PDB-4bej: Nucleotide-free Dynamin 1-like protein (DNM1L, DRP1, DLP1)

ID or keywords:

Entry

Database: PDB / ID: 4bej

Title

Nucleotide-free Dynamin 1-like protein (DNM1L, DRP1, DLP1)

Components

DYNAMIN 1-LIKE PROTEIN

Keywords

HYDROLASE / G PROTEIN / MITOCHONDRIAL FISSION / MEMBRANE REMODELING / APOPTOSIS

Function / homology

Function and homology information

mitochondrial membrane fission / regulation of ATP metabolic process / regulation of peroxisome organization / mitocytosis / dynamin GTPase / Apoptotic execution phase / peroxisome fission / mitochondrial fragmentation involved in apoptotic process / regulation of mitophagy / GTP-dependent protein binding ...
Similarity search - Function

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.483 Å

Authors

Froehlich, C. / Schwefel, D. / Faelber, K. / Daumke, O.

Citation

Journal: Embo J. / Year: 2013
Title: Structural Insights Into Oligomerization and Mitochondrial Remodelling of Dynamin 1-Like Protein.
Authors: Frohlich, C. / Grabiger, S. / Schwefel, D. / Faelber, K. / Rosenbaum, E. / Mears, J. / Rocks, O. / Daumke, O.

History

Deposition	Mar 11, 2013	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Apr 24, 2013	Provider: repository / Type: Initial release
Revision 1.1	May 22, 2013	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4bej.cif.gz	851.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4bej.ent.gz	716.8 KB	Display	PDB format
PDBx/mmJSON format	4bej.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4bej_validation.pdf.gz	476.1 KB	Display	wwPDB validaton report
Full document	4bej_full_validation.pdf.gz	529.7 KB	Display
Data in XML	4bej_validation.xml.gz	77.5 KB	Display
Data in CIF	4bej_validation.cif.gz	103.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/be/4bej ftp://data.pdbj.org/pub/pdb/validation_reports/be/4bej	HTTPS FTP

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Related structure data

Related structure data	3snhS S: Starting model for refinement
Similar structure data	2jfk-d 2jfd-d 2ai0-d 5ks9-d 6pxh-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) 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	#58 - Oct 2004 G Proteins similarity (1)

Deposited unit

A: DYNAMIN 1-LIKE PROTEIN

B: DYNAMIN 1-LIKE PROTEIN

C: DYNAMIN 1-LIKE PROTEIN

D: DYNAMIN 1-LIKE PROTEIN

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

1

A: DYNAMIN 1-LIKE PROTEIN

B: DYNAMIN 1-LIKE PROTEIN

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

2

C: DYNAMIN 1-LIKE PROTEIN

D: DYNAMIN 1-LIKE PROTEIN

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

Unit cell

Length a, b, c (Å)	101.470, 80.770, 208.272
Angle α, β, γ (deg.)	90.00, 93.45, 90.00
Int Tables number	3
Space group name H-M	P121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	2
3	3
4	4
5	5

/ NCS ensembles :

ID
1
2
3
4
5

#1: Protein	DYNAMIN 1-LIKE PROTEIN / DNM1P/VPS1P-LIKE PROTEIN / DVLP / DYNAMIN FAMILY MEMBER PROLINE-RICH CARBOXYL-TERMINAL DOMAIN LESS ...DNM1P/VPS1P-LIKE PROTEIN / DVLP / DYNAMIN FAMILY MEMBER PROLINE-RICH CARBOXYL-TERMINAL DOMAIN LESS / DYMPLE / DYNAMIN-LIKE PROTEIN / DYNAMIN-LIKE PROTEIN 4 / DYNAMIN-LIKE PROTEIN IV / HDYNIV / DYNAMIN-RELATED PROTEIN 1 Mass: 69210.516 Da / Num. of mol.: 4 / Fragment: DNM1L DELTA B INSERT, RESIDUES 1-516,632-725 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: MODIFIED PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: O00429, dynamin GTPase
Sequence details	HUMAN DNM1L ISOFORM 2

#1: Protein

DYNAMIN 1-LIKE PROTEIN / DNM1P/VPS1P-LIKE PROTEIN / DVLP / DYNAMIN FAMILY MEMBER PROLINE-RICH CARBOXYL-TERMINAL DOMAIN LESS ...

Mass: 69210.516 Da / Num. of mol.: 4 / Fragment: DNM1L DELTA B INSERT, RESIDUES 1-516,632-725 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

HOMO SAPIENS (human) / Plasmid: MODIFIED PET28A / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: O00429, dynamin GTPase

Sequence details

HUMAN DNM1L ISOFORM 2

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.66 Å³/Da / Density % sol: 53.83 % / Description: NONE
Crystal grow	pH: 7.5 / Details: 12% PEG3350, 50 MM K(HCOO), pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 24, 2010 / Details: MIRRORS
Radiation	Monochromator: SI111 DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 3.48→50 Å / Num. obs: 42403 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 3.94 % / B_iso Wilson estimate: 75.8 Å² / R_merge(I) obs: 0.21 / Net I/σ(I): 10.19
Reflection shell	Resolution: 3.48→3.69 Å / Redundancy: 3.68 % / R_merge(I) obs: 0.68 / Mean I/σ(I) obs: 2.41 / % possible all: 84.3

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Processing

Software

Name	Classification
Coot	model building
XDS	data scaling
XDS	phasing
CCP4	phasing
PHENIX	phasing
Coot	phasing
PHENIX	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SNH

3snh

Resolution: 3.483→47.574 Å / SU ML: 0.48 / σ(F): 1.99 / Phase error: 28.78 / Stereochemistry target values: ML / Details: TORSION NCS USED.

	R_factor	Num. reflection	% reflection
R_free	0.2761	2121	5 %
R_work	0.2509	-	-
obs	0.2522	42384	97.27 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.483→47.574 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17076	0	0	0	17076

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	17286
X-RAY DIFFRACTION	f_angle_d	1.618	23356
X-RAY DIFFRACTION	f_dihedral_angle_d	15.048	6596
X-RAY DIFFRACTION	f_chiral_restr	0.081	2844
X-RAY DIFFRACTION	f_plane_restr	0.006	2960

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 (%)
3.483-3.564	0.3583	86	0.3364	1674	X-RAY DIFFRACTION	62
3.564-3.6531	0.3544	137	0.3183	2760	X-RAY DIFFRACTION	100
3.6531-3.7518	0.3222	148	0.3125	2708	X-RAY DIFFRACTION	100
3.7518-3.8622	0.3561	138	0.2981	2758	X-RAY DIFFRACTION	100
3.8622-3.9868	0.2932	138	0.2907	2741	X-RAY DIFFRACTION	100
3.9868-4.1292	0.2753	155	0.2714	2705	X-RAY DIFFRACTION	100
4.1292-4.2944	0.2912	158	0.2409	2736	X-RAY DIFFRACTION	100
4.2944-4.4897	0.2848	137	0.2354	2756	X-RAY DIFFRACTION	100
4.4897-4.7262	0.2478	152	0.2245	2746	X-RAY DIFFRACTION	100
4.7262-5.0221	0.2868	123	0.2266	2780	X-RAY DIFFRACTION	100
5.0221-5.4093	0.2635	145	0.2458	2759	X-RAY DIFFRACTION	100
5.4093-5.9527	0.2732	149	0.2677	2765	X-RAY DIFFRACTION	100
5.9527-6.812	0.3201	140	0.2755	2782	X-RAY DIFFRACTION	100
6.812-8.5742	0.2332	141	0.2239	2792	X-RAY DIFFRACTION	100
8.5742-47.5781	0.2259	174	0.2015	2801	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	7.7148	-1.6877	-4.7945	7.8873	1.2845	2.9884	-0.2047	-0.5287	-0.3726	0.0529	0.2187	0.1002	0.4526	0.5059	0.1427	0.3937	0.2777	-0.0051	0.6018	-0.0575	0.2225	-41.9089	12.2537	18.2084
2	4.7462	-0.9294	-4.1672	6.1804	2.5967	9.5058	-0.2444	0.2199	-0.233	-0.3767	0.0096	0.6117	0.4728	0.1189	0.1107	0.8106	0.0573	-0.0742	0.6324	-0.4086	0.812	28.3859	-41.9242	-103.3135
3	1.9665	0.9373	1.8711	3.6106	1.6752	3.1533	0.1935	0.2274	-0.2459	-0.1745	0.0977	-0.1237	0.3877	0.5464	-0.4459	0.4794	0.1391	-0.3043	0.9223	-0.5918	0.8656	-19.7389	-11.3281	19.8418
4	8.3822	0.7178	-3.0741	7.8424	-0.2911	7.2346	-0.0406	-0.5962	0.4862	0.3315	0.1981	0.0184	-0.0522	0.4113	-0.0903	0.1513	-0.0269	0.0925	0.5934	-0.171	0.4569	42.2793	-103.1032	-81.1217
5	2.2332	-0.6754	-0.2297	1.9584	0.0144	2.3029	0.045	0.056	0.3199	0.2681	-0.0324	-0.0242	-0.5865	0.1263	-0.1222	0.4335	0.3013	0.1171	0.4854	-0.1559	0.3215	-40.5408	28.5038	27.524
6	1.5296	0.9574	0.1438	2.2284	0.2981	1.9281	-0.091	-0.299	-0.1295	-0.0438	-0.5483	0.2106	0.4466	-0.5685	-0.4762	0.4752	-0.1378	-0.1049	0.4958	-0.5265	0.4357	34.955	-59.1446	-107.7838
7	1.8339	0.1942	-0.094	2.4161	0.306	2.2464	0.2524	0.5023	-0.4478	-0.1351	-0.1235	-0.3843	0.1477	0.6978	-0.1073	0.237	0.08	-0.0321	0.676	-0.1903	0.4684	-7.4911	2.1926	25.0025
8	1.5698	0.3017	-0.2575	1.2023	0.1848	2.2455	-0.2625	-0.4166	-0.0292	0.7855	-0.1063	-0.6468	0.5776	0.1031	-0.885	0.6559	-0.1452	-0.3518	0.3269	-0.374	0.5087	50.6379	-119.0988	-74.4966
9	2.0357	-0.4204	-0.1144	1.8775	-0.0056	1.7485	0.0114	-0.359	0.2115	-0.0664	0.0743	0.2425	-0.0594	-0.1441	0.0115	-0.0867	-0.1734	-0.044	0.0155	-0.0036	0.0641	-24.6927	-4.8882	-45.9827
10	2.0483	0.5001	0.2991	2.8694	0.5742	2.0983	-0.0075	0.3936	-0.2118	-0.2882	0.0834	-0.1402	0.3709	0.3648	0.1286	0.2517	-0.0696	-0.0204	0.028	0.0049	0.1101	-17.1603	-24.0885	-57.2461
11	2.5242	-0.8266	0.1091	2.5817	0.1168	2.4048	0.0193	-0.2344	0.4293	-0.1328	0.0143	-0.1659	-0.7281	-0.06	-0.0224	0.1958	-0.064	-0.0254	0.0318	-0.0957	0.2097	-17.3261	-43.8467	-43.7575
12	2.6746	0.1843	0.3993	2.4209	0.1878	1.937	0.0662	0.1402	-0.5824	0.0212	-0.0817	-0.1455	0.1637	0.1532	0.087	0.0866	-0.0865	0.0651	-0.0515	-0.0922	0.2894	-12.9525	-66.4275	-51.816
13	1.6798	0.1293	-0.2394	5.1251	1.4123	6.8993	-0.0055	0.4436	-0.2603	-0.2948	0.0378	-0.0285	0.2324	0.0656	0.2385	0.7788	0.0401	0.056	0.8169	-0.3629	0.3863	-42.0004	5.5657	2.3256
14	3.7911	-1.7744	-5.0954	1.2713	2.2907	6.8691	0.0978	0.3095	0.0776	-0.6745	-0.1047	-0.4535	-0.2303	0.5728	0.1287	0.7168	0.0404	0.1266	0.7021	-0.0278	0.4451	-33.3408	5.8537	4.5788
15	2.5488	-0.5816	-0.702	3.7463	3.042	2.4938	-0.036	-0.2131	-0.0305	0.3761	-0.0727	0.5177	0.4219	-0.0729	0.263	0.8989	0.3663	-0.0732	1.0511	-0.5845	1.2057	15.4865	-33.613	-95.2929
16	1.3656	-1.7676	-0.8607	7.4347	2.9331	2.9234	-0.0436	0.3971	-0.3072	-0.7561	0.0513	-0.1997	0.2806	0.0936	-0.0924	0.9539	-0.1516	-0.1159	0.7419	-0.4611	0.831	-26.8976	-18.1022	5.382
17	8.3022	-4.9906	-2.6046	3.0362	1.8837	3.5689	0.2225	-0.3355	0.2256	0.3309	-0.0898	0.9125	-0.404	-0.7397	-0.0647	0.5394	0.191	0.0242	0.6085	-0.0699	0.6771	27.5194	-95.7657	-82.3843
18	2.3785	-0.6711	-2.3547	0.2509	0.6957	2.3474	0.1338	-0.3159	-0.0831	0.1601	0.2036	0.3595	-0.2885	0.189	-0.1266	0.8671	0.3511	-0.0808	0.7111	-0.333	1.0213	22.5124	-34.7544	-90.7594
19	3.6668	-3.2385	-4.3426	2.8626	3.8353	5.1364	0.0815	0.111	-0.3676	0.3282	-0.0553	0.0428	0.5427	0.2907	0.009	0.8613	-0.1751	-0.1599	1.1223	-0.5889	1.0584	-21.5447	-21.2706	10.2128
20	4.2181	-2.8792	-1.7326	6.1878	4.7384	7.2728	-0.1237	-0.6383	0.3684	0.4536	-0.2246	0.1998	-0.3946	-0.1941	0.2588	0.4603	0.0093	-0.1557	0.4788	-0.0508	0.6643	32.2259	-91.8987	-75.9767

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 1:25)
2	X-RAY DIFFRACTION	2	CHAIN B AND (RESSEQ 1:25)
3	X-RAY DIFFRACTION	3	CHAIN C AND (RESSEQ 1:25)
4	X-RAY DIFFRACTION	4	CHAIN D AND (RESSEQ 1:25)
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESSEQ 26:302)
6	X-RAY DIFFRACTION	6	CHAIN B AND (RESSEQ 26:302)
7	X-RAY DIFFRACTION	7	CHAIN C AND (RESSEQ 26:302)
8	X-RAY DIFFRACTION	8	CHAIN D AND (RESSEQ 26:302)
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESSEQ 326:674)
10	X-RAY DIFFRACTION	10	CHAIN B AND (RESSEQ 326:674)
11	X-RAY DIFFRACTION	11	CHAIN C AND (RESSEQ 326:674)
12	X-RAY DIFFRACTION	12	CHAIN D AND (RESSEQ 326:674)
13	X-RAY DIFFRACTION	13	CHAIN A AND (RESSEQ 303:325)
14	X-RAY DIFFRACTION	14	CHAIN A AND (RESSEQ 675:705)
15	X-RAY DIFFRACTION	15	CHAIN B AND (RESSEQ 303:325)
16	X-RAY DIFFRACTION	16	CHAIN C AND (RESSEQ 303:325)
17	X-RAY DIFFRACTION	17	CHAIN D AND (RESSEQ 303:325)
18	X-RAY DIFFRACTION	18	CHAIN B AND (RESSEQ 675:705)
19	X-RAY DIFFRACTION	19	CHAIN C AND (RESSEQ 675:705)
20	X-RAY DIFFRACTION	20	CHAIN D AND (RESSEQ 675:705)

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