PDB-5et1: Crystal structure of Myo3b-ARB1 in complex with Espin1-AR

ID or keywords:

Entry

Database: PDB / ID: 5et1

Title

Crystal structure of Myo3b-ARB1 in complex with Espin1-AR

Components

Espin
Myosin-IIIb

Keywords

PROTEIN BINDING/MOTOR PROTEIN / unconventional myosin /

complex /

protein binding / PROTEIN BINDING-MOTOR PROTEIN complex

Function / homology

Function and homology information

microvillar actin bundle assembly / negative regulation of cytoskeleton organization / regulation of actin filament length / parallel actin filament bundle assembly / actin filament network formation / cochlea morphogenesis / stereocilium tip / stereocilium bundle / filopodium tip / stereocilium ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Liu, H. / Li, J. / liu, W. / Zhang, M.

Funding support

Hong Kong, 1items

Citation

Journal: Elife / Year: 2016
Title: Myosin III-mediated cross-linking and stimulation of actin bundling activity of Espin
Authors: Liu, H. / Li, J. / Raval, M.H. / Yao, N. / Deng, X. / Lu, Q. / Nie, S. / Feng, W. / Wan, J. / Yengo, C.M. / Liu, W. / Zhang, M.

History

Deposition	Nov 17, 2015	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Feb 3, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5et1.cif.gz	284.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5et1.ent.gz	230 KB	Display	PDB format
PDBx/mmJSON format	5et1.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/et/5et1 ftp://data.pdbj.org/pub/pdb/validation_reports/et/5et1	HTTPS FTP

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Related structure data

Related structure data	5et0C 1n0rS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6q3z-d 1koo-1 5kj4-3 4h09-3 4nbz-2 1koh-1 4h09-4 2gem-1 1gml-2 2ifq-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	#18 - Jun 2001 Myosin similarity (8) #174 - Jun 2014 GFP-like Proteins similarity (5) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (2) #64 - Apr 2005 Kinesin similarity (1) #175 - Jul 2014 Microtubules similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Espin

B: Espin

C: Myosin-IIIb

D: Myosin-IIIb

hetero molecules

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

1

A: Espin

C: Myosin-IIIb

hetero molecules

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

2

B: Espin

D: Myosin-IIIb

hetero molecules

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

Unit cell

Length a, b, c (Å)	72.740, 71.142, 76.883
Angle α, β, γ (deg.)	90.00, 96.88, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Espin / / Ectoplasmic specialization protein Mass: 37921.555 Da / Num. of mol.: 2 / Fragment: UNP residues 1-352 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Espn / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ET47
#2: Protein/peptide	Myosin-IIIb Mass: 4322.861 Da / Num. of mol.: 2 / Fragment: UNP residues 1216-1251 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Myo3b / Production host: Escherichia coli (E. coli) / References: UniProt: Q1EG27
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.38 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 0.2 M Lithium Acetate, 20%(w/v) PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2014
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9791 Å / Relative weight: 1
Reflection	Resolution: 1.65→50 Å / Num. obs: 93433 / % possible obs: 99.8 % / Redundancy: 3.7 % / Net I/σ(I): 18.5
Reflection shell	Resolution: 1.65→1.68 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.916 / Mean I/σ(I) obs: 1.7 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.10_2155: ???)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1N0R

1n0r

Resolution: 1.65→32.242 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1911	4345	4.65 %
R_work	0.1694	-	-
obs	0.1704	93405	99.58 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.65→32.242 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5282	0	30	378	5690

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	5540
X-RAY DIFFRACTION	f_angle_d	0.795	7575
X-RAY DIFFRACTION	f_dihedral_angle_d	14.079	3301
X-RAY DIFFRACTION	f_chiral_restr	0.047	857
X-RAY DIFFRACTION	f_plane_restr	0.006	995

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 (%)
1.6491-1.6679	0.295	145	0.2735	2735	X-RAY DIFFRACTION	93
1.6679-1.6875	0.2753	151	0.2593	2960	X-RAY DIFFRACTION	100
1.6875-1.7081	0.2908	138	0.2429	2948	X-RAY DIFFRACTION	100
1.7081-1.7297	0.2762	164	0.2385	2953	X-RAY DIFFRACTION	100
1.7297-1.7524	0.2586	147	0.2346	2967	X-RAY DIFFRACTION	100
1.7524-1.7764	0.2532	144	0.2305	2991	X-RAY DIFFRACTION	100
1.7764-1.8018	0.2477	155	0.2145	2898	X-RAY DIFFRACTION	100
1.8018-1.8287	0.2475	137	0.2131	2978	X-RAY DIFFRACTION	100
1.8287-1.8573	0.2255	135	0.2045	2970	X-RAY DIFFRACTION	100
1.8573-1.8877	0.2464	152	0.1989	2968	X-RAY DIFFRACTION	100
1.8877-1.9203	0.2204	152	0.1961	2992	X-RAY DIFFRACTION	100
1.9203-1.9552	0.2361	155	0.1818	2908	X-RAY DIFFRACTION	100
1.9552-1.9928	0.1757	157	0.1715	2969	X-RAY DIFFRACTION	100
1.9928-2.0335	0.2004	120	0.1595	3028	X-RAY DIFFRACTION	100
2.0335-2.0777	0.1693	154	0.1663	2946	X-RAY DIFFRACTION	100
2.0777-2.126	0.2158	155	0.1636	2932	X-RAY DIFFRACTION	100
2.126-2.1791	0.2088	140	0.1651	2968	X-RAY DIFFRACTION	100
2.1791-2.238	0.1764	147	0.1619	2943	X-RAY DIFFRACTION	100
2.238-2.3039	0.1924	167	0.1609	2974	X-RAY DIFFRACTION	100
2.3039-2.3782	0.2127	153	0.1669	2974	X-RAY DIFFRACTION	100
2.3782-2.4632	0.1832	145	0.1645	2943	X-RAY DIFFRACTION	100
2.4632-2.5618	0.1732	145	0.1663	2997	X-RAY DIFFRACTION	100
2.5618-2.6783	0.1851	144	0.162	2977	X-RAY DIFFRACTION	100
2.6783-2.8194	0.1739	138	0.1715	2991	X-RAY DIFFRACTION	100
2.8194-2.996	0.1952	140	0.1742	2976	X-RAY DIFFRACTION	99
2.996-3.2271	0.1714	127	0.167	3011	X-RAY DIFFRACTION	100
3.2271-3.5515	0.1643	145	0.1641	2998	X-RAY DIFFRACTION	100
3.5515-4.0645	0.1625	132	0.141	3032	X-RAY DIFFRACTION	100
4.0645-5.1176	0.1543	146	0.1388	3023	X-RAY DIFFRACTION	100
5.1176-32.248	0.1724	115	0.1553	3110	X-RAY DIFFRACTION	100

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	0.7234	-0.5727	-0.1037	4.3863	0.299	1.9432	-0.0591	0.2273	0.5299	-0.1721	0.0089	-0.08	-0.3535	0.1321	-0.0429	0.2361	-0.0479	0.0071	0.1717	0.085	0.332	9.64	48.142	63.7518
2	1.9514	-0.6306	-0.0045	3.048	-0.3668	2.4103	-0.0226	0.0007	0.2845	-0.0515	-0.019	0.0232	-0.0788	-0.0372	0.0376	0.0888	-0.0038	-0.0031	0.1167	0.0141	0.1392	5.8374	39.0594	68.9783
3	0.6894	-0.0351	-0.1041	2.3571	0.3075	0.6824	-0.0247	0.003	0.0193	0.0472	0.017	-0.0165	0.0566	0.0808	0.0108	0.0852	0.0104	-0.0081	0.1174	0.007	0.0981	14.3537	20.2486	75.423
4	2.159	-0.8819	-0.3042	1.8848	0.2007	1.2832	-0.0628	-0.016	0.019	0.0496	0.0606	0.0094	0.1803	0.2091	0.006	0.1375	0.051	-0.0025	0.1532	-0.0005	0.1263	23.7919	3.1622	65.0541
5	1.0466	0.1024	0.4276	0.791	0.1169	3.1398	0.0584	0.1698	-0.0662	-0.189	-0.0599	-0.0259	0.4487	0.1901	0.005	0.2784	0.0456	0.0109	0.2004	-0.0305	0.1824	22.9714	-3.5234	49.3307
6	2.6853	0.5548	0.2906	4.2978	1.2193	1.0288	0.0897	0.5069	-0.2995	-0.4317	0.0127	-0.0945	0.5713	0.169	0.0024	0.4583	0.0444	-0.0067	0.3168	-0.048	0.1877	19.7804	-5.1062	34.765
7	4.9607	-2.2478	0.9746	3.5594	-0.0606	3.834	-0.247	0.0914	0.1139	-0.6616	0.1537	0.382	0.2164	-0.3173	0.1206	0.3683	-0.1005	-0.0395	0.1892	0.0047	0.2527	-23.5903	4.0419	58.1088
8	1.8224	1.3004	-1.0865	1.069	-1.0329	1.1181	-0.279	-0.0798	-0.0864	-1.43	0.0542	-0.6695	0.2393	0.4381	0.2633	0.6344	-0.0464	0.1275	0.2898	-0.0227	0.2828	-14.6035	8.1318	52.7804
9	0.6727	0.6187	-0.019	4.3405	-0.983	0.702	-0.0501	-0.0291	-0.1483	-0.1092	0.0061	-0.163	0.1137	-0.0166	0.0434	0.1619	-0.0074	0.0066	0.1569	0.0143	0.1919	-14.7818	22.3665	64.7733
10	1.5018	-0.7027	0.2135	2.3718	-0.2045	1.7585	-0.0077	-0.0227	-0.0375	0.1001	-0.0043	-0.0586	0.0611	-0.0241	0.0137	0.1429	-0.0061	0.01	0.1269	-0.0006	0.1332	-18.5258	44.5278	62.1536
11	2.8207	0.0044	-0.1858	1.568	-0.3634	3.686	0.0394	0.2232	0.1146	-0.1278	-0.0549	-0.0479	-0.1586	0.0084	0.0004	0.1464	0.0033	0.0205	0.1125	0.0192	0.1342	-21.0979	53.3886	53.4879
12	0.848	0.2956	-0.0251	0.864	-0.0503	4.0577	0.0036	0.0461	0.0346	-0.0082	-0.0692	0.0094	-0.3593	-0.0584	0.0615	0.2366	0.0072	0.0065	0.1924	0.0204	0.1577	-24.7122	58.1276	40.4986
13	2.1486	1.2629	-0.8659	3.1438	0.2755	1.649	-0.0082	0.3611	0.0608	-0.1788	0.0759	0.074	-0.3697	-0.1846	-0.0196	0.2736	0.0154	-0.0167	0.2331	0.0324	0.1114	-25.9723	59.0273	25.6462
14	1.6436	-1.8604	-2.1593	3.9702	3.3354	4.6368	0.3584	0.4517	-0.2046	-0.5961	-0.1668	0.1844	-0.1442	-0.0746	-0.0867	0.2848	0.0592	-0.0522	0.3214	-0.0281	0.25	12.1014	8.2991	55.0795
15	4.9527	-2.5397	0.8149	7.2121	3.2112	7.1328	0.1273	0.1192	-0.2856	-0.419	-0.0508	0.2645	0.1966	0.0114	-0.0343	0.1727	0.0261	0.0067	0.1619	0.0198	0.1282	9.8693	25.0239	60.9715
16	1.1998	-2.53	1.5243	5.4062	-3.2716	1.9827	0.3723	0.2975	-0.0458	-1.2052	-0.2727	0.1397	0.6781	-0.1953	0.0023	0.4101	0.028	0.0251	0.3101	0.0011	0.2402	-17.4401	42.5018	43.5072
17	7.5569	2.2851	-0.7831	4.7337	-3.8842	5.1759	-0.2436	0.2692	0.1229	-0.8169	0.4389	0.4464	0.3761	-0.6148	-0.0991	0.2837	-0.0422	-0.0388	0.2068	0.0079	0.2018	-19.2613	26.017	51.2442

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 23 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 72 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 73 through 174 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 175 through 228 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 229 through 293 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 294 through 330 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 0 through 23 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 24 through 38 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 39 through 140 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 141 through 194 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 195 through 228 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 229 through 293 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 294 through 330 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1250 through 1261 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 1262 through 1272 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1250 through 1261 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1262 through 1272 )

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