PDB-5gw1: Crystal structure of SNX16 PX-Coiled coil in space group P212121

ID or keywords:

Entry

Database: PDB / ID: 5gw1

Title

Crystal structure of SNX16 PX-Coiled coil in space group P212121

Components

Sorting nexin-16

Keywords

PROTEIN TRANSPORT / Sortin nexin / PX domain / Endosome sorting

Function / homology

Function and homology information

receptor recycling / protein targeting to lysosome / early endosome to late endosome transport / 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: 3.35 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	Nov 6, 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

-
Download

PDBx/mmCIF format	5gw1.cif.gz	588.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5gw1.ent.gz	497.8 KB	Display	PDB format
PDBx/mmJSON format	5gw1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gw/5gw1 ftp://data.pdbj.org/pub/pdb/validation_reports/gw/5gw1	HTTPS FTP

-
Related structure data

Related structure data	5gw0C 5gw8 C: citing same article (ref.)
Similar structure data	5gw0-2 1c8n-d 5gw0-1 4sbv-d 6rj0-d 1smv-d 1tnv-d 5gw0-3 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

5gw0C

5gw8

C: citing same article (ref.)

Similar structure data

-
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

G: Sorting nexin-16

H: Sorting nexin-16

172 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Sorting nexin-16

B: Sorting nexin-16

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

2

C: 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

E: 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)

4

G: Sorting nexin-16

H: 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)	75.670, 133.060, 215.370
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Sorting nexin-16 Mass: 21451.066 Da / Num. of mol.: 8 / 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

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.18 Å³/Da / Density % sol: 61.32 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
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

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRF

/ Beamline: BL17U / Wavelength: 0.97915 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: 0.97915 Å / Relative weight: 1

Reflection

Resolution: 3.35→61.91 Å / Num. obs: 32016 / % possible obs: 99.7 % / Redundancy: 4.3 % / B_iso Wilson estimate: 106.23 Å² / CC_1/2: 0.994 / R_merge(I) obs: 0.098 / R_pim(I) all: 0.053 / R_rim(I) all: 0.112 / Net I/σ(I): 13.8 / Num. measured all: 139054 / Scaling rejects: 25

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	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
3.35-3.53	4.5	0.704	20585	4605	0.683	0.371	0.799	2.5	99.9
10.59-61.91	4	0.057	4270	1081	0.986	0.032	0.066	43.3	96.2

-
Processing

Software

Name	Version	Classification
Aimless	0.5.12	data scaling
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.2	data extraction
Aimless		data reduction
MOLREP		phasing

Refinement

Resolution: 3.35→19.995 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 0.86 / Phase error: 31.23
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS

	R_factor	Num. reflection	% reflection
R_free	0.2863	2960	4.95 %
R_work	0.2572	-	-
obs	0.2586	31948	99.36 %

Solvent computation

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

Displacement parameters

B_iso max: 248.02 Å² / B_iso mean: 87.54 Å² / B_iso min: 9.63 Å²

Refinement step

Cycle: final / Resolution: 3.35→19.995 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11563	0	0	0	11563
Num. residues	-	-	-	-	1381

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11801
X-RAY DIFFRACTION	f_angle_d	1.468	15890
X-RAY DIFFRACTION	f_chiral_restr	0.081	1724
X-RAY DIFFRACTION	f_plane_restr	0.006	2051
X-RAY DIFFRACTION	f_dihedral_angle_d	16.896	4618

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
3.3501-3.4047	0.4405	133	0.3469	2779	2912	100
3.4047-3.4631	0.3696	145	0.3553	2707	2852	100
3.4631-3.5258	0.3529	153	0.33	2658	2811	100
3.5258-3.5932	0.3124	175	0.3152	2707	2882	99
3.5932-3.6661	0.3258	131	0.2944	2714	2845	100
3.6661-3.7453	0.319	158	0.3037	2690	2848	100
3.7453-3.8319	0.3771	131	0.2987	2723	2854	99
3.8319-3.927	0.3007	159	0.3005	2708	2867	100
3.927-4.0323	0.3036	124	0.278	2733	2857	100
4.0323-4.1499	0.3258	128	0.278	2712	2840	99
4.1499-4.2826	0.2828	124	0.2695	2707	2831	100
4.2826-4.4341	0.2761	145	0.2642	2700	2845	99
4.4341-4.6096	0.3061	157	0.2528	2700	2857	99
4.6096-4.8166	0.3011	131	0.2475	2704	2835	99
4.8166-5.0666	0.2789	158	0.2431	2709	2867	99
5.0666-5.3782	0.3087	158	0.2654	2672	2830	99
5.3782-5.7841	0.3102	140	0.2826	2652	2792	98
5.7841-6.3492	0.3438	128	0.2878	2677	2805	98
6.3492-7.2297	0.2758	135	0.2619	2701	2836	100
7.2297-8.9697	0.2432	113	0.2271	2757	2870	100
8.9697-19.995	0.1915	134	0.1767	2686	2820	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	0.4773	0.0325	0.0166	1.8122	-0.5701	1.2577	-0.0054	0.0229	0.0474	-0.7017	0.2372	-0.4677	-0.0573	0.5025	-0.5339	0.6126	0.0495	0.142	0.6499	-0.5679	0.2594	-21.2734	8.2167	49.3881
2	1.4954	0.1449	0.4248	0.7792	0.3048	0.7612	0.4986	0.3285	-0.4009	-0.3377	0.0382	-0.1049	0.4353	0.2455	0.4916	0.3275	0.0039	0.1492	0.0449	-0.7505	-0.4771	-24.1974	3.3903	44.0865
3	1.0519	0.4045	0.1646	1.3675	-1.0437	3.6424	0.2985	0.1987	0.5624	-0.2879	0.6408	-0.4066	-0.67	0.2649	7.0936	0.3455	-0.0742	0.198	0.1664	-0.904	-0.2032	-23.8325	6.2225	44.6861
4	0.729	0.4888	0.8159	0.4342	0.5253	0.7446	-0.1589	1.0106	-0.1015	-0.4103	-0.0318	-0.2925	0.0364	0.6009	-0.0686	1.1261	-0.0597	-0.1206	0.8983	-0.283	0.8581	-34.0749	2.312	8.4223
5	0.4401	-0.2545	-0.2067	0.3171	-0.1757	0.5949	0.2953	0.1192	0.2238	-0.3576	-0.1719	0.619	-1.7792	-0.3682	0.0056	2.1643	-0.5196	0.3333	1.3325	-0.3584	1.2893	-8.2223	34.1186	20.9456
6	2.9611	-0.1102	0.0549	0.0061	0.0042	0.0047	-0.4918	0.697	0.804	-0.7437	0.1614	-0.0968	-1.1145	-0.0476	-0.0621	2.4315	-0.3578	0.2715	0.6805	0.0401	0.8482	-9.8655	38.2268	19.5017
7	0.6888	-0.0019	0.0222	0.1178	-0.1296	0.6151	0.193	0.3738	-0.0475	-0.3533	-0.1626	0.4058	-0.7772	-0.4065	1.0692	1.8495	0.1012	0.1968	0.6603	-0.1491	0.8726	-20.631	26.631	12.789
8	1.7584	0.55	-1.295	0.7687	-0.3181	0.9832	0.4297	-0.5962	0.2327	-0.4783	-0.3406	-0.0484	-1.974	0.44	0.0085	1.9741	-0.3684	0.0644	0.7342	-0.131	0.9561	-12.7183	30.5115	15.7299
9	0.5336	0.2753	0.1521	0.1847	0.2275	0.2134	0.254	-0.317	0.3791	0.4354	-0.3806	0.4399	0.5465	-1.0416	-0.002	0.9965	-0.1173	-0.0975	0.8343	-0.0086	0.6291	-38.1565	3.278	14.4392
10	7.0768	0.5561	1.4154	0.05	-0.0094	2.8624	0.4797	0.2927	2.015	0.4272	0.1227	0.5257	-2.116	-0.5977	-0.4869	1.4435	0.1951	0.2854	1.3895	0.4703	0.9637	-43.1059	89.7787	43.3803
11	2.466	-0.7027	0.3042	1.6242	-1.0029	2.8881	0.3632	0.5501	-0.2424	-0.1918	0.1811	-0.6031	0.7615	-0.3263	0.0667	0.3196	-0.0502	-0.0901	0.1823	0.2454	-0.0329	-44.3937	71.8555	36.9312
12	4.3595	2.1261	-1.0939	1.0366	-0.5338	0.2739	-0.2541	-0.9329	-1.6053	0.053	-0.9966	-0.5697	0.9035	-0.0285	-0.3706	1.9099	0.3229	-0.2454	0.838	-0.0582	1.0482	-35.8789	55.7483	34.6648
13	2.39	0.788	-1.4181	1.4731	-0.0273	3.0117	0.3205	0.3451	-0.2666	-0.3091	0.1661	0.1419	0.5987	-0.4862	0.217	0.2962	-0.0112	0.083	0.5932	0.2704	0.1353	-45.5208	74.979	37.4275
14	0.1763	0.0068	-0.1441	0.1448	-0.2503	0.3793	-0.5081	0.7827	-1.4472	-0.4086	-0.2719	-0.0151	0.5966	-0.7901	-0.0105	1.1777	-0.3121	0.1058	1.2163	-0.0216	0.8007	-34.245	66.189	0.8735
15	2.3794	0.9729	0.34	0.4379	-0.0337	0.7511	-0.2315	0.1414	-0.0962	-0.0519	-0.5043	-0.1135	0.6525	-0.3922	-4.8439	2.388	-1.3634	0.178	1.8392	0.0132	0.9304	-61.6158	33.7048	16.3124
16	1.9484	-0.9335	1.3191	0.5067	-0.6041	1.111	0.685	-0.7803	-0.0541	-0.0579	-0.7352	0.0558	0.5859	0.7333	0.432	2.5399	-0.5479	0.3317	1.5318	0.007	0.781	-59.8536	40.5409	24.3468
17	1.5273	1.0727	-1.6272	1.2999	-2.6215	6.9754	-0.5594	-0.0483	-0.9314	0.425	-0.3087	-0.3575	1.4266	0.4485	-0.4005	1.7805	-0.6647	-0.0245	1.0126	-0.0803	0.991	-51.1753	41.6495	15.2269
18	1.1529	-0.7073	1.2434	1.3861	0.0965	2.1215	1.3386	0.3912	0.2323	-0.828	0.206	-0.0318	1.3537	0.1369	0.2578	1.3602	-0.111	-0.0586	0.6832	0.0067	0.9819	-53.0055	43.7684	3.8474
19	0.0123	-0.011	0.0013	0.0401	0.0345	0.0368	0.7134	0.1101	0.0124	0.1621	0.214	1.3311	-0.39	-0.5608	0.0002	2.6661	-0.1294	-0.291	1.8384	-0.0649	1.8331	-62.8238	56.1388	15.6085
20	2.4211	-0.884	-1.0588	0.6998	0.3881	0.4692	0.516	-0.4217	0.1714	-0.0979	-0.7413	0.1462	-0.0937	-0.8278	0.3832	1.9468	-0.3592	-0.4242	1.2838	-0.1751	0.6979	-62.111	40.8533	10.5681
21	0.2524	0.2461	0.1325	0.2338	0.1289	0.0666	0.9676	-0.5131	-0.7689	0.9908	-1.176	0.4743	1.1928	-0.5658	-0.0058	2.2602	-0.1806	-0.2345	1.1878	-0.2157	1.3994	-49.5074	31.2428	18.9441
22	0.7348	0.0676	-0.0909	0.0436	0.1541	0.461	-0.0279	0.1063	-0.8613	0.6946	0.1971	-0.6123	0.037	-0.2472	0.0066	1.4961	-0.1558	0.3315	1.1297	-0.084	0.7613	-34.3143	61.3194	11.9081
23	0.0727	-0.0164	-0.0252	0.0061	0.0149	0.0527	-0.7335	0.087	0.2569	-0.1833	-0.3922	-0.0479	-0.2517	-0.2885	-0.0036	1.077	-0.0479	0.0152	0.9114	-0.3268	0.8102	-15.1462	84.7469	-14.3338
24	0.0443	0.4607	0.0573	4.2707	0.6409	0.0811	0.5531	1.1606	-0.2704	-1.5483	0.1098	-0.0331	0.8815	2.2859	0.4026	1.2269	0.811	0.1593	2.4235	-0.0067	1.0661	-58.0763	93.609	12.5514
25	0.0663	-0.3564	-0.1503	2.0043	1.0171	0.8993	0.3537	1.1947	-0.0737	1.4506	0.0035	-0.7281	1.8162	1.1733	0.0156	1.6242	0.7276	-0.0533	1.9867	-0.1622	1.5901	-58.909	82.3959	20.0417
26	4.9937	2.5415	2.1566	2.6063	1.5573	1.4149	-0.6452	2.069	0.3042	-1.1874	-0.7114	-1.0643	-0.6444	0.9828	-0.5414	1.5185	0.821	0.0931	2.1463	0.2241	1.199	-65.002	89.1557	6.5957
27	-0.0042	0.1274	-0.0359	0.1908	-0.0696	0.0136	0.6835	-0.4706	-0.1932	0.6375	-0.218	0.7637	1.212	-0.2747	-0.0002	2.3949	-0.0652	-0.0455	1.3068	0.2239	1.691	-84.7333	62.2911	31.5867
28	4.5241	-0.1318	1.2329	4.5353	-0.6231	2.5018	0.0468	0.226	0.1127	0.3427	0.1735	-0.0123	0.4189	0.1106	0.0573	-0.1963	0.0618	0.1058	0.1741	-0.038	0.0785	-95.762	95.4932	28.3441
29	-0.0854	0.01	-0.0141	-0.0111	-0.0459	-0.0541	0.2239	-0.5176	-0.6537	0.2753	-0.3412	-2.1159	1.4926	-0.2961	0.0094	2.1316	-0.159	-0.0204	0.89	0.3829	2.3697	-77.496	62.2655	35.3476
30	0.9941	-0.1354	-0.2755	0.6711	-0.249	1.1674	0.877	-1.7683	-1.1364	0.9354	-0.1502	-0.5115	0.0835	-1.3279	0.0072	0.6971	-0.1024	-0.1656	0.9471	0.1269	1.0605	-46.8344	107.86	41.7799
31	2.7644	-0.3429	-0.3552	3.2753	0.4339	2.0371	0.1016	-0.6442	-0.9623	0.252	0.0076	0.4627	0.5527	-0.5448	-0.0077	0.2915	-0.0545	-0.2061	0.8977	-0.0769	0.7679	-46.6504	115.1021	42.6498
32	-0.0423	-0.0326	0.0426	0.1297	-0.2655	0.6162	0.1229	-0.6883	1.3954	-0.3123	0.4815	0.3771	-1.3393	0.8096	0.3876	2.0155	-0.5119	0.1296	1.2717	-0.5046	2.4516	-64.929	147.1203	42.227
33	5.4157	-1.054	-0.3489	2.7115	-0.0755	0.0397	0.3729	0.7249	0.6515	-0.9553	-0.0209	0.2056	0.0559	0.2763	0.0995	0.6926	-0.2613	0.288	0.4952	-0.3686	0.7442	-85.7695	116.7678	25.4672
34	1.6439	0.6571	-1.2052	1.7341	-0.2816	2.0487	0.0664	0.8455	0.4467	-0.1272	-0.0347	0.2127	-0.6794	0.0948	0.0126	0.3849	0.0941	0.0037	0.3476	-0.0224	0.7395	-80.7795	123.4916	25.6317
35	1.1511	0.5398	0.6916	0.4261	0.2315	0.4687	1.3412	-0.5878	-0.5155	0.6579	0.7967	-1.4321	0.3817	0.4214	0.0464	1.4739	-0.1498	-0.1498	1.1924	-0.1157	1.1618	-78.0098	118.8557	43.7471
36	1.2633	-0.1772	0.603	0.6939	0.8219	1.5491	-0.6698	0.0662	1.3229	-0.4904	-0.2548	0.0547	-0.3821	-0.2858	-2.4526	0.7872	0.0694	-0.1294	0.125	-0.3326	0.7342	-83.4299	122.8892	23.0042
37	0.4447	0.5151	0.4063	0.4841	0.4026	0.3228	0.8193	-0.2775	0.4571	0.8568	0.2985	-1.1675	-0.9069	0.511	0.0364	1.6877	-0.3459	0.3752	1.2615	-0.3051	1.7961	-58.8506	143.6003	37.8098

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 104 through 122 )	A	104 - 122
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 123 through 168 )	A	123 - 168
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 169 through 232 )	A	169 - 232
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 233 through 278 )	A	233 - 278
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 105 through 122 )	B	105 - 122
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 123 through 145 )	B	123 - 145
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 146 through 158 )	B	146 - 158
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 159 through 232 )	B	159 - 232
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 233 through 277 )	B	233 - 277
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 103 through 110 )	E	103 - 110
11	X-RAY DIFFRACTION	11	chain 'E' and (resid 111 through 168 )	E	111 - 168
12	X-RAY DIFFRACTION	12	chain 'E' and (resid 169 through 177 )	E	169 - 177
13	X-RAY DIFFRACTION	13	chain 'E' and (resid 178 through 232 )	E	178 - 232
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 233 through 278 )	E	233 - 278
15	X-RAY DIFFRACTION	15	chain 'F' and (resid 105 through 117 )	F	105 - 117
16	X-RAY DIFFRACTION	16	chain 'F' and (resid 118 through 138 )	F	118 - 138
17	X-RAY DIFFRACTION	17	chain 'F' and (resid 139 through 158 )	F	139 - 158
18	X-RAY DIFFRACTION	18	chain 'F' and (resid 159 through 168 )	F	159 - 168
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 169 through 180 )	F	169 - 180
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 181 through 197 )	F	181 - 197
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 198 through 224 )	F	198 - 224
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 225 through 272 )	F	225 - 272
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 273 through 278 )	F	273 - 278
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 109 through 140 )	G	109 - 140
25	X-RAY DIFFRACTION	25	chain 'G' and (resid 141 through 206 )	G	141 - 206
26	X-RAY DIFFRACTION	26	chain 'G' and (resid 207 through 232 )	G	207 - 232
27	X-RAY DIFFRACTION	27	chain 'G' and (resid 233 through 277 )	G	233 - 277
28	X-RAY DIFFRACTION	28	chain 'H' and (resid 106 through 232 )	H	106 - 232
29	X-RAY DIFFRACTION	29	chain 'H' and (resid 233 through 278 )	H	233 - 278
30	X-RAY DIFFRACTION	30	chain 'C' and (resid 103 through 131 )	C	103 - 131
31	X-RAY DIFFRACTION	31	chain 'C' and (resid 132 through 232 )	C	132 - 232
32	X-RAY DIFFRACTION	32	chain 'C' and (resid 233 through 278 )	C	233 - 278
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 106 through 119 )	D	106 - 119
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 120 through 168 )	D	120 - 168
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 169 through 177 )	D	169 - 177
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 178 through 227 )	D	178 - 227
37	X-RAY DIFFRACTION	37	chain 'D' and (resid 228 through 277 )	D	228 - 277

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
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

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
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

-
Yorodumi

-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

-Yorodumi

-
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

-
Yorodumi