PDB-5x3e: kinesin 6

ID or keywords:

Entry

Database: PDB / ID: 5x3e

Title

kinesin 6

Components

Kinesin-like protein

Keywords

MOTOR PROTEIN / kinesin 6 / apo state / neck linker

Function / homology

Function and homology information

pronuclear migration / regulation of actomyosin contractile ring contraction / meiotic spindle midzone assembly / polar body extrusion after meiotic divisions / mitotic spindle midzone assembly / mitotic spindle midzone / plus-end-directed microtubule motor activity / microtubule motor activity / kinesin complex / microtubule-based movement ...
Similarity search - Function

Biological species

Caenorhabditis elegans (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.61 Å

Authors

Chen, Z. / Guan, R. / Zhang, L.

Funding support

China, 5items

Organization	Grant number	Country
Chinese Key Research Plan-Protein Sciences	2014CB910100	China
National Natural Science Foundation of China	31630046,31270762	China
Junior One Thousand Talents program		China
National Science Foundation of China	31271423	China
863 Program	SS2015AA020406	China

Citation

Journal: Nat Commun / Year: 2017
Title: Crystal structure of Zen4 in the apo state reveals a missing conformation of kinesin
Authors: Guan, R. / Zhang, L. / Su, Q.P. / Mickolajczyk, K.J. / Chen, G.Y. / Hancock, W.O. / Sun, Y. / Zhao, Y. / Chen, Z.

History

Deposition	Feb 4, 2017	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 19, 2017	Provider: repository / Type: Initial release
Revision 1.1	Mar 27, 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	5x3e.cif.gz	320.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5x3e.ent.gz	263.9 KB	Display	PDB format
PDBx/mmJSON format	5x3e.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5x3e_validation.pdf.gz	470.5 KB	Display	wwPDB validaton report
Full document	5x3e_full_validation.pdf.gz	484.6 KB	Display
Data in XML	5x3e_validation.xml.gz	30.1 KB	Display
Data in CIF	5x3e_validation.cif.gz	41.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x3/5x3e ftp://data.pdbj.org/pub/pdb/validation_reports/x3/5x3e	HTTPS FTP

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Related structure data

Similar structure data	6xib-d 4qfu-1 2quk-d 3hbp-d 2a9b-d 6gl6-d 4p4u-d 4tq2-1 3wk1-1 2zz7-1 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	#64 - Apr 2005 Kinesin similarity (8) #175 - Jul 2014 Microtubules similarity (7) #18 - Jun 2001 Myosin similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (7) #174 - Jun 2014 GFP-like Proteins similarity (1)

Deposited unit

A: Kinesin-like protein

B: Kinesin-like protein

hetero molecules

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

1

A: Kinesin-like protein

hetero molecules

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

2

B: Kinesin-like protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	244.152, 244.152, 42.217
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	168
Space group name H-M	P6

#1: Protein	Kinesin-like protein Mass: 50813.535 Da / Num. of mol.: 2 / Fragment: UNP residues 1-441 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: zen-4, CELE_M03D4.1, M03D4.1 Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others) References: UniProt: G5EG83
#2: Chemical	... ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 38 Source method: isolated from a genetically manipulated source Formula: SO₄
#3: Chemical	ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 148 / 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: 3.61 Å³/Da / Density % sol: 65.89 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 1.5M (NH4)2SO4, 100mM MES, 200mM NaI, 4% dioxane, 10mM DTT, pH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.987 Å / Relative weight: 1
Reflection	Resolution: 2.61→31.845 Å / Num. obs: 44542 / % possible obs: 99.54 % / Redundancy: 5.2 % / Net I/σ(I): 13.3
Reflection shell	Resolution: 2.61→2.7 Å / Mean I/σ(I) obs: 1.05 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Resolution: 2.61→31.845 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.63

	R_factor	Num. reflection	% reflection
R_free	0.2397	1999	4.49 %
R_work	0.2092	-	-
obs	0.2107	44542	99.54 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.61→31.845 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5803	0	197	148	6148

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	6047
X-RAY DIFFRACTION	f_angle_d	0.736	8185
X-RAY DIFFRACTION	f_dihedral_angle_d	13.651	3627
X-RAY DIFFRACTION	f_chiral_restr	0.048	920
X-RAY DIFFRACTION	f_plane_restr	0.004	1029

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 (%)
2.6097-2.675	0.3695	139	0.322	2970	X-RAY DIFFRACTION	99
2.675-2.7472	0.3518	141	0.3048	2989	X-RAY DIFFRACTION	99
2.7472-2.828	0.3273	142	0.2728	3027	X-RAY DIFFRACTION	100
2.828-2.9193	0.3184	140	0.2751	2986	X-RAY DIFFRACTION	100
2.9193-3.0235	0.2707	143	0.2599	3041	X-RAY DIFFRACTION	99
3.0235-3.1445	0.2859	141	0.2441	2980	X-RAY DIFFRACTION	100
3.1445-3.2874	0.2709	141	0.2209	3017	X-RAY DIFFRACTION	99
3.2874-3.4606	0.2503	142	0.2091	3011	X-RAY DIFFRACTION	100
3.4606-3.6771	0.2533	142	0.2037	3016	X-RAY DIFFRACTION	100
3.6771-3.9605	0.2151	143	0.1828	3040	X-RAY DIFFRACTION	99
3.9605-4.3582	0.2027	145	0.171	3071	X-RAY DIFFRACTION	100
4.3582-4.9867	0.1969	143	0.1648	3060	X-RAY DIFFRACTION	100
4.9867-6.2749	0.2553	147	0.2136	3113	X-RAY DIFFRACTION	100
6.2749-31.8478	0.1975	150	0.2066	3222	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	6.0487	3.7075	1.533	5.2588	2.6564	8.2879	0.3419	0.8006	-0.988	-0.817	-0.5094	1.0502	1.1226	-1.0011	0.2594	0.9752	-0.041	-0.1949	0.545	-0.1231	0.6668	-396.3967	5.102	-0.2462
2	2.5312	1.1483	1.4841	3.3988	1.2658	3.8158	0.1099	0.1928	-0.1986	-0.2249	-0.1236	0.2507	0.4248	-0.1519	-0.0157	0.5253	0.0853	-0.014	0.3075	-0.0002	0.3622	-383.8895	16.3048	6.4318
3	2.0791	0.4478	-6.9079	8.6821	-0.4687	5.6849	-0.463	-0.6974	-0.8282	0.6665	-0.3695	-1.0953	0.0579	1.0215	0.8169	0.7858	-0.1375	-0.2341	0.6525	0.1707	0.6579	-360.3463	30.9298	21.0362
4	2.7437	1.0985	-0.0557	5.3586	-1.2425	4.1876	0.1191	0.2515	-0.3167	-0.6695	-0.1652	-0.5337	0.7393	0.2579	0.0899	0.5434	0.0935	-0.0342	0.3333	-0.0355	0.3468	-375.7734	20.6543	10.7847
5	2.479	-3.8645	-2.9182	8.9108	1.7378	6.9872	-0.3457	-1.0098	0.2717	0.647	0.4491	-0.396	0.5843	0.2441	-0.1155	0.7756	0.0124	-0.0873	0.3989	-0.0673	0.3514	-376.3224	14.9994	28.0122
6	3.6996	1.0555	1.9906	2.1105	-2.2321	8.3067	0.103	0.4828	-0.4239	-0.5191	-0.041	-0.5212	0.5163	0.71	0.0345	0.5563	0.1015	0.0104	0.4969	-0.0707	0.3853	-369.0142	15.9337	12.6446
7	6.9458	-2.5774	-1.8291	0.9542	0.6628	0.4632	-0.0343	0.5899	-2.0396	-0.2369	0.1291	0.1336	2.0024	0.1552	-0.1393	1.3298	0.1543	-0.1095	0.7334	-0.0628	0.8306	-374.3833	-1.646	17.5522
8	1.6707	0.4759	0.5059	5.1394	-0.0303	1.0917	0.0337	-0.2028	0.227	0.7813	-0.0496	-0.1047	0.0777	0.0117	0.0323	0.6738	0.0741	-0.0314	0.3411	-0.0027	0.3869	-376.6187	31.8181	16.7985
9	8.1959	-0.7562	0.5236	5.0395	-1.3315	7.0419	0.1782	-0.5839	-0.7003	0.2096	0.0163	1.0315	0.5881	-0.5162	-0.1564	0.6246	-0.1808	0.0036	0.4102	0.0062	0.5386	-394.8404	10.4662	21.3917
10	4.0554	3.3324	0.7351	5.7595	2.7204	2.9664	-0.0823	0.0053	-0.9942	0.2406	0.1407	0.6494	1.8719	-0.8712	-0.0309	1.1725	-0.2128	-0.0104	0.6075	0.011	0.8839	-397.5691	1.2848	6.2965
11	2.779	-3.3982	-1.5765	5.8891	1.9246	3.8396	-0.0996	-1.2163	0.796	0.8949	-0.048	0.5021	-1.2345	-0.9013	0.05	1.4019	0.4087	0.0735	0.931	-0.2176	0.8302	-398.2514	-26.3549	25.5238
12	2.7663	-0.7445	-0.2801	4.9054	0.677	4.0026	-0.0592	-0.4724	0.4218	0.6196	0.1274	0.232	-0.8882	-0.3105	-0.0925	0.5444	0.0824	0.0475	0.4379	0.0072	0.3552	-389.4368	-43.9902	17.966
13	9.619	-2.4565	4.2881	7.2253	-1.6004	2.0583	0.1209	0.1477	1.0116	0.4863	-0.0929	-0.545	-0.6807	0.1377	0.0154	0.3294	0.0172	0.0212	0.3415	-0.0037	0.3807	-373.3338	-64.6821	2.1543
14	3.5141	0.4564	-0.7181	6.151	-1.253	4.3052	0.0028	-0.6088	0.1402	0.6593	-0.0672	-0.1989	-0.7927	0.2392	0.0639	0.4088	0.0198	-0.0397	0.3864	-0.0511	0.2812	-384.859	-49.0093	13.8132
15	7.0481	2.6044	3.3752	7.1987	0.5425	7.3928	0.2011	1.3306	-0.1764	-0.6102	0.1728	-0.3036	-0.4976	0.7185	-0.2478	0.7956	0.0696	0.1151	0.5053	-0.0644	0.353	-382.4751	-42.8645	-3.262
16	7.1746	7.3247	-1.9517	2.1763	0.2701	9.2635	-0.0163	-0.5436	0.736	0.3043	0.1142	-0.5416	-0.8024	0.6862	-0.061	0.4656	0.0236	-0.0892	0.4328	-0.1146	0.5663	-375.8647	-45.8439	11.6399
17	3.2428	0.3085	0.6521	0.0113	0.081	0.1148	-0.3077	-0.3311	0.8973	0.3711	-0.2592	-0.9489	-1.1857	0.2041	0.5758	1.231	0.0341	-0.2053	0.8011	-0.0563	1.2156	-376.5238	-28.3005	7.859
18	1.7716	-0.1953	0.0805	5.0393	-0.3385	2.7822	0.1219	-0.0014	-0.2485	-0.1546	-0.0635	0.1161	-0.1616	-0.2106	-0.093	0.2477	-0.0281	0.0289	0.2684	-0.0047	0.2701	-388.0546	-58.8867	7.4644
19	7.1458	1.3121	-0.7995	6.5106	-0.6036	5.79	-0.2795	0.3165	1.1217	-0.1918	0.3876	1.1486	-1.1963	-0.8058	-0.1254	0.8106	0.2642	-0.0821	0.4968	-0.0107	0.6982	-399.27	-33.9428	3.5312
20	3.1854	-3.6629	0.1305	7.2572	1.9668	4.6723	-0.3778	0.0396	1.2083	1.232	0.5616	0.4755	-2.2648	-0.2656	-0.0107	1.6355	0.2171	0.1509	0.6065	-0.0049	0.853	-398.335	-24.0872	18.872

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 25:53)
2	X-RAY DIFFRACTION	2	(chain A and resid 54:162)
3	X-RAY DIFFRACTION	3	(chain A and resid 163:180)
4	X-RAY DIFFRACTION	4	(chain A and resid 181:220)
5	X-RAY DIFFRACTION	5	(chain A and resid 221:252)
6	X-RAY DIFFRACTION	6	(chain A and resid 253:272)
7	X-RAY DIFFRACTION	7	(chain A and resid 273:287)
8	X-RAY DIFFRACTION	8	(chain A and resid 288:324)
9	X-RAY DIFFRACTION	9	(chain A and resid 325:397)
10	X-RAY DIFFRACTION	10	(chain A and resid 398:426)
11	X-RAY DIFFRACTION	11	(chain B and resid 26:56)
12	X-RAY DIFFRACTION	12	(chain B and resid 71:162)
13	X-RAY DIFFRACTION	13	(chain B and resid 163:178)
14	X-RAY DIFFRACTION	14	(chain B and resid 189:220)
15	X-RAY DIFFRACTION	15	(chain B and resid 221:252)
16	X-RAY DIFFRACTION	16	(chain B and resid 253:273)
17	X-RAY DIFFRACTION	17	(chain B and resid 274:287)
18	X-RAY DIFFRACTION	18	(chain B and resid 288:324)
19	X-RAY DIFFRACTION	19	(chain B and resid 325:397)
20	X-RAY DIFFRACTION	20	(chain B and resid 398:426)

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