PDB-5cx3: Crystal structure of FYCO1 LIR in complex with LC3A

ID or keywords:

Entry

Database: PDB / ID: 5cx3

Title

Crystal structure of FYCO1 LIR in complex with LC3A

Components

FYVE and coiled-coil domain-containing protein 1
Microtubule-associated proteins 1A/1B light chain 3A

Keywords

PROTEIN BINDING / autophagy adaptor

Function / homology

Function and homology information

plus-end-directed vesicle transport along microtubule / cellular response to oxygen-glucose deprivation / SMAD protein signal transduction / autophagy of mitochondrion / phosphatidylethanolamine binding / positive regulation of autophagosome maturation / cellular response to nitrogen starvation / response to iron(II) ion / Receptor Mediated Mitophagy / Macroautophagy ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.3 Å

Authors

Cheng, X. / Pan, L.

Funding support

China, 2items

Citation

Journal: Autophagy / Year: 2016
Title: Structural basis of FYCO1 and MAP1LC3A interaction reveals a novel binding mode for Atg8-family proteins.
Authors: Cheng, X. / Wang, Y. / Gong, Y. / Li, F. / Guo, Y. / Hu, S. / Liu, J. / Pan, L.

History

Deposition	Jul 28, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 10, 2016	Group: Database references / Structure summary
Revision 1.2	Aug 17, 2016	Group: Database references
Revision 1.3	Jan 8, 2020	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5cx3.cif.gz	246.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5cx3.ent.gz	203 KB	Display	PDB format
PDBx/mmJSON format	5cx3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5cx3_validation.pdf.gz	498.4 KB	Display	wwPDB validaton report
Full document	5cx3_full_validation.pdf.gz	513.6 KB	Display
Data in XML	5cx3_validation.xml.gz	24.1 KB	Display
Data in CIF	5cx3_validation.cif.gz	32.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cx/5cx3 ftp://data.pdbj.org/pub/pdb/validation_reports/cx/5cx3	HTTPS FTP

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Related structure data

Similar structure data	6hyq-1 6hyq-4 6h4g-1 3me8-d 6nl1-d 4r3a-2 6lzk-1 1kkh-d 4jgg-d 6hyq-3 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	#87 - Mar 2007 Zinc Fingers similarity (5) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (2) #60 - Dec 2004 Ubiquitin similarity (2) #141 - Sep 2011 O-GlcNAc Transferase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1)

Deposited unit

A: Microtubule-associated proteins 1A/1B light chain 3A

B: Microtubule-associated proteins 1A/1B light chain 3A

C: Microtubule-associated proteins 1A/1B light chain 3A

D: Microtubule-associated proteins 1A/1B light chain 3A

E: FYVE and coiled-coil domain-containing protein 1

F: FYVE and coiled-coil domain-containing protein 1

G: FYVE and coiled-coil domain-containing protein 1

H: FYVE and coiled-coil domain-containing protein 1

hetero molecules

70.9 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Microtubule-associated proteins 1A/1B light chain 3A

C: Microtubule-associated proteins 1A/1B light chain 3A

E: FYVE and coiled-coil domain-containing protein 1

G: FYVE and coiled-coil domain-containing protein 1

hetero molecules

defined by author&software
35.4 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Microtubule-associated proteins 1A/1B light chain 3A

D: Microtubule-associated proteins 1A/1B light chain 3A

F: FYVE and coiled-coil domain-containing protein 1

H: FYVE and coiled-coil domain-containing protein 1

hetero molecules

defined by author&software
35.4 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	35.426, 115.257, 73.517
Angle α, β, γ (deg.)	90.00, 102.29, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Microtubule-associated proteins 1A/1B light chain 3A / Autophagy-related protein LC3 A / Autophagy-related ubiquitin-like modifier LC3 A / MAP1 light ...Autophagy-related protein LC3 A / Autophagy-related ubiquitin-like modifier LC3 A / MAP1 light chain 3-like protein 1 / MAP1A/MAP1B light chain 3 A / MAP1A/MAP1B LC3 A / Microtubule-associated protein 1 light chain 3 alpha Mass: 14293.451 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H492
#2: Protein/peptide	FYVE and coiled-coil domain-containing protein 1 / Zinc finger FYVE domain-containing protein 7 Mass: 3376.661 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FYCO1, ZFYVE7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQS8
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.72 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 1.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES sodium PH range: 6.9-8.0

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97945 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97945 Å / Relative weight: 1
Reflection	Resolution: 2.3→50 Å / Num. obs: 25680 / % possible obs: 99.1 % / Redundancy: 3 % / Net I/σ(I): 16.9

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Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
HKL-2000		data reduction
HKL-2000		data scaling
REFMAC	5.7.0029	phasing

Refinement

Resolution: 2.3→34.615 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.02 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2445	1235	5.14 %
R_work	0.1776	-	-
obs	0.1811	24033	93.77 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.3→34.615 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4551	0	12	95	4658

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4703
X-RAY DIFFRACTION	f_angle_d	1.161	6353
X-RAY DIFFRACTION	f_dihedral_angle_d	16.347	1841
X-RAY DIFFRACTION	f_chiral_restr	0.053	698
X-RAY DIFFRACTION	f_plane_restr	0.006	841

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 (%)
2.3-2.3921	0.3257	95	0.2252	1741	X-RAY DIFFRACTION	64
2.3921-2.501	0.3096	110	0.2308	2338	X-RAY DIFFRACTION	87
2.501-2.6328	0.272	151	0.2147	2623	X-RAY DIFFRACTION	98
2.6328-2.7976	0.3223	153	0.2248	2649	X-RAY DIFFRACTION	99
2.7976-3.0135	0.2997	144	0.2066	2676	X-RAY DIFFRACTION	99
3.0135-3.3166	0.3004	149	0.1967	2676	X-RAY DIFFRACTION	99
3.3166-3.796	0.2367	148	0.1688	2688	X-RAY DIFFRACTION	100
3.796-4.7805	0.1833	142	0.1351	2679	X-RAY DIFFRACTION	99
4.7805-34.6186	0.1914	143	0.152	2728	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	5.3278	4.5936	-4.2716	4.307	-2.7563	5.6709	-0.3012	0.0696	0.0572	-0.3282	0.1437	-0.041	0.5315	0.6591	0.1734	0.3953	0.0423	-0.004	0.4293	-0.0195	0.2325	20.6115	-30.1926	62.5532
2	5.6202	1.0069	1.2808	3.9899	1.1711	3.1744	0.0775	0.0139	0.0159	0.3019	-0.0109	-0.0844	-0.1563	0.0356	-0.0798	0.2232	0.0268	0.0319	0.2307	0.0444	0.1704	22.3536	-23.095	78.0553
3	5.3337	-4.0608	-5.6141	3.2663	3.4185	8.9745	-0.4508	0.1789	-0.2798	0.1892	0.1976	0.1691	0.6101	-0.2219	0.2225	0.4101	0.0315	0.0277	0.5016	0.0804	0.3053	31.9632	-29.0221	50.6025
4	2.4448	-2.0825	-0.037	3.8457	-0.3836	3.6246	0.0808	0.1254	-0.3478	-0.3105	-0.0762	0.1933	0.098	-0.1584	-0.0717	0.2503	-0.0448	-0.0218	0.3685	-0.0363	0.2223	30.594	-23.2648	35.5804
5	2.4471	4.0569	0.8895	7.6753	3.2065	5.4829	-0.1546	0.2647	-0.1668	-0.4555	0.0231	0.8258	-0.3915	-0.4946	0.0458	0.2792	0.018	-0.0789	0.4319	-0.027	0.3237	28.1089	-14.9971	33.0781
6	4.7939	-1.367	-0.9761	6.4714	-1.4393	4.6008	-0.0742	-0.3952	0.076	-0.0122	0.1233	-0.1393	-0.498	0.3218	0.0083	0.2492	-0.0179	0.0402	0.3213	-0.1106	0.178	30.8681	-16.0671	41.6181
7	1.2665	1.1708	1.3617	6.3575	-1.8738	4.1466	0.5199	-0.0643	0.0919	-0.2143	-0.167	0.4861	0.1925	-0.3508	-0.3541	0.3297	0.011	0.07	0.3346	-0.0318	0.4364	21.0762	11.3615	69.7107
8	1.7272	0.8895	-1.2304	8.585	-0.2985	7.3132	0.0572	-0.0464	-0.0166	1.1103	-0.1798	0.1866	-0.1863	-0.0784	0.1146	0.4654	0.0043	0.0059	0.2344	0.0602	0.5576	26.8878	4.3742	82.5066
9	3.0434	-0.5935	-2.2643	2.0666	2.5017	5.9803	-0.1235	-0.0589	0.3573	0.6291	0.0035	0.3642	0.3813	0.4091	0.0349	0.6386	-0.0361	0.1818	0.263	0.0026	0.4393	26.4303	-4.2124	84.4869
10	2.7913	1.4031	0.0238	4.2042	-4.3274	5.2676	-0.1297	0.2086	0.0863	0.0644	-0.0173	-0.1006	0.173	0.2411	0.0188	0.4132	-0.0045	0.0903	0.2559	-0.0377	0.4653	26.081	-2.2691	76.0038
11	4.1413	-6.2307	-4.5733	9.4994	6.9492	5.0907	0.1086	-0.306	0.9709	-0.9247	0.4104	-2.2625	-0.2613	1.167	-0.5161	0.4761	0.0356	0.2066	0.5579	-0.0793	0.7571	38.1669	10.7273	48.547
12	3.9954	3.9952	4.1215	7.9278	0.9948	8.5652	-0.627	-1.3018	0.6344	-0.1206	-0.1651	0.0175	-0.5067	-0.1741	0.7196	0.4923	0.072	0.0075	0.5013	-0.029	0.3621	26.2127	13.5704	55.964
13	2.4715	-1.6549	-2.6688	7.4688	3.5944	7.3952	0.3684	0.3201	0.1771	-1.3503	-0.0435	-0.2616	-1.3809	-0.4029	-0.2402	0.6958	0.0741	0.0113	0.3284	0.0095	0.4169	26.7138	8.8418	40.3135
14	3.6076	3.7421	-2.221	5.4503	0.3491	6.3171	0.6867	0.4776	0.3526	-2.0415	-0.6642	1.0198	-0.1081	-0.6475	-0.119	1.23	0.4278	-0.1231	0.5314	-0.1139	0.5963	20.6877	7.6193	33.6048
15	2.9435	0.4966	-0.56	2.3537	-2.4547	8.4757	0.3035	0.2997	0.164	-0.5306	-0.3625	-0.0058	-0.2214	-0.5365	0.3269	0.7005	0.2152	0.031	0.3745	-0.0855	0.4386	25.6458	0.6154	34.693
16	3.8655	3.4242	4.1153	9.4635	5.0403	4.6902	0.1915	-0.8686	-0.9128	0.394	-1.1609	0.9812	0.8292	-1.5007	1.0824	0.585	0.0853	0.1892	0.6423	-0.0258	0.5314	19.4024	0.0702	49.1503
17	3.1793	-0.8914	-1.647	5.5761	6.2035	7.7009	0.033	-0.0525	-0.0353	-0.3159	0.178	-0.0159	-0.1948	0.0785	-0.2659	0.5009	0.0571	0.0911	0.2794	0.0667	0.3359	29.5439	0.557	40.7541
18	2.1629	-0.9464	-1.1383	3.1504	1.5466	7.0441	0.1439	0.7417	-0.4697	0.2594	-0.1639	-0.9954	0.5362	0.538	-0.0182	0.3533	0.1313	-0.0291	0.533	0.0312	0.5613	24.0162	-35.5009	74.2536
19	4.6944	-1.6479	3.2611	4.8781	-2.8594	2.9492	0.3737	-2.2006	1.0808	2.023	-1.3276	0.002	-0.605	-0.7552	0.8053	0.699	-0.2003	0.1294	0.9383	-0.1118	0.4611	12.9323	-33.2423	89.7296
20	4.9443	5.0869	-5.2583	5.4839	-5.5559	5.6949	-0.3637	0.5001	-0.7169	-0.7775	-0.0088	0.8795	1.1399	-0.4186	0.5384	0.4147	0.005	0.0608	0.387	-0.0403	0.5354	31.6671	-32.4158	38.5197
21	2.8924	0.179	-1.7157	3.6777	-3.3104	3.8347	-1.1088	1.0953	-1.4806	-0.4437	0.0272	-0.4134	0.9412	0.255	0.9079	0.5508	0.0071	0.0401	0.5522	-0.0951	0.4945	38.2773	-26.8165	24.6023
22	9.8316	6.9758	-6.3	5.2661	-4.3157	4.1104	1.3568	-0.9288	0.5957	2.4953	-1.1134	0.6003	-0.1862	0.5166	-0.1159	0.6347	-0.1441	0.0241	0.5404	-0.0705	0.3777	43.3434	-13.935	18.6926
23	7.3531	-6.814	6.9968	6.3409	-6.5008	6.6674	-0.2786	-1.3789	0.7886	1.2561	0.2944	-0.4625	-0.4029	-0.9464	0.227	0.4752	0.0155	-0.1057	0.4743	-0.0198	0.5277	26.3551	14.4413	80.0789
24	8.8357	-4.2616	3.0319	4.2421	-3.6153	3.2153	-0.6931	-0.1341	0.1323	0.8222	-0.6716	-1.1348	-0.1901	0.0494	1.735	0.7761	-0.042	-0.0873	0.7527	0.124	0.7098	39.2888	6.6748	90.456
25	9.6579	4.4548	-0.6346	3.8029	0.8351	0.9458	-0.3361	-0.9575	-0.6203	-1.1682	0.1581	-0.1053	0.6022	-0.0538	0.0051	1.7684	0.5986	-0.197	1.0323	0.3185	1.1262	24.5928	17.5166	43.2194
26	4.1207	2.6649	3.9209	2.5935	1.9152	4.1602	0.8613	-0.3827	-0.8909	-0.3623	0.1381	0.2708	-1.0651	-0.7099	-0.9007	1.0493	0.2452	-0.0489	1.158	-0.0004	0.8481	12.8937	13.686	32.79

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 26 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 27 through 121 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 4 through 26 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 27 through 70 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 71 through 94 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 95 through 121 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 3 through 26 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 27 through 71 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 72 through 94 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 95 through 121 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 5 through 12 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 13 through 26 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 27 through 59 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 60 through 70 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 71 through 94 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 95 through 102 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 103 through 121 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 1273 through 1284 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 1285 through 1292 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 1276 through 1284 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 1285 through 1292 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 1293 through 1300 )
23	X-RAY DIFFRACTION	23	chain 'G' and (resid 1276 through 1284 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 1285 through 1294 )
25	X-RAY DIFFRACTION	25	chain 'H' and (resid 1277 through 1284 )
26	X-RAY DIFFRACTION	26	chain 'H' and (resid 1285 through 1292 )

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