PDB-6ikn: Crystal structure of the GAS7 F-BAR domain

ID or keywords:

Entry

Database: PDB / ID: 6ikn

Title

Crystal structure of the GAS7 F-BAR domain

Components

Growth arrest-specific protein 7

Keywords

LIPID BINDING PROTEIN / membrane deformation / phagocytosis / F-BAR domain

Function / homology

Function and homology information

actin filament bundle assembly / ruffle / actin filament polymerization / neuron projection morphogenesis / actin filament / neuron differentiation / actin filament binding / regulation of cell shape / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3 Å

Authors

Hanawa-Suetsugu, K. / Itoh, Y. / Kohda, D. / Shimada, A. / Suetsugu, S.

Funding support

Japan, 11items

Organization	Grant number	Country
Japan Society for the Promotion of Science	KAKENHI 24687014	Japan
Japan Society for the Promotion of Science	KAKENHI 25121726	Japan
Japan Society for the Promotion of Science	KAKENHI 17K07309	Japan
Japan Society for the Promotion of Science	KAKENHI 26291037	Japan
Japan Society for the Promotion of Science	KAKENHI 15H0164	Japan
Japan Society for the Promotion of Science	KAKENHI 15H05902	Japan
Japan Society for the Promotion of Science	KAKENHI 17H03674	Japan
Japan Society for the Promotion of Science	KAKENHI 17H06006	Japan
Japan Society for the Promotion of Science	NEXT program LS031	Japan
Japan Society for the Promotion of Science	KAKENHI 16K07351	Japan
Japan Society for the Promotion of Science	KAKENHI 23121507	Japan

Citation

Journal: Nat Commun / Year: 2019
Title: Phagocytosis is mediated by two-dimensional assemblies of the F-BAR protein GAS7.
Authors: Hanawa-Suetsugu, K. / Itoh, Y. / Ab Fatah, M. / Nishimura, T. / Takemura, K. / Takeshita, K. / Kubota, S. / Miyazaki, N. / Wan Mohamad Noor, W.N.I. / Inaba, T. / Nguyen, N.T.H. / Hamada- ...

History

Deposition	Oct 16, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Oct 16, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6ikn.cif.gz	513.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6ikn.ent.gz	440.4 KB	Display	PDB format
PDBx/mmJSON format	6ikn.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6ikn_validation.pdf.gz	448.2 KB	Display	wwPDB validaton report
Full document	6ikn_full_validation.pdf.gz	464.1 KB	Display
Data in XML	6ikn_validation.xml.gz	41.2 KB	Display
Data in CIF	6ikn_validation.cif.gz	56.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ik/6ikn ftp://data.pdbj.org/pub/pdb/validation_reports/ik/6ikn	HTTPS FTP

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Related structure data

Related structure data	6ikoC C: citing same article (ref.)
Similar structure data	6iko-d 6xj1-d 4dyl-1 2efl-1 1ojv-d 1ok3-d 1ojy-2 1ok1-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	#245 - May 2020 Spliceosomes similarity (6) #88 - Apr 2007 Clathrin similarity (1)

Deposited unit

A: Growth arrest-specific protein 7

B: Growth arrest-specific protein 7

C: Growth arrest-specific protein 7

D: Growth arrest-specific protein 7

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

1

A: Growth arrest-specific protein 7

B: Growth arrest-specific protein 7

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

2

C: Growth arrest-specific protein 7

D: Growth arrest-specific protein 7

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

Unit cell

Length a, b, c (Å)	53.264, 87.281, 88.793
Angle α, β, γ (deg.)	80.98, 74.72, 79.73
Int Tables number	1
Space group name H-M	P1

#1: Protein	Growth arrest-specific protein 7 / GAS-7 Mass: 39618.117 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gas7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q60780*PLUS
Sequence details	The authors state the reference sequence is GenBank XM_006532202.1 and that residues 146-165 are ...The authors state the reference sequence is GenBank XM_006532202.1 and that residues 146-165 are expression tags.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 49.92 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: PEG 4000, PEG 8000, ammonium sulfate, 80 mM HEPES-NaOH (pH 7.5), MES (pH 6.5) PH range: 6.5-7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.9789 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 23, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9789 Å / Relative weight: 1
Reflection	Resolution: 3→50 Å / Num. obs: 30444 / % possible obs: 99.1 % / Redundancy: 6.4 % / CC_1/2: 0.97 / Net I/σ(I): 7
Reflection shell	Resolution: 3→3.05 Å / Num. unique obs: 1515 / CC_1/2: 0.49

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Processing

Software

Name	Version	Classification
PHENIX	1.8.2_1309	refinement
HKL-2000		data reduction
HKL-2000		data scaling
autoSHARP		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3→32.029 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.45

	R_factor	Num. reflection	% reflection
R_free	0.2547	1501	5.04 %
R_work	0.194	-	-
obs	0.197	29801	98.83 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3→32.029 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10017	0	0	0	10017

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	10181
X-RAY DIFFRACTION	f_angle_d	0.934	13660
X-RAY DIFFRACTION	f_dihedral_angle_d	16.573	4032
X-RAY DIFFRACTION	f_chiral_restr	0.037	1473
X-RAY DIFFRACTION	f_plane_restr	0.005	1778

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 (%)
3-3.0968	0.3244	135	0.2875	2520	X-RAY DIFFRACTION	97
3.0968-3.2074	0.3222	135	0.2521	2550	X-RAY DIFFRACTION	99
3.2074-3.3356	0.2941	129	0.2543	2610	X-RAY DIFFRACTION	99
3.3356-3.4873	0.2904	128	0.2362	2592	X-RAY DIFFRACTION	99
3.4873-3.6709	0.2822	151	0.2077	2543	X-RAY DIFFRACTION	99
3.6709-3.9005	0.2588	136	0.1908	2577	X-RAY DIFFRACTION	99
3.9005-4.2011	0.2411	144	0.1819	2585	X-RAY DIFFRACTION	99
4.2011-4.6227	0.2398	145	0.164	2571	X-RAY DIFFRACTION	99
4.6227-5.289	0.2141	133	0.1631	2592	X-RAY DIFFRACTION	99
5.289-6.6538	0.2727	139	0.2077	2599	X-RAY DIFFRACTION	100
6.6538-32.031	0.2029	126	0.1528	2561	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	2.0003	-0.4553	1.9071	0.9492	-0.1821	1.8676	-0.2275	1.8081	0.0059	-0.2857	0.327	0.4352	-0.0269	-1.268	-0.034	0.4314	-0.0105	-0.1033	0.9119	0.088	0.3317	25.3977	10.2387	-1.5928
2	6.0671	-3.9946	2.2644	2.4973	-1.0958	1.1496	-0.6864	-0.8829	0.0735	0.4762	0.5891	-0.1637	-0.2119	-0.2847	0.0442	0.3719	0.0621	0.0281	0.3718	0.0491	0.3618	59.8166	-12.8255	21.0967
3	3.9568	-4.4624	3.79	5.1955	-2.7688	4.9955	-0.0701	-0.8878	0.2022	0.1847	0.2588	0.5935	0.5855	-0.0857	-0.0516	0.4979	0.0866	-0.0521	0.5012	0.0968	0.4969	22.3692	11.4162	16.3927
4	3.1922	-1.9708	0.3587	2.6762	-0.5998	0.5696	-0.0857	-0.1711	1.2403	-0.0563	0.1103	-0.4088	0.0134	-0.1036	0.009	0.4578	0.0087	-0.0273	0.3177	-0.0597	0.2779	30.9818	10.894	12.2067
5	3.272	-4.2273	1.5309	4.6673	-0.8428	2.4946	-0.0275	0.1618	0.5531	0.2828	-0.2423	-0.3398	-0.091	0.4458	0.2859	0.2589	0.0513	-0.0108	0.3987	0.0537	0.4635	106.4005	-40.4837	29.1652
6	1.7731	-2.001	-0.1359	5.5216	-2.1728	6.1216	0.1804	0.1516	0.5871	-0.1366	-0.3516	-0.9229	0.6446	0.4838	0.2075	0.4442	0.0357	-0.0748	0.5455	-0.0426	0.656	115.3196	-52.4564	36.5186
7	4.745	-5.8019	4.8054	6.4713	-4.7284	3.4705	-0.4891	-0.9321	-1.0505	0.1739	0.7536	0.4193	-0.2708	-0.3557	-0.1858	0.3805	0.0892	0.0354	0.3671	0.0778	0.4835	81.5209	-39.6787	26.3935
8	7.0023	-5.3524	1.5403	7.3855	-1.7441	1.973	0.144	-0.3902	-0.343	-0.5365	0.0303	0.2252	0.1833	-0.0988	-0.0464	0.3443	-0.0155	-0.0031	0.3472	0.0405	0.2622	68.5843	-28.3711	14.443
9	6.9627	-4.9994	1.5493	6.7847	-2.7979	3.1376	0.0075	-0.4163	-0.3262	-0.1355	-0.0979	0.1849	0.619	0.4481	-0.0341	0.7718	0.1909	-0.0609	0.5865	0.057	0.4875	118.2051	-74.737	39.3434
10	7.4444	-6.3836	2.0721	5.6192	-1.8723	0.8106	0.2044	-0.0334	0.0403	-0.307	-0.12	-0.1251	0.2431	0.1276	0.0217	0.4507	0.0486	-0.0342	0.3308	-0.0297	0.3071	90.4063	-40.6282	19.8835
11	7.8314	-2.0559	-1.6095	5.4043	3.5603	2.5463	-0.7895	-2.4772	0.0493	1.4256	0.5915	0.7364	-0.4001	-1.3669	0.2122	0.7004	0.0708	0.1993	1.02	0.0338	0.5516	-0.6341	-36.874	5.1663
12	5.8856	3.7972	-1.8978	2.6874	-1.2681	1.0827	-0.4648	0.916	0.0042	-0.2764	0.5452	0.0504	0.0303	-0.1602	-0.0573	0.4108	-0.0831	0.0339	0.4382	-0.0397	0.3611	33.4518	-13.7336	-17.1379
13	3.6416	4.1733	-1.456	3.6322	-1.8815	1.966	0.2964	1.5179	0.0086	-0.5674	0.3313	0.6646	-0.3118	-0.2357	0.0222	0.4402	-0.1676	0.1192	0.7372	-0.034	0.682	-7.3978	-38.6356	-11.7282
14	1.0204	-0.1736	-0.105	1.6578	-1.2558	0.9756	0.0522	0.1308	-0.1176	-0.3041	0.2881	1.605	0.3676	-0.7982	-0.0815	0.843	-0.1004	0.0097	1.2887	0.0166	1.1862	-43.9782	-51.0846	-0.2617
15	5.2741	3.3016	-1.0361	2.5572	-0.7742	0.4625	-0.1743	0.1959	-0.7196	-0.1357	0.1187	-0.342	0.0728	-0.02	0.1416	0.4187	-0.0703	0.0677	0.2793	-0.1669	0.2639	32.638	-20.643	-14.0008
16	5.6182	3.2784	-3.1931	6.952	-6.6031	9.5567	-0.1882	-0.0396	-0.0247	-0.0776	0.1149	-0.4682	-0.2505	-0.0439	0.0228	0.6115	-0.117	0.1859	0.765	-0.3965	0.6173	90.31	25.4986	-30.544
17	6.2219	8.1959	-5.921	8.913	-4.7201	3.7433	0.1383	-0.0434	0.4286	-0.1281	-0.0067	0.0223	-0.1323	0.1458	-0.2376	0.4678	-0.1318	0.0223	0.4951	0.051	0.3829	55.4977	12.9143	-22.2272
18	8.0911	7.4562	-1.4455	9.1202	-0.8962	0.3634	0.4484	0.0542	0.2019	0.5315	-0.2399	0.1355	-0.0546	0.1805	-0.2907	0.3525	-0.015	0.0383	0.476	0.0755	0.2305	36.6279	-4.1994	-8.9593
19	2.5848	-0.2628	-1.4775	5.8806	-2.8911	2.0033	0.6597	0.1497	2.8135	-0.0668	-0.142	-0.8731	-3.0586	0.4245	-0.8885	-0.0029	-0.3502	0.3891	1.0365	0.3152	1.2337	59.2148	20.4319	-15.5052
20	2.9439	1.064	-0.0818	3.8953	-0.7821	1.7501	0.326	0.7554	0.6758	-0.0556	-0.1397	0.3281	-0.6688	0.0263	-0.1023	1.0976	-0.2577	0.4363	0.7175	-0.0536	1.0868	94.5873	47.2568	-34.8253
21	8.5096	6.597	-2.6655	5.9011	-2.1388	1.4097	0.6514	-0.1921	0.4188	0.6325	-0.253	-0.0848	-0.591	0.2786	-0.2303	0.5444	-0.1154	0.143	0.4569	-0.1367	0.4983	63.9437	12.4997	-14.8126

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 171 through 192 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 193 through 308 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 309 through 351 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 352 through 440 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 441 through 475 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 172 through 218 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 219 through 259 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 260 through 310 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 311 through 360 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 361 through 475 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 172 through 192 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 193 through 308 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 309 through 355 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 356 through 363 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 364 through 475 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 172 through 218 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 219 through 259 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 260 through 299 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 300 through 310 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 311 through 362 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 363 through 475 )

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