PDB-6b0t: Structural Insights into the Induced-fit Inhibition of Fascin by ...

ID or keywords:

Entry

Database: PDB / ID: 6b0t

Title

Structural Insights into the Induced-fit Inhibition of Fascin by a Small Molecule

Components

Fascin

Keywords

PROTEIN BINDING / Metastaic cancers / Small-molecule inhibitors / actin-bundling / Domain rotation

Function / homology

Function and homology information

microspike / parallel actin filament bundle assembly / regulation of microvillus assembly / positive regulation of extracellular matrix disassembly / establishment of apical/basal cell polarity / microspike assembly / cell projection membrane / cell-cell junction assembly / positive regulation of podosome assembly / positive regulation of filopodium assembly ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.8 Å

Authors

Dey, R. / Huang, X.Y.

Funding support

United States, 1items

Citation

Journal: J. Mol. Biol. / Year: 2018
Title: Structural Insights into the Induced-fit Inhibition of Fascin by a Small-Molecule Inhibitor.
Authors: Huang, J. / Dey, R. / Wang, Y. / Jakoncic, J. / Kurinov, I. / Huang, X.Y.

History

Deposition	Sep 15, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 18, 2018	Provider: repository / Type: Initial release
Revision 1.1	May 9, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2	Feb 20, 2019	Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6b0t.cif.gz	1.6 MB	Display	PDBx/mmCIF format
PDB format	pdb6b0t.ent.gz	1.4 MB	Display	PDB format
PDBx/mmJSON format	6b0t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6b0t_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	6b0t_full_validation.pdf.gz	2.3 MB	Display
Data in XML	6b0t_validation.xml.gz	103.4 KB	Display
Data in CIF	6b0t_validation.cif.gz	137 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b0/6b0t ftp://data.pdbj.org/pub/pdb/validation_reports/b0/6b0t	HTTPS FTP

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Related structure data

Related structure data	3llpS S: Starting model for refinement
Similar structure data	4gov-2 6i16-d 1dfc-2 4gp0-2 6i14-d 6i17-d 6i12-d 6i15-d 3llp-2 6i18-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

3llpS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Fascin

B: Fascin

C: Fascin

D: Fascin

E: Fascin

F: Fascin

hetero molecules

327 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Fascin

hetero molecules

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

2

B: Fascin

hetero molecules

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

3

C: Fascin

hetero molecules

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

4

D: Fascin

hetero molecules

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

5

E: Fascin

hetero molecules

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

6

F: Fascin

hetero molecules

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

Unit cell

Length a, b, c (Å)	102.577, 59.255, 293.651
Angle α, β, γ (deg.)	90.00, 90.03, 90.00
Int Tables number	3
Space group name H-M	P121

#1: Protein	Fascin / 55 kDa actin-bundling protein / Singed-like protein / p55 Mass: 54026.242 Da / Num. of mol.: 6 / Fragment: residues 7-493 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FSCN1, FAN1, HSN, SNL / Production host: Escherichia coli (E. coli) / References: UniProt: Q16658
#2: Chemical	ChemComp-C7V / 4-methyl-N-(1-{[4-(trifluoromethyl)phenyl]methyl}-1H-indazol-3-yl)-1,2-oxazole-5-carboxamide Mass: 400.354 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₀H₁₅F₃N₄O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.75 Å³/Da / Density % sol: 55.32 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 24% PEG 4000, 50mM Tris HCL (pH 8), 3.3% glycerol, 142mM NaCl, 5mM MgCl2, 10mM CaCl2 and 0.004% NaN3

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.3 Å
Detector	Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.3 Å / Relative weight: 1
Reflection	Resolution: 2.8→45.44 Å / Num. obs: 87042 / % possible obs: 98.61 % / Redundancy: 4.2 % / CC_1/2: 0.99 / R_merge(I) obs: 0.09 / Net I/σ(I): 13.59
Reflection shell	Resolution: 2.8→2.9 Å / R_merge(I) obs: 0.44 / Num. unique obs: 8516 / CC_1/2: 0.87

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829)	refinement
XDS		data reduction
XDS		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3LLP

3llp

Resolution: 2.8→45.44 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3028	4260	4.9 %
R_work	0.2651	-	-
obs	0.267	86895	98.64 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.8→45.44 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22818	0	174	344	23336

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	23688
X-RAY DIFFRACTION	f_angle_d	0.603	32106
X-RAY DIFFRACTION	f_dihedral_angle_d	18.472	8640
X-RAY DIFFRACTION	f_chiral_restr	0.047	3426
X-RAY DIFFRACTION	f_plane_restr	0.004	4218

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 (%)
2.8001-2.8319	0.3471	133	0.3384	2702	X-RAY DIFFRACTION	98
2.8319-2.8652	0.3709	154	0.3351	2636	X-RAY DIFFRACTION	98
2.8652-2.9001	0.3988	117	0.3225	2774	X-RAY DIFFRACTION	98
2.9001-2.9368	0.4	127	0.338	2763	X-RAY DIFFRACTION	98
2.9368-2.9755	0.368	162	0.3169	2652	X-RAY DIFFRACTION	98
2.9755-3.0162	0.3521	159	0.3138	2728	X-RAY DIFFRACTION	98
3.0162-3.0593	0.318	154	0.3036	2662	X-RAY DIFFRACTION	98
3.0593-3.105	0.3389	117	0.2988	2843	X-RAY DIFFRACTION	99
3.105-3.1535	0.2941	139	0.2969	2644	X-RAY DIFFRACTION	98
3.1535-3.2052	0.33	142	0.2994	2794	X-RAY DIFFRACTION	98
3.2052-3.2604	0.351	151	0.3114	2691	X-RAY DIFFRACTION	99
3.2604-3.3197	0.3665	165	0.3015	2717	X-RAY DIFFRACTION	99
3.3197-3.3835	0.3352	125	0.2962	2734	X-RAY DIFFRACTION	99
3.3835-3.4526	0.3502	165	0.2804	2714	X-RAY DIFFRACTION	99
3.4526-3.5276	0.3089	155	0.2767	2764	X-RAY DIFFRACTION	99
3.5276-3.6096	0.277	124	0.2773	2740	X-RAY DIFFRACTION	99
3.6096-3.6999	0.3012	150	0.2716	2800	X-RAY DIFFRACTION	99
3.6999-3.7999	0.3306	170	0.2682	2672	X-RAY DIFFRACTION	99
3.7999-3.9116	0.2989	118	0.2552	2815	X-RAY DIFFRACTION	99
3.9116-4.0378	0.3082	100	0.2557	2767	X-RAY DIFFRACTION	99
4.0378-4.182	0.2689	150	0.2354	2787	X-RAY DIFFRACTION	99
4.182-4.3494	0.249	121	0.2247	2796	X-RAY DIFFRACTION	99
4.3494-4.5471	0.2405	165	0.2067	2778	X-RAY DIFFRACTION	99
4.5471-4.7866	0.2235	140	0.2148	2742	X-RAY DIFFRACTION	99
4.7866-5.0862	0.2798	145	0.2218	2791	X-RAY DIFFRACTION	99
5.0862-5.4783	0.2966	136	0.2387	2823	X-RAY DIFFRACTION	99
5.4783-6.0285	0.3219	130	0.2524	2830	X-RAY DIFFRACTION	99
6.0285-6.8984	0.287	146	0.2625	2817	X-RAY DIFFRACTION	99
6.8984-8.6817	0.2948	136	0.2547	2861	X-RAY DIFFRACTION	99
8.6817-46.1154	0.2613	164	0.2578	2798	X-RAY DIFFRACTION	94

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	3.8534	-0.1313	-0.6792	4.0769	-1.7928	4.4765	0.3517	0.5462	0.7549	-0.066	0.134	0.011	-0.6929	-0.9499	-0.2702	0.6067	0.1237	0.1305	0.5097	0.1122	0.3706	64.8045	94.3609	-283.4886
2	1.5887	0.0703	-1.409	1.117	-0.3265	1.3181	-0.7806	0.5908	-0.9008	0.5866	0.1844	0.7965	1.4068	-0.7696	0.3069	1.1238	-0.2838	0.5032	0.5178	-0.1223	0.7841	52.2845	74.2567	-269.5414
3	2.0254	0.0716	0.5882	1.1777	0.2229	0.9162	0.2562	-0.2065	-0.3544	0.2172	-0.2851	-0.1856	-0.3939	-0.2483	-0.0211	1.1978	0.3675	-0.0558	0.9082	0.0085	0.7406	74.7526	62.895	-249.8666
4	2.0343	-0.7602	0.9375	1.1059	-0.9404	1.8067	-1.0041	-0.1554	-0.6358	0.9329	0.1755	0.0308	1.0715	0.1798	-1.1131	1.3755	0.2067	0.5097	0.4098	-0.0319	0.5076	77.3336	64.5813	-276.138
5	4.336	-0.0148	-1.85	4.3133	0.6575	3.5637	0.2552	0.3015	-0.3455	-0.0438	-0.2811	-0.0521	-0.0859	-0.1541	0.0048	0.2419	0.0742	-0.0318	0.304	-0.0502	0.2311	100.0198	105.163	-185.4427
6	2.7526	1.1488	-0.1364	2.0581	-0.5492	3.4485	0.0698	0.1232	0.2364	-0.0923	-0.0898	0.0986	-0.2437	-0.0454	0.012	0.2841	0.0554	-0.0103	0.2483	-0.0335	0.3498	89.1085	126.5144	-171.9295
7	2.7113	1.32	-0.4018	3.1521	-0.7005	3.5432	-0.1249	-0.2101	-0.4151	0.2455	-0.0337	0.1612	0.4467	-0.1765	0.1739	0.2956	0.0082	0.0779	0.3437	-0.0038	0.4865	67.7574	112.7445	-151.9399
8	2.9398	-0.2635	-0.648	1.418	0.4621	2.1473	0.0799	0.2548	-0.3127	-0.2573	-0.3079	0.492	0.1613	-0.4156	0.1654	0.2597	0.0187	-0.04	0.4784	-0.174	0.5276	68.1954	110.5004	-178.4507
9	3.7744	-0.9094	-0.7233	2.756	0.9232	2.3985	0.1692	-0.1117	-0.0933	-0.2279	0.2706	-0.3987	-0.5338	0.7494	-0.3294	0.3124	-0.0511	0.0592	0.7012	-0.1653	0.4045	48.4285	76.6035	-185.9998
10	1.1835	0.1213	-0.2525	2.684	0.2669	2.1829	0.3588	-0.0107	0.5196	-0.5256	0.2227	-0.4364	-0.9737	0.5773	-0.3262	0.6191	-0.0868	0.1604	0.3303	-0.1131	0.5457	36.6024	96.1457	-170.9091
11	3.3362	1.1724	0.4064	3.3114	-1.7283	3.6303	0.1449	-0.3422	0.039	0.3272	-0.1232	0.1067	-0.1943	0.0106	-0.0377	0.2315	0.0096	0.0421	0.299	-0.0245	0.2393	17.2818	78.9476	-151.6611
12	2.8133	1.7757	-0.9208	1.9824	0.4572	3.7918	-0.0208	0.0819	-0.0411	-0.1478	0.0087	-0.0634	-0.1038	-0.0259	0.0053	0.2308	0.0697	-0.0209	0.2396	-0.0042	0.3037	16.404	79.2302	-178.0057
13	3.1807	-1.0953	1.5175	2.2525	0.1651	2.6249	0.3583	-0.0813	-0.4513	0.5287	0.3327	-0.5953	1.2384	0.4897	-0.4081	0.699	0.1786	-0.2937	0.4662	-0.1272	0.5524	62.0743	99.2589	-205.9473
14	1.1568	-0.6623	0.6534	2.1324	1.4152	2.2367	0.495	-0.0348	-0.3205	-0.2407	-1.3068	1.2607	0.1542	-1.5493	-0.0751	0.3955	0.064	-0.2156	1.1599	-0.4384	0.7643	38.4016	98.5927	-219.9476
15	1.2388	-0.1547	-0.5883	2.6729	-0.419	0.9709	-0.214	0.5841	0.6559	0.4142	0.145	-0.4437	-0.0554	0.0791	-0.052	0.9723	0.3073	-0.1235	0.8866	0.1009	0.8008	39.7085	123.3543	-239.8225
16	1.2164	-0.5387	0.7599	1.9506	-0.2443	0.8878	0.3369	0.3962	0.3985	-0.9538	-0.8825	0.1563	-0.6621	-0.5706	0.0698	0.6762	0.5191	-0.0629	0.7265	-0.2255	0.4945	42.5471	124.9082	-213.46
17	3.8059	-0.1787	1.2802	4.2617	-0.1348	3.3297	0.0857	0.146	-0.2787	0.3193	0.1565	-0.4586	0.8462	0.461	-0.1676	0.5236	0.1118	-0.1149	0.3932	-0.0711	0.3582	113.3656	69.2301	-205.9812
18	0.8858	-0.7944	0.1477	1.6525	0.9749	1.4142	0.3215	0.2352	-0.4474	-0.24	-1.3235	1.5183	0.0988	-1.3312	0.0773	0.4768	0.0235	-0.1383	1.0748	-0.551	0.8503	89.7121	68.4466	-219.9424
19	1.2869	0.0813	-0.9402	3.1467	-0.354	1.4417	-0.063	0.5097	0.2801	0.6376	0.2613	-0.4019	0.168	-0.0659	-0.3018	0.9294	0.3059	-0.115	0.8884	0.0646	0.6899	91.0127	93.6396	-239.5086
20	0.3471	-0.2037	0.1857	1.235	0.6513	0.8355	0.1409	0.3094	0.322	-0.9106	-0.8639	0.6286	-0.7341	-0.8483	-0.7373	0.6739	0.6975	-0.2025	0.7894	-0.3777	0.6257	93.747	94.836	-213.2807
21	2.7615	-0.4089	-0.1396	3.9867	-1.7106	3.435	0.4378	0.3927	0.7466	-0.4018	0.0334	-0.1641	-0.8551	-0.8471	-0.2834	0.7688	0.1952	0.1895	0.5553	0.0948	0.4307	13.5476	123.9531	-283.4066
22	2.2012	-0.2336	-1.7074	2.1338	-0.2566	2.3192	-0.8014	0.5472	-1.0271	0.6537	0.1261	1.0176	1.3058	-0.8397	0.5287	0.7904	-0.1341	0.3735	0.5339	-0.111	0.7882	1.0648	103.8218	-269.413
23	1.5325	0.0332	0.5044	0.9677	0.1134	0.6983	0.1362	-0.0557	-0.3175	0.3466	-0.1337	-0.3896	-0.0756	-0.0196	-0.0697	1.2199	0.3855	-0.1383	0.8918	-0.0366	0.8433	23.4599	92.5046	-249.6023
24	2.0613	-1.0112	-0.2553	2.3614	-1.1258	1.0182	-0.8623	-0.3171	-0.4098	0.8463	0.4074	-0.1402	1.2017	0.3202	0.3172	0.9054	0.2541	0.2025	0.4117	-0.0092	0.4616	25.966	94.2064	-276.0038

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 138 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 139 through 260 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 261 through 382 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 383 through 493 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 7 through 138 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 139 through 260 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 261 through 382 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 383 through 493 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 7 through 138 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 139 through 260 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 261 through 382 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 383 through 493 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 7 through 138 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 139 through 260 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 261 through 382 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 383 through 493 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 7 through 138 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 139 through 260 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 261 through 382 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 383 through 493 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 7 through 138 )
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 139 through 260 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 261 through 382 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 383 through 493 )

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Yorodumi