PDB-9jcw: Crystal structure of human MIGA1 LD targeting domain

ID or keywords:

Entry

Database: PDB / ID: 9jcw

Title

Crystal structure of human MIGA1 LD targeting domain

Components

Mitoguardin 1

Keywords

LIPID BINDING PROTEIN / LD targeting domain / MIGA1

Function / homology

Function and homology information

Synthesis of PA / mitochondrial fusion / mitochondrial outer membrane / protein heterodimerization activity / protein homodimerization activity / mitochondrion / plasma membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Yang, K.L. / Zhang, L.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: Structural basis for mitoguardin-1 mediated lipid transport at ER-mitochondrial membrane contact sites.
Authors: Yang, K.L. / Zhang, L.

History

Deposition	Aug 30, 2024	Deposition site: PDBJ / Processing site: PDBC
Revision 1.0	Mar 11, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9jcw.cif.gz	627.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9jcw.ent.gz	525.5 KB	Display	PDB format
PDBx/mmJSON format	9jcw.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/jc/9jcw ftp://data.pdbj.org/pub/pdb/validation_reports/jc/9jcw	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	#239 - Nov 2019 Phospholipase A2 similarity (1)

Deposited unit

C: Mitoguardin 1

F: Mitoguardin 1

A: Mitoguardin 1

E: Mitoguardin 1

B: Mitoguardin 1

D: Mitoguardin 1

hetero molecules

184 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: light scattering

Unit cell

Length a, b, c (Å)	88.645, 157.782, 163.907
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Mitoguardin 1 / Protein FAM73A Mass: 30112.723 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MIGA1, FAM73A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NAN2
#2: Chemical	ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL Mass: 691.959 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃₇H₇₄NO₈P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.17 Å³/Da / Density % sol: 61.22 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: potassium chloride,Ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 24, 2023
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.6→50.08 Å / Num. obs: 71396 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC_1/2: 0.999 / Net I/σ(I): 22.6
Reflection shell	Resolution: 2.6→2.66 Å / Num. unique obs: 4518 / CC_1/2: 0.757

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Processing

Software

Name	Version	Classification
PHENIX	(1.19_4092: ???)	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.6→50.08 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 24.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.244	3709	5.2 %
R_work	0.2105	-	-
obs	0.2122	71313	99.9 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.6→50.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12175	0	235	72	12482

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	12673
X-RAY DIFFRACTION	f_angle_d	0.74	17098
X-RAY DIFFRACTION	f_dihedral_angle_d	17.931	4647
X-RAY DIFFRACTION	f_chiral_restr	0.046	1885
X-RAY DIFFRACTION	f_plane_restr	0.004	2174

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 (%)
2.6-2.63	0.3324	135	0.2692	2545	X-RAY DIFFRACTION	100
2.63-2.67	0.3167	153	0.2537	2556	X-RAY DIFFRACTION	100
2.67-2.71	0.2991	164	0.2456	2526	X-RAY DIFFRACTION	100
2.71-2.75	0.3309	134	0.2461	2595	X-RAY DIFFRACTION	100
2.75-2.79	0.2925	137	0.2483	2567	X-RAY DIFFRACTION	100
2.79-2.84	0.3252	135	0.2687	2592	X-RAY DIFFRACTION	100
2.84-2.89	0.3405	132	0.2966	2587	X-RAY DIFFRACTION	100
2.89-2.94	0.3559	158	0.2851	2554	X-RAY DIFFRACTION	100
2.94-3	0.334	137	0.2644	2557	X-RAY DIFFRACTION	100
3-3.06	0.297	158	0.248	2608	X-RAY DIFFRACTION	100
3.06-3.12	0.3013	147	0.2478	2550	X-RAY DIFFRACTION	100
3.12-3.2	0.2843	129	0.2365	2583	X-RAY DIFFRACTION	100
3.2-3.28	0.2726	144	0.2459	2603	X-RAY DIFFRACTION	100
3.28-3.36	0.2801	139	0.2489	2582	X-RAY DIFFRACTION	100
3.36-3.46	0.2869	151	0.2346	2580	X-RAY DIFFRACTION	100
3.46-3.57	0.256	138	0.2203	2595	X-RAY DIFFRACTION	100
3.57-3.7	0.2586	129	0.2132	2625	X-RAY DIFFRACTION	100
3.7-3.85	0.2277	143	0.2046	2604	X-RAY DIFFRACTION	100
3.85-4.03	0.2311	126	0.1929	2623	X-RAY DIFFRACTION	100
4.03-4.24	0.2214	109	0.1883	2643	X-RAY DIFFRACTION	100
4.24-4.5	0.1898	145	0.1742	2606	X-RAY DIFFRACTION	100
4.5-4.85	0.2137	134	0.1745	2628	X-RAY DIFFRACTION	100
4.85-5.34	0.2257	173	0.1939	2607	X-RAY DIFFRACTION	100
5.34-6.11	0.2485	149	0.22	2658	X-RAY DIFFRACTION	100
6.11-7.69	0.2597	138	0.2252	2684	X-RAY DIFFRACTION	100
7.69-50.08	0.1768	172	0.1701	2746	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	4.931	-0.8003	1.8949	2.2139	0.0747	3.7938	-0.0631	0.473	0.3482	-0.103	0.0082	-0.3594	-0.2619	0.6838	0.0709	0.5084	-0.1743	-0.0283	0.5308	-0.0048	0.3844	-38.3039	-58.1037	-18.2317
2	3.656	-0.41	-2.8112	0.072	-0.0526	4.8536	-0.0023	-0.2683	-0.0015	0.2297	0.0369	0.2639	-0.4428	0.0079	-0.0679	0.529	-0.1514	-0.0056	0.5084	-0.0468	0.4124	-52.1878	-56.8963	-5.8027
3	2.105	1.8118	-0.0408	5.1758	-0.0326	6.0498	-0.0456	0.9127	-0.7513	-0.2025	0.1459	-0.2633	0.6538	0.1218	-0.2378	0.6428	-0.0468	-0.0808	0.5376	-0.054	0.4422	-37.8168	-72.4995	-20.4864
4	3.4375	0.8538	-0.9969	3.7922	0.0254	5.6901	-0.2519	0.831	-0.0808	-0.4275	0.5725	0.5529	0.6824	-2.5869	-0.1898	1.1328	-0.6254	-0.0229	1.7571	0.2483	0.7138	-64.9028	-94.6215	-14.9903
5	3.5727	0.4895	2.8674	3.4714	1.8925	3.2269	0.2792	0.0601	-0.9685	-0.6735	0.0697	-0.491	1.4553	-0.8981	-0.2592	1.6504	-0.6135	0.0878	0.9408	-0.0333	0.7874	-53.3348	-103.0461	-17.5005
6	7.3482	2.0923	0.7798	3.4216	-0.967	6.0767	-0.164	0.236	-0.5656	-0.6047	0.3965	-0.606	1.4943	-0.2816	-0.3529	1.1219	0.0012	-0.1218	0.5898	-0.0372	0.7362	-38.5362	-102.1136	0.3592
7	5.1881	3.6211	2.28	5.6923	1.7824	1.165	0.0029	-0.0323	-0.8105	-0.267	-0.3581	-0.5778	1.7696	-0.7351	0.4164	1.5589	-0.3716	-0.0852	0.7481	-0.1446	1.0378	-46.0287	-105.1159	-12.8635
8	6.8183	0.4543	0.7478	5.744	-1.05	6.2759	0.0546	-0.2766	0.2974	-0.1625	0.3994	0.2285	0.5185	-1.876	-0.4951	0.8281	-0.349	-0.0319	1.006	0.0819	0.4537	-56.7684	-85.4151	-14.2007
9	5.57	0.7179	-2.4472	2.7882	-0.9942	4.9496	0.0337	-0.9487	0.3093	0.4112	-0.0116	-0.0669	-0.3877	0.3359	-0.0372	0.3824	0.0517	-0.0721	0.48	-0.1142	0.4699	-23.055	-56.8559	37.3949
10	2.4256	-0.1625	1.473	-0.0187	-0.4169	7.5132	-0.1435	0.157	0.274	-0.2113	0.0606	0.0888	-0.2723	-0.3442	0.0722	0.3541	0.0356	-0.0428	0.4203	-0.0478	0.4781	-28.3688	-56.3768	19.2506
11	8.713	-1.8775	-4.0965	6.4333	3.1859	2.1931	-0.2339	-0.8779	-0.4694	0.5772	0.2397	-0.3529	0.0949	0.1586	-0.0127	0.4303	0.0293	-0.0974	0.6095	-0.0042	0.6409	-21.4781	-71.1617	38.4203
12	4.7214	0.9228	-0.2023	3.887	-0.1118	2.9166	0.2468	-0.7018	-0.2253	0.567	-0.1824	-0.2722	0.2437	0.2064	-0.0533	0.4793	-0.0122	0.0185	0.4209	0.0871	0.351	-65.8933	-97.1775	41.662
13	2.5838	1.0095	-0.9275	0.6554	0.3446	6.7385	-0.2466	0.3024	-0.2612	-0.4578	0.1889	-0.196	0.5675	0.2311	0.054	0.5152	0.0598	0.07	0.4384	0.0603	0.4287	-63.7873	-98.8001	22.8642
14	6.541	-1.1342	6.4591	7.39	-2.5435	7.5167	0.1834	-0.6424	0.6555	0.5899	-0.1135	0.0194	-0.0038	-0.6351	0.0861	0.4821	-0.0351	0.1737	0.5427	-0.0156	0.508	-67.17	-83.1488	42.2351
15	2.5966	-0.3996	-1.2485	6.0116	0.121	5.7282	0.1042	0.4246	0.2503	-0.4804	0.0172	0.3112	-0.4768	-0.8706	-0.0967	0.3682	0.1138	0.0099	0.5227	0.0941	0.4871	-78.7873	-58.5517	21.2137
16	2.618	-3.0695	0.8764	0.6391	-0.5406	1.2558	0.0118	0.4274	1.0367	0.0653	0.0247	-0.5542	-0.5125	0.1882	-0.0544	0.5182	-0.0377	-0.0094	0.5631	0.0668	1.0557	-59.5973	-51.9092	28.8352
17	5.1891	-0.53	2.8529	5.1158	0.2437	9.5961	-0.0477	0.0035	-0.4366	-0.2012	0.0143	-0.0397	0.2634	-0.5242	0.0441	0.3691	0.046	0.1262	0.3562	0.0368	0.5334	-74.6188	-71.5065	23.0311
18	2.4233	2.5784	-0.9349	4.3372	-3.9349	5.79	0.3997	0.1333	0.0858	-0.0872	-1.0736	0.1242	-0.1684	-0.3986	0.5925	0.9649	-0.0087	-0.0786	1.4216	-0.6839	1.1138	-17.4493	-101.0187	3.2198
19	3.9374	0.1782	4.8857	6.5707	1.1855	6.1682	0.2996	0.9094	-0.2324	-1.6288	0.3224	-1.3409	0.6078	1.0243	-0.311	1.1569	-0.2224	0.3959	1.3115	-0.5117	1.277	-14.0897	-91.7991	6.7327
20	3.5743	-0.3131	1.0439	9.3936	1.2629	3.7778	-0.0995	0.439	-1.2066	0.5152	0.6098	-0.7476	0.6442	0.9194	-0.5354	0.6419	0.1735	-0.067	0.7393	-0.3427	1.1563	-14.623	-99.1066	24.2119
21	7.222	-0.5694	-0.2158	0.0545	0.7499	2.8301	0.1833	0.0263	-1.7878	0.1004	0.287	-0.3552	0.9172	0.1162	-0.4441	0.7699	0.0237	0.0447	0.587	-0.1032	1.4411	-31.6295	-102.7373	27.2028
22	6.8191	0.4553	0.0881	7.7786	-0.1635	5.5436	-0.5586	0.5924	-0.3137	-0.6572	0.511	-0.5268	-0.2169	0.4359	0.0028	0.5183	-0.0508	0.0638	0.4681	-0.1947	0.7701	-17.9837	-83.9559	19.3194

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 351 through 481 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 482 through 570 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 571 through 606 )
4	X-RAY DIFFRACTION	4	chain 'F' and (resid 352 through 422 )
5	X-RAY DIFFRACTION	5	chain 'F' and (resid 423 through 481 )
6	X-RAY DIFFRACTION	6	chain 'F' and (resid 482 through 518 )
7	X-RAY DIFFRACTION	7	chain 'F' and (resid 519 through 546 )
8	X-RAY DIFFRACTION	8	chain 'F' and (resid 547 through 606 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 351 through 472 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 473 through 570 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 571 through 606 )
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 349 through 472 )
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 473 through 570 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 571 through 606 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 351 through 481 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 482 through 546 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 547 through 606 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 362 through 371 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 372 through 401 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 402 through 481 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 482 through 546 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 547 through 606 )

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