PDB-6aag: Crystal structure of budding yeast Atg8 complexed with the helica...

ID or keywords:

Entry

Database: PDB / ID: 6aag

Title

Crystal structure of budding yeast Atg8 complexed with the helical AIM of Hfl1.

Components

Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8

Keywords

MEMBRANE PROTEIN / VACUOLE AUTOPHAGY

Function / homology

Function and homology information

Cvt vesicle membrane / autophagosome membrane / autophagy / protein transport / membrane => GO:0016020 / endoplasmic reticulum
Similarity search - Function

Biological species

Saccharomyces cerevisiae (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.445 Å

Authors

Yamasaki, A. / Noda, N.N.

Funding support

Japan, 1items

Citation

Journal: Elife / Year: 2018
Title: Lipidation-independent vacuolar functions of Atg8 rely on its noncanonical interaction with a vacuole membrane protein
Authors: Liu, X.M. / Yamasaki, A. / Du, X.M. / Coffman, V.C. / Ohsumi, Y. / Nakatogawa, H. / Wu, J.Q. / Noda, N.N. / Du, L.L.

History

Deposition	Jul 18, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 12, 2018	Provider: repository / Type: Initial release
Revision 1.1	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	6aag.cif.gz	396.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6aag.ent.gz	327 KB	Display	PDB format
PDBx/mmJSON format	6aag.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6aag_validation.pdf.gz	467.8 KB	Display	wwPDB validaton report
Full document	6aag_full_validation.pdf.gz	477.9 KB	Display
Data in XML	6aag_validation.xml.gz	36.1 KB	Display
Data in CIF	6aag_validation.cif.gz	49.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aa/6aag ftp://data.pdbj.org/pub/pdb/validation_reports/aa/6aag	HTTPS FTP

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Related structure data

Related structure data	6aafC 2zpnS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5yu5-d 6kmf-d 3eka-d 4371 2yw0-d 2c3f-d 2yx2-d 2946 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 (2)

Deposited unit

A: Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8

B: Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8

C: Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8

D: Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8

E: Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8

F: Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8

G: Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8

113 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8

B: Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8

C: Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8

F: Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8

D: Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8

E: Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8

G: Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8

defined by author&software
Evidence: isothermal titration calorimetry
113 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	90.468, 61.650, 100.112
Angle α, β, γ (deg.)	90.00, 96.37, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8 / Autophagy-related ubiquitin-like modifier ATG8 / Cytoplasm to vacuole targeting protein 5 Mass: 16191.364 Da / Num. of mol.: 7 / Mutation: K26P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Saccharomyces cerevisiae (strain YJM789) (yeast) Strain: ATCC 204508 / S288c, YJM789 / Gene: YKR051W, ATG8, APG8, AUT7, CVT5, SCY_0144 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P36142, UniProt: A6ZKM4
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Transmembrane protein 184 homolog YKR051W,Autophagy-related protein 8 / Autophagy-related ubiquitin-like modifier ATG8 / Cytoplasm to vacuole targeting protein 5

Mass: 16191.364 Da / Num. of mol.: 7 / Mutation: K26P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.)

Saccharomyces cerevisiae (strain YJM789) (yeast)
Strain: ATCC 204508 / S288c, YJM789 / Gene: YKR051W, ATG8, APG8, AUT7, CVT5, SCY_0144 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P36142, UniProt: A6ZKM4

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.45 Å³/Da / Density % sol: 49.76 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 6% PEG6000, 0.1 M sodium citrate pH 5.0

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Data collection

Diffraction	Mean temperature: 95 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.445→45.73 Å / Num. obs: 40557 / % possible obs: 99.6 % / Redundancy: 3.3 % / R_merge(I) obs: 0.112 / Net I/σ(I): 6.5
Reflection shell	Resolution: 2.45→2.49 Å / R_merge(I) obs: 0.647 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2002 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2ZPN

2zpn

Resolution: 2.445→45.73 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.11

	R_factor	Num. reflection	% reflection
R_free	0.2442	2010	4.96 %
R_work	0.1928	-	-
obs	0.1954	40501	98.97 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.445→45.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7664	0	0	195	7859

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	7872
X-RAY DIFFRACTION	f_angle_d	0.79	10712
X-RAY DIFFRACTION	f_dihedral_angle_d	14.285	4815
X-RAY DIFFRACTION	f_chiral_restr	0.054	1156
X-RAY DIFFRACTION	f_plane_restr	0.007	1413

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 (%)
2.4447-2.5058	0.3036	128	0.2732	2529	X-RAY DIFFRACTION	92
2.5058-2.5736	0.3607	142	0.2863	2749	X-RAY DIFFRACTION	99
2.5736-2.6493	0.3356	131	0.2779	2721	X-RAY DIFFRACTION	99
2.6493-2.7348	0.3319	132	0.2698	2779	X-RAY DIFFRACTION	99
2.7348-2.8326	0.3241	150	0.2518	2719	X-RAY DIFFRACTION	100
2.8326-2.9459	0.3416	146	0.2616	2773	X-RAY DIFFRACTION	100
2.9459-3.08	0.2838	139	0.2502	2751	X-RAY DIFFRACTION	100
3.08-3.2423	0.2846	135	0.2337	2790	X-RAY DIFFRACTION	100
3.2423-3.4454	0.265	159	0.2146	2725	X-RAY DIFFRACTION	100
3.4454-3.7113	0.2522	172	0.1883	2718	X-RAY DIFFRACTION	100
3.7113-4.0846	0.2006	140	0.1706	2811	X-RAY DIFFRACTION	100
4.0846-4.6751	0.2085	137	0.1417	2791	X-RAY DIFFRACTION	100
4.6751-5.8882	0.1889	149	0.1516	2795	X-RAY DIFFRACTION	99
5.8882-45.7397	0.2011	150	0.1575	2840	X-RAY DIFFRACTION	98

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	4.3241	-1.449	-1.2459	5.2119	1.5766	4.4268	-0.2073	0.1074	-0.6307	0.7004	-0.0035	0.18	0.3018	-0.0754	0.2711	0.3789	-0.0614	-0.0774	0.3668	-0.0353	0.3833	192.0597	18.044	26.3255
2	5.6789	0.1687	1.5533	0.0015	0.0107	0.389	0.2151	2.7837	-0.5302	0.0587	0.4318	0.05	-0.4025	0.151	-0.6247	0.4273	0.0783	0.0163	0.8865	0.0095	0.5167	219.0555	27.0521	19.6918
3	3.6818	2.2524	0.6631	5.3039	-1.0603	2.9024	0.0145	0.5142	0.5768	0.1808	0.0588	0.0041	-0.2452	0.3603	-0.0871	0.2846	0.042	0.0179	0.4421	0.0604	0.5634	226.1356	37.0601	30.9913
4	4.6957	0.4037	1.9841	2.777	-0.4899	2.3322	0.1425	0.2695	-0.4613	0.0188	-0.0183	-0.2293	0.3091	0.2482	-0.1243	0.3288	0.0294	-0.0102	0.3777	-0.0402	0.4063	222.7087	23.5914	37.2151
5	5.764	-0.5713	-0.1352	6.427	-0.1472	5.9828	-0.3034	0.8327	-0.4218	-1.141	0.2227	-0.1326	0.1729	-0.0095	0.0768	0.3802	-0.0205	-0.0244	0.472	-0.0353	0.2466	175.7694	21.3107	-0.7269
6	0.1803	0.2159	0.7836	0.2942	-0.0298	4.5703	-0.7335	-0.3172	0.2499	-0.4047	-0.2677	0.8417	-0.455	-0.9106	1.1141	0.6642	0.059	-0.0898	0.4105	-0.1618	0.67	184.2349	36.987	22.4511
7	5.2704	-1.6674	0.699	2.0496	-2.7291	3.6442	-0.4278	-0.8358	0.5004	0.8476	0.3222	0.4305	0.5899	-0.3308	0.311	0.565	0.0403	0.111	0.6088	-0.1066	0.494	188.4999	32.8585	38.7525
8	4.0959	-0.4486	1.1529	1.7381	0.9273	5.0039	-0.013	0.1255	-0.1274	0.0336	0.0544	-0.0727	-0.0236	0.0751	-0.0801	0.3778	-0.0049	-0.0152	0.2192	-0.0255	0.3407	197.883	24.3199	23.678
9	3.0454	-0.5089	1.7928	6.0218	5.0102	2.0915	-0.1561	0.3945	0.7883	-0.2208	0.0821	0.0597	-1.0236	0.8224	0.2149	0.4423	-0.0327	-0.0883	0.4639	0.1026	0.4935	198.8702	32.6679	24.7846
10	2.1368	-0.2222	-1.0119	2.1542	1.3613	5.7046	-0.061	-0.0207	0.3852	-0.1795	-0.0625	0.2559	-0.8033	-1.0258	0.2105	0.4622	0.1141	-0.1311	0.5862	-0.1336	0.5551	148.8224	34.8589	-9.6005
11	0.0114	-0.0857	0.1302	-0.0315	0.217	1.7535	-0.2102	-0.6182	-0.9726	-0.1571	0.4467	0.4024	0.3359	-0.9829	-0.0653	0.5156	-0.1346	0.0711	0.6823	0.1785	0.607	158.6372	15.4302	10.8026
12	2.3387	-0.6582	0.1773	3.0047	0.1959	2.6729	0.0586	-0.118	-0.5011	-0.1371	-0.1745	0.0619	0.5031	0.1058	0.1135	0.4524	-0.0361	-0.0288	0.3036	0.0097	0.4594	174.3385	9.7249	8.3974
13	3.8412	-0.6793	0.9206	3.5796	-0.5518	2.5616	-0.1118	-0.0888	0.1805	0.0163	-0.0413	0.108	-0.0275	-0.1473	0.1205	0.3198	-0.0416	0.0053	0.3229	-0.0102	0.2976	173.914	25.0574	9.8526
14	1.2233	1.6733	-0.8378	7.8577	-2.169	4.803	0.2124	-0.5987	0.0979	0.8645	-0.459	0.0796	-0.5032	-0.1838	0.2739	0.4943	-0.1423	-0.0545	0.565	-0.0822	0.4041	194.0305	-3.0411	55.3921
15	0.1268	0.2305	0.3172	0.2371	0.3583	0.4706	-0.3929	0.7366	-0.4056	-0.0956	0.2925	-0.4484	-0.0138	1.2529	-0.116	0.4086	0.0101	0.0765	0.818	0.0218	0.4897	188.3245	-3.005	26.5835
16	4.8735	1.8254	0.9199	3.439	1.5329	4.6332	0.1544	1.0696	-0.6841	-0.201	0.3505	-0.3016	0.5732	0.6947	-0.2903	0.392	0.0418	-0.1071	0.5734	-0.1109	0.4877	176.6679	-14.0533	21.6445
17	7.8108	-3.9328	-0.9396	2.0631	0.9219	2.0081	-0.1237	0.42	1.0629	-0.0521	0.3623	-0.4273	-0.0159	1.1914	-0.4034	0.4381	-0.0298	-0.0362	0.4767	-0.08	0.3572	180.8487	-0.9131	35.6762
18	7.2008	1.1859	1.9247	3.8999	1.5327	5.395	0.0965	0.0656	0.7032	0.1548	-0.172	0.3872	-0.1142	-0.1243	0.0509	0.2567	0.0052	0.0084	0.2734	-0.0151	0.3593	169.3546	-5.2176	31.278
19	8.9759	-2.4415	-1.5728	4.8625	2.2831	6.1743	-0.2995	-0.8994	-0.7559	-0.1568	0.0636	0.1767	0.3123	0.5173	0.0012	0.5867	0.1383	-0.1275	0.4799	-0.0095	0.417	179.8917	-16.7072	30.6069
20	9.0074	-0.2247	-2.3221	7.4304	2.6021	8.1223	0.019	-1.6377	0.4077	0.5706	-0.0145	0.6987	0.7151	0.2974	0.029	0.3841	-0.0176	0.0916	0.6678	-0.039	0.3382	164.2384	-9.3688	40.2044
21	4.1062	0.6256	1.4905	0.6791	0.3606	5.6381	-0.5826	-1.1762	1.0514	0.7366	-0.2733	1.0066	-0.3656	0.506	0.3782	0.6688	0.2212	0.0255	0.5524	-0.0896	1.1022	152.8322	8.4141	30.246
22	4.9011	-0.3479	1.5071	2.8049	0.1041	3.3478	-0.2524	0.3413	0.9499	-0.0844	0.2466	0.3252	-0.2957	-0.1079	0.0264	0.2633	-0.0344	-0.005	0.3858	0.0847	0.5665	145.8555	-1.3074	19.7127
23	2.5454	1.2705	-3.0079	5.8563	-1.4598	4.507	0.0371	0.1493	0.0577	-0.0154	0.6267	0.3101	-0.1508	-0.9842	-0.6721	0.2701	-0.0333	-0.1035	0.5217	0.0172	0.506	216.147	32.7364	39.5663
24	3.7171	-1.3407	0.5596	1.0307	-0.3751	0.7071	-0.0656	0.7523	-0.901	-0.6976	0.1288	0.176	0.59	0.0541	-0.0292	0.6771	0.0349	0.0375	0.4907	-0.1592	0.7706	242.5647	9.7921	44.5437
25	5.2703	-1.0916	1.5824	3.7842	0.4173	3.1789	0.0013	0.2424	-0.0043	-0.0679	-0.138	0.1138	0.114	0.0872	0.1452	0.3325	0.0131	-0.0118	0.2702	0.0191	0.2491	246.0629	23.1631	52.6941
26	1.9831	1.0954	-0.2768	6.4532	-0.4993	3.7426	-0.3367	0.484	0.4401	-0.5141	0.0948	-0.7505	-0.233	0.467	0.2199	0.3272	0.0093	0.0029	0.5377	0.1103	0.689	153.4623	-3.4999	13.3482
27	7.1056	0.2662	0.6447	0.0102	0.0216	-0.0775	0.1685	-0.7831	-1.0846	0.0166	0.1446	0.0264	-0.0324	-0.2258	-0.3889	0.4196	-0.0722	0.0254	0.6143	0.1231	0.5821	127.2628	-13.4665	22.3337
28	1.9663	-1.4079	0.0268	2.0294	-1.7258	3.2899	0.2665	-0.6751	0.192	0.188	-0.5182	0.2548	-0.0869	-0.4314	0.284	0.561	-0.0432	-0.0452	0.6674	-0.0938	0.4131	110.9733	-3.6924	23.6941
29	3.7016	-0.7291	0.849	2.2713	0.0053	3.4956	0.1976	0.1827	-0.0218	-0.1432	-0.3381	-0.1307	-0.0007	0.3688	0.1172	0.2997	-0.0029	-0.0286	0.4456	0.0435	0.4216	120.5411	-4.2921	6.777
30	7.8554	0.0246	-4.4647	4.0113	0.6095	7.4193	0.1823	0.3504	0.5011	-0.0299	0.0952	-0.4269	0.5315	-0.2846	-0.3083	0.3603	0.02	-0.0666	0.4834	0.0849	0.3845	117.4538	-10.7729	10.3296

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -22 through -3 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid -2 through 10 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 11 through 35 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 36 through 114 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid -22 through -3 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid -2 through 10 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 11 through 24 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 25 through 98 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 99 through 115 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid -22 through -3 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid -2 through 10 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 11 through 35 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 36 through 116 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid -22 through -3 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid -2 through 10 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 11 through 35 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 36 through 47 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 48 through 114 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid -22 through -13 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid -12 through -2 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid -1 through 10 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 11 through 114 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid -23 through -4 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid -3 through 24 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 25 through 114 )
26	X-RAY DIFFRACTION	26	chain 'G' and (resid -23 through -4 )
27	X-RAY DIFFRACTION	27	chain 'G' and (resid -3 through 10 )
28	X-RAY DIFFRACTION	28	chain 'G' and (resid 11 through 24 )
29	X-RAY DIFFRACTION	29	chain 'G' and (resid 25 through 98 )
30	X-RAY DIFFRACTION	30	chain 'G' and (resid 99 through 114 )

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