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

ID or keywords:

Entry

Database: PDB / ID: 4nxv

Title

Crystal structure of the cytosolic domain of human MiD51

Components

Mitochondrial dynamic protein MID51

Keywords

TRANSFERASE / protein-nucleotide complex / nucleotidyltransferase / protein-protein interaction / ADP / GDP / membrane-anchored / mitochondrial fission / mitochondria

Function / homology

Function and homology information

positive regulation of mitochondrial fusion / mitochondrial fission / positive regulation of mitochondrial fission / positive regulation of protein targeting to membrane / ADP binding / GDP binding / mitochondrial outer membrane / mitochondrion / identical protein binding
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

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

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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Download

PDBx/mmCIF format	4nxv.cif.gz	760.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4nxv.ent.gz	643.8 KB	Display	PDB format
PDBx/mmJSON format	4nxv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4nxv_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	4nxv_full_validation.pdf.gz	1.7 MB	Display
Data in XML	4nxv_validation.xml.gz	51.3 KB	Display
Data in CIF	4nxv_validation.cif.gz	70.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nx/4nxv ftp://data.pdbj.org/pub/pdb/validation_reports/nx/4nxv	HTTPS FTP

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Related structure data

Related structure data	4nxtC 4nxuC 4nxwC 4nxxC C: citing same article (ref.)
Similar structure data	4nxu-2 4woy-1 4nxu-1 4nxt-4 3mc0-1 3byt-2 5q6l-d 4nxt-3 3owe-8 4oai-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) 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

158 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
39.4 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
39.6 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
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
39.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

A: Mitochondrial dynamic protein MID51

hetero molecules

D: Mitochondrial dynamic protein MID51

hetero molecules

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

6

B: Mitochondrial dynamic protein MID51

hetero molecules

C: Mitochondrial dynamic protein MID51

hetero molecules

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

Unit cell

Length a, b, c (Å)	72.343, 79.093, 80.052
Angle α, β, γ (deg.)	65.81, 84.36, 64.08
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-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 356 / 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: 2.41 Å³/Da / Density % sol: 48.92 %
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, 0.01M GDP, 0.02M manganese chloride, 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: Aug 23, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.3→40 Å / Num. obs: 63108 / % possible obs: 98.1 % / Redundancy: 2.5 % / B_iso Wilson estimate: 27.4 Å² / R_merge(I) obs: 0.078 / Net I/σ(I): 9.4
Reflection shell	Resolution: 2.3→2.42 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.447 / Mean I/σ(I) obs: 2.2 / Num. unique all: 63108

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHENIX		model building
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
XDS		data reduction
SCALA		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→39.046 Å / SU ML: 0.28 / σ(F): 1.97 / Phase error: 25.72 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2375	3169	5.02 %	random
R_work	0.1913	-	-	-
obs	-	63108	98.1 %	-

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→39.046 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10363	0	138	356	10857

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	10754
X-RAY DIFFRACTION	f_angle_d	0.903	14703
X-RAY DIFFRACTION	f_dihedral_angle_d	14.928	3965
X-RAY DIFFRACTION	f_chiral_restr	0.05	1695
X-RAY DIFFRACTION	f_plane_restr	0.004	1870

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 (%)
2.3-2.3343	0.3351	134	0.2818	2610	X-RAY DIFFRACTION	97
2.3343-2.3708	0.3537	126	0.2616	2583	X-RAY DIFFRACTION	98
2.3708-2.4097	0.3116	144	0.2554	2602	X-RAY DIFFRACTION	97
2.4097-2.4512	0.2964	124	0.2444	2588	X-RAY DIFFRACTION	98
2.4512-2.4958	0.2906	147	0.2321	2642	X-RAY DIFFRACTION	98
2.4958-2.5438	0.2939	138	0.2329	2567	X-RAY DIFFRACTION	98
2.5438-2.5957	0.2951	158	0.2204	2588	X-RAY DIFFRACTION	99
2.5957-2.6521	0.2598	131	0.2147	2579	X-RAY DIFFRACTION	98
2.6521-2.7138	0.2664	131	0.2121	2639	X-RAY DIFFRACTION	98
2.7138-2.7816	0.2487	128	0.2177	2642	X-RAY DIFFRACTION	98
2.7816-2.8568	0.2455	125	0.212	2607	X-RAY DIFFRACTION	98
2.8568-2.9409	0.2721	142	0.2154	2584	X-RAY DIFFRACTION	98
2.9409-3.0358	0.2995	143	0.2051	2615	X-RAY DIFFRACTION	98
3.0358-3.1442	0.2812	136	0.2126	2629	X-RAY DIFFRACTION	99
3.1442-3.27	0.2719	153	0.1971	2581	X-RAY DIFFRACTION	98
3.27-3.4188	0.2267	141	0.1875	2625	X-RAY DIFFRACTION	98
3.4188-3.5989	0.2152	132	0.1842	2624	X-RAY DIFFRACTION	98
3.5989-3.8242	0.2337	147	0.1773	2589	X-RAY DIFFRACTION	98
3.8242-4.1192	0.1924	128	0.1596	2607	X-RAY DIFFRACTION	98
4.1192-4.5332	0.1957	121	0.1473	2644	X-RAY DIFFRACTION	99
4.5332-5.1878	0.1823	158	0.1533	2578	X-RAY DIFFRACTION	98
5.1878-6.5311	0.2499	144	0.1903	2589	X-RAY DIFFRACTION	98
6.5311-39.0513	0.1662	138	0.1629	2627	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	8.5898	0.434	-2.5392	1.2929	-0.406	3.4947	0.666	0.4501	1.4502	0.0386	-0.1748	0.4821	-0.7622	-0.1457	-0.53	0.4007	0.0205	0.0841	0.3254	-0.0105	0.5409	1.2582	-9.7803	-16.8523
2	3.9399	-1.0032	-0.3248	2.3409	-0.8879	2.8415	-0.0978	-0.9743	0.0087	0.5033	0.2639	0.4365	-0.2134	-0.3894	-0.2598	0.2824	0.0316	0.0285	0.631	-0.0371	0.3018	-15.3714	-29.2532	-1.09
3	1.2471	-1.0108	0.3234	3.4578	-0.7519	1.4555	0.0089	-0.2299	-0.5046	-0.1403	0.4403	0.4166	-0.0054	-0.4658	-0.4031	0.2947	-0.0262	-0.0302	0.4557	0.1358	0.4156	-7.9231	-52.4938	-0.8723
4	3.2951	-1.6842	0.7763	4.6284	-0.8725	0.349	-0.0776	-0.1283	0.0073	-0.5527	0.3972	1.0766	0.2053	-0.7813	-0.277	0.4254	0.0028	-0.0199	0.7219	0.1395	0.6224	-26.8193	-31.4836	-7.0071
5	5.5721	-3.299	1.2722	4.4936	-0.5718	1.4277	-0.161	0.0235	0.1275	-0.3175	0.042	-0.0562	-0.3164	-0.453	0.1723	0.3561	-0.046	-0.0292	0.3656	0.0495	0.2259	-11.4432	-34.9043	-9.199
6	1.5566	1.4622	-0.2478	2.7225	-1.2886	1.0596	0.1781	-0.2021	0.2169	0.2398	-0.1623	0.1454	-0.1131	0.0439	-0.0631	0.2293	0.0243	0.0502	0.3055	-0.048	0.2973	2.0792	-26.9227	-8.998
7	2.3846	1.8971	-0.0833	4.0421	-0.5476	1.5263	0.0579	-0.0862	-0.0643	0.0622	-0.1159	-0.3294	0.0731	0.2364	0.0918	0.1807	-0.0032	0.0339	0.2407	-0.002	0.248	11.5208	-27.039	-12.2813
8	3.3201	0.4298	-0.7523	0.1493	-0.3436	1.9921	-0.2785	0.4988	0.1306	-0.6989	0.3655	0.1391	0.2276	-0.1602	0.0365	0.2978	-0.0272	0.0028	0.3469	0.0196	0.2777	6.7792	-25.1253	-27.5513
9	1.5969	-0.3699	0.0812	1.5523	0.6622	1.5854	0.1431	0.1158	-0.0814	0.0408	0.1922	-0.5496	0.0238	0.3162	-0.3925	0.2648	-0.0077	0.0121	0.3633	0.0202	0.321	-25.264	-8.3097	-30.0973
10	2.0649	1.2661	-0.8084	1.4162	1.0079	2.1342	-0.0082	-0.0346	-0.2694	0.1481	-0.018	-0.0756	0.1341	0.1147	0.03	0.267	0.0172	-0.0164	0.243	0.044	0.2273	-45.1967	-22.6651	-35.0212
11	4.841	-1.8326	6.8983	3.0294	-0.6287	2.1645	0.544	-0.9201	-0.698	0.4157	-0.276	-0.133	0.5663	-0.1961	-0.5903	0.4122	-0.0221	-0.1158	0.6109	0.0297	0.4259	-21.7096	-20.5108	-23.5433
12	1.3129	0.7443	0.4527	4.0869	1.1944	0.6456	0.0704	-0.1436	0.1344	0.188	-0.093	-0.0037	-0.0519	0.0305	0.0351	0.2515	-0.0252	-0.0005	0.2742	0.008	0.1877	-39.1766	0.8202	-22.8782
13	3.2435	-2.3754	-0.648	2.7017	0.7893	0.569	0.1007	-0.1672	0.1221	-0.0447	-0.0238	-0.483	0.2477	-0.0136	-0.1462	0.2277	-0.0262	-0.0124	0.3132	-0.001	0.4852	11.1088	5.6339	7.0076
14	3.3666	0.2532	-0.8965	0.6538	-0.1549	1.0909	0.0373	0.0266	-0.1479	0.0199	-0.0066	-0.0988	0.041	0.1109	-0.0494	0.1856	0.0206	-0.0172	0.2303	0.0036	0.1732	-22.4985	9.0326	17.2416
15	3.087	-0.154	-1.2533	0.6429	0.0294	2.7615	-0.1415	0.2591	-0.2311	0.1999	0.0755	0.0432	0.1515	-0.2108	0.0334	0.182	0.0107	-0.0198	0.2335	0.0008	0.2745	-42.1263	1.9704	16.2274
16	6.1326	5.3123	0.1966	9.5137	0.2431	0.8565	-0.4329	0.7928	0.5628	-0.7588	0.5995	0.0828	-0.3825	-0.0036	-0.1893	0.3014	-0.0128	-0.0316	0.3732	0.0601	0.3906	-26.1687	21.6989	11.4446
17	4.3712	0.2997	-1.3354	2.1801	0.2537	1.2718	-0.0216	0.2842	-0.1049	-0.0722	0.0051	-0.1067	-0.1036	0.1	-0.0129	0.2597	-0.0205	-0.0272	0.3075	-0.0175	0.1939	-13.097	5.4511	10.6582
18	6.4246	1.4667	-0.1175	2.8357	0.9169	1.8976	-0.0875	0.5846	-0.8766	-0.3366	0.0818	-0.5255	0.0266	0.1886	0.0633	0.2967	0.0089	0.0713	0.3609	-0.0968	0.5126	-2.4859	-5.1229	3.4394
19	2.1822	1.0983	-0.1802	0.7809	-0.2226	2.3665	0.0193	0.3456	0.3282	-0.2466	0.1362	-0.1564	-0.4449	-0.0281	-0.136	0.4065	0.0005	0.0001	0.3262	0.037	0.3256	3.9704	15.0033	-50.9315
20	1.2859	-2.6746	-0.832	6.5477	2.0153	2.3658	-0.059	-0.2291	-0.0477	0.5648	0.0688	0.0216	0.1385	0.0896	0.0069	0.3116	0.0194	-0.0149	0.2626	-0.0194	0.2882	8.3616	-13.3254	-51
21	7.8417	-0.8618	2.1017	5.6365	1.6649	1.196	0.4631	-0.5537	-0.1208	0.6226	-0.2372	-1.0183	-0.7604	1.0205	-0.2503	0.5266	-0.1583	0.0285	0.6266	-0.1346	0.6659	20.5842	12.356	-48.3115
22	2.9462	-0.2849	-1.7592	2.8108	0.9565	3.1428	0.0062	0.3145	0.1983	0.1345	-0.0429	0.3197	-0.2667	-0.3388	0.0121	0.3242	0.0398	-0.0082	0.3032	0.025	0.2365	-7.4105	7.499	-43.9307
23	0.1329	-0.1943	-0.1113	2.6079	0.544	0.2382	-0.0645	-0.4978	0.2068	0.6329	0.2238	0.4919	-0.199	-0.2053	0.1042	0.6275	-0.0291	0.1067	0.667	-0.0015	0.5381	-13.083	13.3082	-27.6976

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 132 through 150 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 151 through 208 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 209 through 271 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 272 through 296 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 297 through 333 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 334 through 381 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 382 through 439 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 440 through 462 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 132 through 200 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 201 through 283 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 284 through 305 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 306 through 462 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 126 through 150 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 151 through 235 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 236 through 258 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 259 through 296 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 297 through 381 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 382 through 462 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 132 through 207 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 208 through 273 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 274 through 296 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 297 through 439 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 440 through 462 )

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi