PDB-4nxt: Crystal structure of the cytosolic domain of human MiD51

ID or keywords:

Entry

Database: PDB / ID: 4nxt

Title

Crystal structure of the cytosolic domain of human MiD51

Components

Mitochondrial dynamic protein MID51

Keywords

TRANSFERASE /

nucleotidyltransferase /

protein-protein interaction /

ADP / GDP /

mitochondrial fission /

mitochondria / membrane-anchored

Function / homology

Function and homology information

mitochondrial fission / positive regulation of mitochondrial fission / positive regulation of protein targeting to membrane /

ADP binding / GDP binding / cellular response to hypoxia / mitochondrial outer membrane /

mitochondrion / identical protein binding
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.12 Å

Authors

Richter, V. / Ryan, M.T. / Kvansakul, M.

Citation

Journal: J.Cell Biol. / Year: 2014
Title: Structural and functional analysis of MiD51, a dynamin receptor required for mitochondrial fission.
Authors: Richter, V. / Palmer, C.S. / Osellame, L.D. / Singh, A.P. / Elgass, K. / Stroud, D.A. / Sesaki, H. / Kvansakul, M. / Ryan, M.T.

History

Deposition	Dec 9, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 25, 2013	Provider: repository / Type: Initial release
Revision 1.1	Mar 19, 2014	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nx/4nxt ftp://data.pdbj.org/pub/pdb/validation_reports/nx/4nxt	HTTPS FTP

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Related structure data

Related structure data	4nxuC 4nxvC 4nxwC 4nxxC C: citing same article (ref.)
Similar structure data	4gqo-3 6s93-d 6wo0-d 7apv-d 7af1-d 5aq9-3 3ldf-d 2zyo-d 3obj-d 1jw4-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Mitochondrial dynamic protein MID51

B: Mitochondrial dynamic protein MID51

C: Mitochondrial dynamic protein MID51

D: Mitochondrial dynamic protein MID51

hetero molecules

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

1

A: Mitochondrial dynamic protein MID51

hetero molecules

defined by author&software
39 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Mitochondrial dynamic protein MID51

hetero molecules

defined by author&software
38.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Mitochondrial dynamic protein MID51

hetero molecules

defined by author&software
39.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Mitochondrial dynamic protein MID51

hetero molecules

defined by author&software
39.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	72.720, 78.735, 79.362
Angle α, β, γ (deg.)	66.26, 84.93, 64.07
Int Tables number	1
Space group name H-M	P1

#1: Protein	Mitochondrial dynamic protein MID51 / Mitochondrial dynamic protein of 51 kDa / Mitochondrial elongation factor 1 / Smith-Magenis ...Mitochondrial dynamic protein of 51 kDa / Mitochondrial elongation factor 1 / Smith-Magenis syndrome chromosomal region candidate gene 7 protein-like Mass: 38822.656 Da / Num. of mol.: 4 / Fragment: unp residues 119-463 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) Gene: candidate 7-like, MID51, MIEF1, SMCR7L, Smith-Magenis syndrome chromosome region Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9NQG6
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.4 Å³/Da / Density % sol: 48.65 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16% PEG 8000, 0.1M HEPES, 10% 2-propanol, 0.2M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 21, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.12→40.67 Å / Num. obs: 79550 / % possible obs: 97.3 % / Redundancy: 2.7 % / B_iso Wilson estimate: 32 Å² / R_merge(I) obs: 0.066 / Net I/σ(I): 11
Reflection shell	Resolution: 2.12→2.23 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.5 / Mean I/σ(I) obs: 2.8 / Num. unique all: 79550

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
XDS		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.12→39.007 Å / SU ML: 0.28 / σ(F): 1.96 / Phase error: 28.41 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2626	3964	4.98 %	random
R_work	0.2228	-	-	-
obs	-	79549	97.3 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.12→39.007 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10276	0	75	527	10878

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	10587
X-RAY DIFFRACTION	f_angle_d	0.802	14442
X-RAY DIFFRACTION	f_dihedral_angle_d	13.591	3888
X-RAY DIFFRACTION	f_chiral_restr	0.031	1676
X-RAY DIFFRACTION	f_plane_restr	0.004	1846

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 (%)
2.12-2.1459	0.334	148	0.2995	2695	X-RAY DIFFRACTION	97
2.1459-2.173	0.3151	146	0.3011	2651	X-RAY DIFFRACTION	97
2.173-2.2016	0.3391	142	0.2889	2713	X-RAY DIFFRACTION	97
2.2016-2.2318	0.3311	153	0.2858	2715	X-RAY DIFFRACTION	97
2.2318-2.2636	0.329	145	0.2824	2660	X-RAY DIFFRACTION	97
2.2636-2.2974	0.3025	132	0.2662	2694	X-RAY DIFFRACTION	98
2.2974-2.3333	0.2644	118	0.2693	2781	X-RAY DIFFRACTION	98
2.3333-2.3716	0.3049	128	0.2569	2687	X-RAY DIFFRACTION	98
2.3716-2.4125	0.2933	151	0.2537	2720	X-RAY DIFFRACTION	98
2.4125-2.4563	0.3026	122	0.2628	2724	X-RAY DIFFRACTION	98
2.4563-2.5036	0.2959	146	0.2575	2723	X-RAY DIFFRACTION	97
2.5036-2.5547	0.2967	146	0.2536	2678	X-RAY DIFFRACTION	98
2.5547-2.6102	0.2706	131	0.2472	2771	X-RAY DIFFRACTION	98
2.6102-2.6709	0.2683	147	0.2386	2670	X-RAY DIFFRACTION	98
2.6709-2.7377	0.2659	145	0.2496	2727	X-RAY DIFFRACTION	98
2.7377-2.8117	0.2769	130	0.2515	2757	X-RAY DIFFRACTION	98
2.8117-2.8944	0.2781	147	0.2398	2679	X-RAY DIFFRACTION	98
2.8944-2.9878	0.2939	149	0.2299	2714	X-RAY DIFFRACTION	98
2.9878-3.0945	0.241	132	0.223	2708	X-RAY DIFFRACTION	98
3.0945-3.2184	0.2795	160	0.2216	2704	X-RAY DIFFRACTION	97
3.2184-3.3648	0.2816	146	0.2233	2673	X-RAY DIFFRACTION	97
3.3648-3.542	0.2582	144	0.2163	2683	X-RAY DIFFRACTION	97
3.542-3.7638	0.2559	139	0.2007	2719	X-RAY DIFFRACTION	97
3.7638-4.0541	0.2367	144	0.1987	2628	X-RAY DIFFRACTION	96
4.0541-4.4616	0.2255	128	0.1809	2697	X-RAY DIFFRACTION	96
4.4616-5.106	0.2346	146	0.1875	2651	X-RAY DIFFRACTION	96
5.106-6.4283	0.276	159	0.2203	2699	X-RAY DIFFRACTION	98
6.4283-39.0139	0.2114	139	0.1975	2665	X-RAY DIFFRACTION	96

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	6.2852	1.1381	0.1279	0.2618	0.0563	2.9245	-0.0938	-0.2647	-0.6231	-0.531	0.1289	-0.875	0.18	0.3586	-0.169	0.3742	0.0379	0.165	0.5212	-0.0046	0.7911	12.2573	4.2348	5.8776
2	5.1203	2.285	-5.5965	1.0147	-2.3175	5.7687	0.7773	-0.8074	0.0749	0.1507	-0.3703	-0.055	-0.4309	0.5116	-0.3546	0.3418	-0.0619	0.0332	0.391	-0.1026	0.3863	-17.0461	20.8941	20.2611
3	5.213	-0.0495	-5.499	3.0704	-0.62	6.8979	-0.1739	-0.7508	-0.3416	0.0823	-0.0249	-0.3049	-0.0233	0.7059	0.2584	0.2332	-0.0355	-0.0186	0.4103	-0.1123	0.3246	-17.0537	11.9718	17.3156
4	6.6228	-1.281	-1.7982	0.3341	0.6048	1.4298	-0.3133	0.536	-1.3067	0.0842	0.0364	0.0887	0.3749	-0.0159	0.3232	0.421	0.0096	0.0931	0.372	-0.1583	0.4283	-29.1446	-2.3978	13.4213
5	7.4198	4.6854	-1.3715	5.7237	-0.0067	4.0956	-0.1134	0.7693	0.0777	-0.1344	0.1274	0.2921	0.0833	-0.2355	-0.0337	0.2152	0.0426	-0.0311	0.421	-0.0247	0.2679	-38.5958	5.471	13.3703
6	3.6519	-3.2636	-2.5876	9.1471	-0.9736	3.605	-0.0256	1.1232	0.3206	-1.0739	0.1112	0.1623	-0.8318	-0.4842	-0.0637	0.4164	0.0283	-0.0115	0.4811	0.0754	0.5021	-22.2045	24.8517	10.6171
7	3.8007	1.7972	0.5282	6.2164	1.4139	3.0544	-0.3014	0.7388	-0.0249	-0.5993	0.1632	-0.0823	-0.0297	0.0994	0.0781	0.2329	0.0357	0.0235	0.4517	-0.0494	0.2479	-20.9317	7.5725	9.1582
8	5.1111	1.0951	-1.2435	3.9187	0.8986	3.1845	0.0293	-0.0143	-0.5441	-0.2008	-0.1796	-0.6827	0.0798	0.1529	0.145	0.2939	0.0384	0.1115	0.3669	-0.0119	0.5574	-2.3881	-3.6473	5.1428
9	7.5026	1.8717	-4.4237	2.8396	-2.9662	4.6853	0.2537	-0.2379	0.6207	0.2433	0.0916	0.4963	-0.1721	-0.1719	-0.3793	0.3018	-0.0008	0.03	0.3777	-0.0679	0.3249	-10.195	-22.8962	-6.1701
10	1.79	-1.5909	0.3617	3.6368	-0.4696	0.9082	-0.0625	-0.2179	-0.4317	-0.0522	0.273	0.5567	-0.0399	-0.2803	-0.1434	0.3063	-0.0383	0.0225	0.4207	0.0616	0.4378	-11.8818	-42.5878	-4.8736
11	3.3683	1.6522	-1.1216	3.7953	-1.1275	2.2441	0.0709	0.0087	0.0666	-0.0733	-0.064	-0.0546	-0.0425	0.0678	-0.0031	0.1915	0.0104	0.0493	0.2826	-0.0054	0.266	7.9572	-26.6505	-14.2965
12	2.639	-3.8764	-1.7551	7.9347	3.1896	3.7393	0.146	-0.8887	0.7444	-0.1254	0.6326	-1.7541	-0.6408	0.4664	-0.6731	0.4835	-0.1348	0.1021	0.5898	-0.2733	0.7028	57.9703	41.5188	54.5704
13	3.837	2.784	2.5162	4.3731	3.6031	6.7764	0.228	0.2825	-0.2876	0.1323	0.127	-0.5891	0.4279	0.4144	-0.3257	0.2426	0.0305	0.0297	0.381	0.0457	0.286	53.9443	16.7653	37.1498
14	3.0768	1.0656	-0.5867	2.283	1.6498	2.1982	-0.057	0.4349	-0.1793	0.1547	-0.0575	0.2678	0.2061	-0.2065	0.1252	0.2948	0.0059	0.0201	0.3509	0.0216	0.2515	31.8517	10.0295	36.483
15	7.6768	1.4729	6.7112	2.2755	0.6546	6.0965	0.4726	-0.0605	-0.9881	0.4834	-0.0748	-0.484	0.9399	-0.1685	-0.3566	0.4707	0.0404	-0.0184	0.4917	0.1381	0.6245	57.1792	6.3049	44.3181
16	5.736	0.4007	-0.1102	3.1439	0.5191	0.5745	0.0276	-0.2859	0.249	0.3289	-0.1443	-0.3526	0.106	0.228	0.0654	0.3111	-0.0063	-0.0319	0.3521	0.0511	0.2556	46	16.609	45.2112
17	0.5986	0.9287	0.7563	4.3192	2.9162	2.3756	0.106	-0.0952	0.1481	-0.3211	0.0659	-0.1072	-0.3696	0.2526	-0.2563	0.2903	0.0023	0.0828	0.3729	-0.0132	0.3624	44.4129	32.3303	45.3612
18	2.5619	1.3871	0.7475	8.9302	0.9212	4.085	0.0526	-0.1487	0.3697	0.01	0.0534	0.4149	-0.607	0.0256	-0.1208	0.3329	-0.0264	0.1042	0.2653	-0.0424	0.288	38.4722	39.4729	48.4136
19	5.016	2.5307	-1.9473	2.6225	1.2476	4.1305	0.5057	-0.5586	0.2247	1.7685	-0.4295	0.3088	0.5293	-0.145	-0.1903	0.7545	-0.0578	0.0362	0.4096	-0.0476	0.3884	41.3251	37.161	63.856
20	4.0609	-5.3507	-2.9298	7.1544	4.2226	4.1951	0.507	-0.3029	1.0666	-0.005	-0.4391	-0.3558	-1.2204	0.0939	-0.2168	0.8647	-0.0512	0.1746	0.4906	0.089	1.0972	69.407	58.6223	30.3993
21	6.8509	-4.8837	-5.0183	5.0586	5.8523	6.8782	0.0773	0.0191	0.7597	-1	0.5873	-0.6604	-0.937	0.6803	-0.7604	0.6848	-0.1921	0.1565	0.5294	0.0013	0.6908	94.1165	45.8002	15.8047
22	7.8445	-2.7739	-2.8813	5.5229	2.934	4.4306	-0.0024	0.596	-0.2367	0.0128	-0.2225	0.3654	-0.3098	-0.0218	0.0457	0.4985	-0.0592	0.1582	0.4233	0.0891	0.4471	87.4665	40.0477	18.7216
23	2.8071	-1.4056	-2.191	6.6645	3.4641	5.1441	-0.0841	0.0849	-0.7588	0.2662	-0.3061	0.0736	0.2969	-0.0094	0.2867	0.2697	0.0622	0.0391	0.426	0.0464	0.5894	82.5472	22.1074	21.7055
24	4.7288	-3.2711	-1.362	5.4147	4.541	5.9981	-0.1182	0.1023	0.2989	1.0682	0.7843	-0.7293	0.6497	0.3494	-0.4736	0.4507	0.1662	0.169	0.5117	0.1216	1.0068	92.8693	13.6268	18.7374
25	2.2914	-1.0099	-1.9438	3.5693	-0.3835	2.0424	-0.1077	-0.1856	-0.2196	0.8505	0.3844	-1.6112	-0.4076	0.8934	-0.4007	0.6173	-0.1036	-0.0508	0.8294	-0.064	1.0621	100.6706	38.6381	23.3924
26	7.1476	4.7688	2.218	3.2614	1.9458	6.7433	0.2871	-0.2991	0.4093	0.8215	-0.1984	-0.2078	-0.8518	0.4488	-0.0351	0.6814	-0.0253	0.1218	0.5311	-0.0882	0.5985	91.8236	42.8041	25.5303
27	6.2745	1.1925	0.809	3.2468	0.6305	5.7648	-0.0685	-0.275	-0.1028	0.0585	0.4486	-0.2267	-0.3783	-0.346	-0.3853	0.432	0.0339	0.1447	0.4308	0.0166	0.4324	76.5323	31.7987	24.2135
28	6.8908	2.18	1.8466	4.6633	0.5482	5.3991	0.4112	-0.0159	1.501	0.0049	-0.2247	-0.1155	-0.5629	-0.6	-0.3499	0.5213	0.0821	0.273	0.4192	0.1049	0.8573	71.2716	47.3712	31.8327
29	4.1796	0.3497	-1.2808	3.8793	0.8367	5.5257	0.3009	-0.1516	0.8919	0.2005	-0.0981	0.4465	-0.4357	-0.2484	-0.2361	0.4195	0.0241	0.1949	0.4547	-0.0017	0.5824	64.6429	41.1047	34.4279

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 125 through 150 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 151 through 175 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 176 through 200 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 201 through 235 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 236 through 271 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 272 through 296 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 297 through 341 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 342 through 461 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 132 through 200 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 201 through 333 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 334 through 462 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 132 through 150 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 151 through 200 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 201 through 271 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 272 through 296 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 297 through 333 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 334 through 381 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 382 through 439 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 440 through 462 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 133 through 150 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 151 through 175 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 176 through 200 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 201 through 235 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 236 through 258 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 259 through 289 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 290 through 318 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 319 through 356 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 357 through 381 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 382 through 462 )

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