PDB-5gw0: Crystal structure of SNX16 PX-Coiled coil

ID or keywords:

Entry

Database: PDB / ID: 5gw0

Title

Crystal structure of SNX16 PX-Coiled coil

Components

Sorting nexin-16

Keywords

PROTEIN TRANSPORT / Sorting nexin / PX domain / endosome sorting

Function / homology

Function and homology information

receptor recycling / early endosome to late endosome transport / protein targeting to lysosome / endosome to lysosome transport / phosphatidylinositol binding / late endosome membrane / late endosome / early endosome membrane / early endosome / lysosome ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 3.3 Å

Authors

Xu, J. / Liu, J.

Citation

Journal: Structure / Year: 2017
Title: SNX16 Regulates the Recycling of E-Cadherin through a Unique Mechanism of Coordinated Membrane and Cargo Binding.
Authors: Xu, J. / Zhang, L. / Ye, Y. / Shan, Y. / Wan, C. / Wang, J. / Pei, D. / Shu, X. / Liu, J.

History

Deposition	Sep 8, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 30, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5gw0.cif.gz	441.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5gw0.ent.gz	371.4 KB	Display	PDB format
PDBx/mmJSON format	5gw0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5gw0_validation.pdf.gz	470.6 KB	Display	wwPDB validaton report
Full document	5gw0_full_validation.pdf.gz	492.6 KB	Display
Data in XML	5gw0_validation.xml.gz	37 KB	Display
Data in CIF	5gw0_validation.cif.gz	50.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gw/5gw0 ftp://data.pdbj.org/pub/pdb/validation_reports/gw/5gw0	HTTPS FTP

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Related structure data

Related structure data	5gw1C 5gw8 C: citing same article (ref.)
Similar structure data	5gw1-4 1c8n-d 5gw1-1 5f4e-d 5gw1-2 6rj0-d 5gw1-3 5jke-2 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

5gw1C

5gw8

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Sorting nexin-16

B: Sorting nexin-16

C: Sorting nexin-16

D: Sorting nexin-16

E: Sorting nexin-16

F: Sorting nexin-16

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

1

A: Sorting nexin-16

F: Sorting nexin-16

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

2

B: Sorting nexin-16

D: Sorting nexin-16

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

3

C: Sorting nexin-16

E: Sorting nexin-16

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

Unit cell

Length a, b, c (Å)	70.380, 196.780, 72.960
Angle α, β, γ (deg.)	90.00, 111.75, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Sorting nexin-16 Mass: 21451.066 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 100-278 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNX16 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P57768
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.67 Å³/Da / Density % sol: 66.49 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS Mosaicity: 0.56 °
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 7.5 Details: 31mM Citric, 69mM Bis-tris Propanol, 18% PEG 5000, 70mM NaF, 2mM TCEP

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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: Apr 18, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9791 Å / Relative weight: 1

Reflection

Resolution: 3.3→56.77 Å / Num. obs: 27200 / % possible obs: 98.3 % / Redundancy: 3.6 % / B_iso Wilson estimate: 110.09 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.087 / R_pim(I) all: 0.052 / R_rim(I) all: 0.102 / Net I/σ(I): 10.6 / Num. measured all: 98589 / Scaling rejects: 8

Reflection shell

Diffraction-ID: 1 / Redundancy: 3.6 % / Rejects: _

Resolution (Å)	R_merge(I) obs	Num. measured all	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Net I/σ(I) obs	% possible all
3.3-3.5	0.633	16305	4480	0.647	0.383	0.741	2.1	99.5
9.9-56.77	0.056	3117	873	0.993	0.034	0.066	33	83.4

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Processing

Software

Name	Version	Classification
PHENIX	1.8.1_1168	refinement
MOSFLM		data collection
Aimless	0.5.12	data scaling
PDB_EXTRACT	3.2	data extraction
Aimless		data reduction
MR-Rosetta		phasing

Refinement

Resolution: 3.3→19.991 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 33.31 / Stereochemistry target values: MLHL
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS

	R_factor	Num. reflection	% reflection
R_free	0.288	2650	5.02 %
R_work	0.2363	-	-
obs	0.239	27163	97.01 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.3→19.991 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8558	0	0	0	8558

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	8729
X-RAY DIFFRACTION	f_angle_d	1.381	11748
X-RAY DIFFRACTION	f_dihedral_angle_d	17.816	3419
X-RAY DIFFRACTION	f_chiral_restr	0.073	1282
X-RAY DIFFRACTION	f_plane_restr	0.006	1514

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 (%)
3.3001-3.3599	0.384	133	0.3711	2695	X-RAY DIFFRACTION	98
3.3599-3.4242	0.377	143	0.3537	2625	X-RAY DIFFRACTION	98
3.4242-3.4937	0.3479	141	0.3477	2731	X-RAY DIFFRACTION	98
3.4937-3.5693	0.4492	106	0.3242	2633	X-RAY DIFFRACTION	98
3.5693-3.6518	0.3121	149	0.3117	2720	X-RAY DIFFRACTION	98
3.6518-3.7426	0.3109	123	0.2824	2600	X-RAY DIFFRACTION	98
3.7426-3.8431	0.3536	146	0.2957	2720	X-RAY DIFFRACTION	97
3.8431-3.9553	0.3452	128	0.2739	2649	X-RAY DIFFRACTION	98
3.9553-4.0819	0.3145	119	0.2654	2702	X-RAY DIFFRACTION	98
4.0819-4.2265	0.2977	153	0.2551	2627	X-RAY DIFFRACTION	98
4.2265-4.394	0.3139	148	0.2436	2701	X-RAY DIFFRACTION	98
4.394-4.5917	0.3233	166	0.2389	2560	X-RAY DIFFRACTION	97
4.5917-4.8305	0.2811	115	0.2221	2679	X-RAY DIFFRACTION	98
4.8305-5.1284	0.2559	128	0.213	2650	X-RAY DIFFRACTION	97
5.1284-5.5166	0.2812	159	0.2312	2634	X-RAY DIFFRACTION	97
5.5166-6.0577	0.3108	125	0.2615	2424	X-RAY DIFFRACTION	89
6.0577-6.9025	0.2913	143	0.2463	2663	X-RAY DIFFRACTION	99
6.9025-8.5805	0.2553	166	0.1948	2703	X-RAY DIFFRACTION	100
8.5805-19.9918	0.2161	159	0.1535	2465	X-RAY DIFFRACTION	91

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	5.702	-0.0418	1.1578	6.7367	-0.1413	5.4247	0.4039	-0.1123	-0.179	-0.3553	-0.2776	-0.1772	0.6131	0.0767	0.0141	0.5376	0.2666	0.108	0.3122	-0.046	0.5395	24.6382	2.3664	22.0825
2	-1.2003	-0.3527	-0.4395	2.0125	-2.2274	2.0457	-0.0671	0.1014	-0.0752	-0.2349	-0.5417	-0.9773	0.2255	0.7159	0.0015	0.9735	0.1791	-0.1199	0.8738	0.3135	1.1828	37.7193	15.1579	5.6593
3	5.41	-2.2437	-1.4464	1.8379	-0.9939	2.8003	-0.1065	0.9152	-0.8178	-0.629	-1.6694	0.5592	0.5664	-1.2798	-2.0725	1.179	0.1655	-0.6523	1.431	-0.3852	0.2968	70.408	20.5405	-7.1097
4	1.862	-0.008	-1.679	-0.0071	0.0665	1.5422	-0.9602	0.5033	-0.8409	-0.8813	0.1618	1.1727	0.769	-1.0193	-0.165	1.0462	0.5229	-0.545	1.1674	-0.1893	0.7439	69.6171	13.5183	-5.8312
5	1.3525	-0.5335	-0.8301	1.5504	0.5388	2.2078	0.2284	-0.3347	-0.2621	-0.3355	-0.3938	0.4099	0.0154	-1.0207	0.0281	0.7979	0.2883	-0.1843	0.7535	-0.1333	0.8656	75.0816	17.2529	6.447
6	0.5068	-0.0498	0.0411	-0.0104	0.0065	0.0781	-0.7374	2.3592	1.2296	-1.756	1.1765	-0.8653	-1.0393	0.1718	-0.0057	1.8004	-0.1349	0.1201	1.4225	-0.0759	1.4233	80.4771	32.6967	-3.7047
7	2.034	-0.7593	1.3531	2.5171	1.3498	2.0677	-0.0239	0.6886	-0.2553	-1.1139	-0.0556	0.9205	0.4909	-0.9507	0.0015	0.938	0.2002	-0.1447	0.9704	-0.1701	1.052	70.9741	14.4452	0.6969
8	0.403	-0.1128	-0.6175	0.8551	0.1537	0.7021	-0.1885	0.2901	0.364	0.661	0.298	0.13	0.8447	0.4857	-0.0237	0.8498	0.349	-0.2094	1.0085	-0.0009	0.6309	81.4642	37.326	30.8643
9	5.2723	0.3577	1.0234	6.3978	1.2771	6.9124	-0.0662	-0.0237	0.4045	-0.137	-0.1563	0.4255	-0.3799	-0.5066	-0.0053	0.4991	0.0317	0.1611	0.3825	-0.108	0.3513	99.3155	72.5877	-32.3751
10	0.5778	0.4104	0.4489	0.9191	-1.1805	1.3655	0.931	-0.4009	-0.3395	1.585	-0.8135	-0.777	-0.1644	0.3909	0.0009	0.7713	-0.1177	0.0922	1.0801	-0.1108	0.9242	73.2326	44.5452	-21.3002
11	2.1434	-1.7543	-0.2643	4.7145	3.5797	3.0648	2.5547	1.6244	2.303	-2.355	-0.7054	0.2639	-2.4838	-0.5369	0.0494	-0.1196	0.2572	-1.0436	1.4191	-0.352	0.39	58.4606	56.3798	1.4997
12	2.2635	-0.5616	-1.2688	1.9524	1.1855	1.368	0.4892	0.182	-0.0428	0.0201	-0.1817	0.0719	-0.1685	0.9586	-0.0077	0.5593	0.0683	-0.0608	0.6216	-0.1284	0.4817	67.7758	54.9578	11.7625
13	3.7686	-2.6025	0.8344	2.8461	0.8704	2.8045	0.0969	0.3847	-0.042	-0.6667	-0.1171	0.4318	-0.0529	-0.2667	0.0029	0.7536	0.1252	-0.1702	0.924	-0.1278	0.514	63.3446	55.3242	6.8041
14	0.7652	0.9854	0.6876	2.0816	0.2613	0.5631	-0.4275	-0.1671	0.3433	-0.2101	0.1922	-0.5454	0.8328	-0.4123	-0.0091	0.7073	0.2014	-0.13	1.2295	-0.3057	0.5816	87.6287	34.5534	27.1916
15	0.2696	0.0665	0.3526	0.0482	-0.0026	0.2876	-0.5676	-1.4003	0.1725	0.4038	-0.6787	-0.9114	0.14	0.8481	0.0022	1.538	-0.0429	0.3023	1.468	0.2634	1.2732	95.0924	62.8793	6.0701
16	0.6762	-0.1478	0.1368	0.4292	0.4163	0.5133	-1.1959	-1.2055	-0.9625	-0.5535	-0.182	-1.4345	-0.9164	2.1686	-0.0597	1.249	-0.0887	0.2874	1.5046	-0.0021	1.204	97.0015	65.6082	0.1525
17	0.0311	0.0254	0.006	0.0144	0.0047	-0.0049	0.2917	0.6034	0.1495	-0.1321	-0.1617	0.016	-0.1951	0.3441	-0.0004	2.3927	-0.0563	-0.054	1.9606	0.0017	1.0187	102.3219	49.3068	16.1629
18	0.3972	0.1128	-0.3813	0.2886	-0.0502	0.2451	0.3125	-0.1535	-2.3023	-0.9613	-0.2872	0.2375	0.5732	0.793	0.0061	1.1418	-0.0084	0.2558	1.3633	0.2281	1.4658	90.5276	51.3609	-2.5906
19	0.0967	-0.0078	0.2035	0.0327	-0.0082	0.425	-1.5931	-0.2848	0.0953	1.0166	-0.0577	1.5276	-1.8355	0.4175	-0.0057	1.5809	-0.29	-0.0255	1.263	0.0123	1.4345	84.1	68.9124	-6.486
20	6.8794	0.4541	4.9252	0.0594	0.0133	7.0756	-0.9978	-2.2403	0.2891	0.5382	-0.8133	0.0934	-0.2302	0.4972	-2.1657	0.8447	0.0626	0.9668	1.2175	0.112	1.5363	85.8311	58.881	5.0462
21	0.0054	-0.0057	0.0125	0.0425	0.0516	0.0998	-1.2076	0.7461	-1.1277	-0.2962	-0.3974	-0.2042	1.6036	0.6144	-0.0007	1.8979	-0.0827	0.4078	1.195	0.311	1.9638	94.6124	43.7641	2.4858
22	0.4541	-0.9513	-0.5396	2.4171	1.2222	0.6414	-1.0201	-0.8479	-0.3771	2.5886	1.1343	1.2623	0.8906	1.8818	0.0135	1.4926	0.1023	0.0176	1.9608	0.2384	1.4328	105.3576	56.9262	1.2727
23	0.1284	-0.455	0.3922	0.9777	-0.6308	0.2161	-0.0676	1.2529	0.6968	-0.0882	0.2041	0.0633	-0.0814	1.074	-0.0001	0.8092	-0.1915	0.1843	1.2474	-0.1572	0.9538	77.5704	42.3903	-27.3263
24	0.6749	0.5691	-0.037	0.7417	0.4869	0.8915	-0.3563	-0.4411	0.0335	0.2615	0.7581	-1.697	-0.2984	0.2772	0.0004	1.1662	0.032	0.0778	1.6142	0.0379	2.144	57.7222	16.7175	31.3632
25	0.7345	0.0666	0.9814	-0.0195	0.1974	0.445	0.94	0.7654	0.6158	-0.9009	0.1548	-2.3092	0.5164	0.4786	0.0016	1.7671	-0.0696	0.5237	1.5807	0.0226	2.9306	60.799	19.148	21.7981
26	-0.2508	0.6582	-0.7614	2.127	-1.5767	1.7773	0.2075	-0.5085	-0.0236	0.6478	-0.0654	-0.1419	0.0495	-0.3093	0.036	0.9079	0.0754	0.0287	0.9774	0.1528	1.2607	42.6182	27.808	14.6787

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 106 through 197 )	A	106 - 197
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 198 through 278 )	A	198 - 278
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 107 through 122 )	B	107 - 122
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 123 through 137 )	B	123 - 137
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 138 through 168 )	B	138 - 168
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 169 through 177 )	B	169 - 177
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 178 through 232 )	B	178 - 232
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 233 through 277 )	B	233 - 277
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 106 through 232 )	C	106 - 232
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 233 through 278 )	C	233 - 278
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 106 through 137 )	D	106 - 137
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 138 through 168 )	D	138 - 168
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 169 through 232 )	D	169 - 232
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 233 through 277 )	D	233 - 277
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 108 through 119 )	E	108 - 119
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 120 through 131 )	E	120 - 131
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 132 through 138 )	E	132 - 138
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 139 through 168 )	E	139 - 168
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 169 through 177 )	E	169 - 177
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 178 through 196 )	E	178 - 196
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 197 through 211 )	E	197 - 211
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 212 through 232 )	E	212 - 232
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 233 through 278 )	E	233 - 278
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 109 through 158 )	F	109 - 158
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 159 through 204 )	F	159 - 204
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 205 through 278 )	F	205 - 278

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

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Yorodumi