	-0.063	0.3862	0.577	-0.0366	0.0738	0.4631	0.0181	0.4678	-22.7175	6.9903	225.1096
2	3.6732	2.8197	-0.1488	4.3236	-0.2881	5.3722	0.0798	0.9523	-0.6169	-1.6044	0.2917	0.9827	2.7664	-0.0093	0.3541	1.7186	-0.1449	0.1334	0.6827	-0.0622	0.4577	-26.7018	-4.0639	217.8115
3	1.641	0.7023	-1.2445	1.5224	0.5965	2.3122	-0.1349	0.2903	-0.3738	-0.5733	-0.1322	0.2558	2.1328	-0.3306	0.3595	1.6451	-0.1918	0.0158	0.6794	-0.0449	0.7583	-26.1444	-12.45	230.7605
4	1.635	0.1853	-0.0665	1.867	0.4353	1.8599	-0.3475	-0.8407	-1.4007	0.1646	0.4667	0.6101	1.4381	-1.5653	-0.4044	1.0513	-0.2324	-0.3013	1.3679	-0.0121	1.3535	-44.2543	8.4791	225.144
5	2.3727	0.588	-1.7735	2.6909	1.6368	5.1762	-0.0235	-0.2603	-0.0317	-0.1005	-0.2624	0.2274	1.0174	-0.007	0.4172	0.4758	-0.1262	0.0645	0.4596	-0.0047	0.5189	-24.0927	1.7169	235.3116
6	1.6414	0.5662	-0.6906	2.3003	-0.6733	5.7134	0.2281	-0.7598	-1.2601	-1.3271	0.0531	0.8571	2.6049	-0.286	-0.2601	2.0466	-0.2945	-0.142	0.6198	-0.0943	0.8055	-28.5089	-13.8137	229.5066
7	2.1818	-1.0922	-0.3952	3.6253	1.1539	0.5356	0.1702	-0.7437	-0.6248	0.0258	0.3252	1.4292	1.6122	-1.5237	-0.2133	1.1101	-0.5276	0.0037	0.9955	-0.0576	0.7943	-35.2822	-1.6276	233.2277
8	1.873	0.5346	-1.2936	3.2818	-0.5727	4.4808	0.019	-0.3794	-0.3853	0.4036	0.0415	0.2891	-0.3963	-0.0635	0.0199	0.4479	-0.115	0.0359	0.5248	0.0429	0.4292	-25.8225	8.1083	252.1495
9	2.1061	0.0229	-0.3417	2.3211	-2.2129	3.0398	-0.0483	-0.1497	-0.0611	0.1687	-0.3969	-0.511	-0.2294	0.5998	0.3602	0.3751	-0.0594	-0.0619	0.5071	0.0446	0.4863	-19.394	13.7431	238.3269
10	3.5792	0.1648	-0.686	3.8813	-0.7444	5.7689	0.0543	-0.7801	-0.5528	1.3433	-0.9319	-0.8434	-1.2181	1.2046	0.3312	0.9904	-0.2963	-0.1664	0.7398	0.186	0.5946	-16.0753	14.612	257.148
11	3.4767	1.2166	-1.0133	3.5009	-0.6221	3.4363	0.0188	-0.6445	0.0222	0.7246	0.357	0.5895	-0.7608	-0.5716	0.0779	1.0728	0.0651	0.0881	0.589	-0.0402	0.5225	-29.267	18.2864	254.7368
12	0.2449	0.025	0.0938	4.4363	3.5871	2.957	0.728	0.7633	0.3332	1.9681	-1.3641	0.9019	-2.7408	0.2633	0.0709	2.067	-0.0536	0.0197	0.7471	-0.0376	1.0498	-35.5534	40.7546	250.0433
13	1.4769	-1.0018	-0.8446	6.4209	-2.9206	3.9622	-0.2151	-0.7476	-0.1633	1.4107	0.6812	0.6053	-0.9701	-1.0125	0.1687	0.7661	-0.0416	0.1204	0.7082	-0.1091	0.6135	-28.6624	11.0043	256.2978
14	3.2506	-0.3568	3.3527	5.2558	-1.485	7.6229	-0.0226	-0.7696	-0.485	-0.0295	0.1509	0.3352	0.8636	-0.764	-0.1332	0.5039	-0.0947	0.1887	0.5962	0.0608	0.6162	-24.5409	-2.598	251.8905
15	3.3407	1.003	-0.7029	5.9857	-2.1272	4.6826	0.5263	-0.714	0.724	0.5845	0.317	1.651	-1.9474	-1.3652	-0.4876	1.3113	0.415	0.1689	0.7753	0.0784	0.819	-33.0069	25.42	237.4211
16	2.8987	1.0451	-0.79	5.3697	-0.8319	5.9831	0.4094	0.1584	0.133	0.686	-0.3744	-0.6051	-0.9853	0.2717	-0.502	0.7853	-0.1375	-0.001	0.4775	-0.0447	0.5648	-22.0988	22.9083	239.9697
17	1.2306	0.9323	-1.6431	1.1455	-2.3194	6.1995	0.3857	-0.2481	0.1123	1.3418	-0.0599	0.2064	-1.7122	-0.4182	-0.1107	1.4654	-0.3249	0.1048	0.6988	-0.0879	0.4149	-25.7159	18.2264	257.4287
18	1.6469	0.1606	-1.9469	8.3793	-1.4349	2.6715	0.821	0.202	0.9735	-0.5605	0.0335	1.0577	-0.4853	0.7012	-1.0534	1.5567	0.065	0.0635	0.9203	0.1424	1.1967	-37.1569	5.5091	271.132
19	2.0037	1.2383	-4.2205	7.2789	3.3947	3.6716	-0.1867	0.6333	1.7987	-0.0084	-0.3823	1.3866	-3.2895	-3.459	1.2671	2.3285	0.3659	-0.5101	2.5184	-0.3837	1.2556	-49.6037	-7.0621	270.3741
20	2.9767	-0.7018	0.8689	2.7326	0.275	3.6017	-0.1477	-0.2982	-0.7811	0.1781	-0.04	0.3125	0.1392	-0.4041	0.0571	0.3011	0.0493	0.026	0.4943	0.0209	0.5372	-28.5289	45.7953	221.4646
21	4.2793	-0.3094	-1.0338	1.5329	-2.3879	4.4808	0.072	0.3284	0.1481	0.8587	-0.3862	-2.7213	-0.5962	1.0745	0.4499	0.5026	-0.0958	-0.1298	0.7746	0.1461	0.669	-8.7237	46.0654	216.2929
22	1.338	-1.1343	-1.3823	5.1998	0.1075	1.5713	-0.3546	-0.1102	-0.5783	1.6384	-0.1732	-0.7327	0.26	0.4151	0.4321	0.6283	-0.0423	-0.0318	0.5062	0.0724	0.5225	-18.1759	39.9157	222.1283
23	3.2321	-1.0869	-2.8628	3.6132	0.2143	5.0828	0.5216	-0.2038	0.5141	0.3741	-0.0781	0.1429	-1.2393	-0.1962	-0.3064	0.6754	0.0621	0.0115	0.5232	-0.0064	0.5294	-25.3612	60.0182	219.5227
24	0.0721	0.0904	0.1757	0.0613	0.0939	0.7397	-0.2228	-1.3809	0.0109	0.1017	0.135	0.5112	0.2214	-1.7639	0.3288	0.7317	-0.0258	-0.3126	1.1248	0	1.471	-39.7174	40.464	213.4402
25	1.1278	0.0657	-1.2957	2.316	-1.1942	2.5178	-0.0875	0.3098	0.0134	-0.0388	-0.0927	0.5046	0.1447	-0.1865	0.2388	0.232	0.036	-0.1622	0.4707	-0.0108	0.5386	-24.0218	43.8067	211.2992
26	1.4963	-2.1395	-1.8694	4.2433	0.0448	6.4391	0.6654	-0.261	1.333	0.6457	-0.2597	-0.1137	-1.5669	0.5026	-0.0309	0.8474	-0.1571	0.0954	0.48	-0.0515	0.7818	-14.852	62.4449	214.2544
27	4.3059	0.0763	0.8698	2.4406	0.3272	0.3187	0.7124	0.1085	1.1699	-0.9797	0.1318	2.3574	-0.6599	-1.2957	-0.3387	1.0441	0.2696	0.1479	0.6946	0.145	1.3642	-29.0997	67.6677	208.9803
28	2.0432	-0.4292	0.1718	2.7209	1.936	1.588	-0.303	1.1882	0.6726	-1.4782	0.3109	1.0489	0.1777	-0.8899	-0.1947	0.3909	0.2237	-0.1091	0.8207	0.1259	0.709	-30.7772	52.3354	208.5003
29	1.6274	0.1318	-1.3749	5.3254	-1.8603	3.9184	0.1308	0.1383	-0.0228	-0.6265	-0.2795	-0.0802	0.3234	0.3139	0.1161	0.3314	0.1075	-0.0053	0.4705	0.0803	0.4023	-14.2774	39.948	202.9386
30	1.803	0.2291	1.1345	4.3862	0.9503	0.7381	-0.1926	0.1449	-0.0044	-1.0832	-0.1827	-0.3827	0.4097	0.0948	0.4016	0.9935	0.0841	0.2737	0.6306	-0.002	0.5705	-11.4146	30.9623	192.4445
31	1.7334	0.644	-0.7247	6.0969	1.4671	4.5245	0.2409	0.4346	0.1488	-0.5958	-0.1524	-0.1455	-0.1508	-0.1073	-0.1098	0.6275	0.1441	-0.0667	0.5215	0.0802	0.4353	-14.4057	48.2228	193.3239
32	2.4836	-0.3959	-2.2157	4.0765	-1.2515	6.7596	-0.1702	0.3023	-0.2989	-0.7804	-0.1733	-0.0515	1.3992	-0.4278	0.3981	0.8949	0.0512	0.0554	0.4824	-0.0624	0.5957	-19.7959	28.3191	202.9545
33	0.2935	0.4296	0.3751	1.4659	1.2103	1.1517	-0.6879	-0.6434	0.3217	1.2406	0.4452	0.4737	1.3568	-0.9388	0.3499	1.3639	0.024	0.14	1.1694	0.1073	1.1933	-25.5567	52.2451	172.6019

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 6 through 58 )	A	6 - 58
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 59 through 78 )	A	59 - 78
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 79 through 103 )	A	79 - 103
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 104 through 114 )	A	104 - 114
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 115 through 147 )	A	115 - 147
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 148 through 168 )	A	148 - 168
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 169 through 190 )	A	169 - 190
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 31 )	B	1 - 31
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 32 through 69 )	B	32 - 69
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 70 through 90 )	B	70 - 90
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 91 through 106 )	B	91 - 106
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 107 through 114 )	B	107 - 114
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 115 through 133 )	B	115 - 133
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 134 through 161 )	B	134 - 161
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 162 through 176 )	B	162 - 176
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 177 through 189 )	B	177 - 189
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 190 through 196 )	B	190 - 196
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 197 through 204 )	B	197 - 204
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 205 through 211 )	B	205 - 211
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 6 through 32 )	C	6 - 32
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 33 through 42 )	C	33 - 42
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 43 through 58 )	C	43 - 58
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 59 through 103 )	C	59 - 103
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 104 through 115 )	C	104 - 115
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 116 through 133 )	C	116 - 133
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 134 through 157 )	C	134 - 157
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 158 through 168 )	C	158 - 168
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 169 through 190 )	C	169 - 190
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 1 through 69 )	D	1 - 69
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 70 through 114 )	D	70 - 114
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 115 through 161 )	D	115 - 161
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 162 through 196 )	D	162 - 196
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 197 through 216 )	D	197 - 216

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