PDB-5x87: Crystal structure of a bacterial Bestrophin homolog from Klebsiel...

ID or keywords:

Entry

Database: PDB / ID: 5x87

Title

Crystal structure of a bacterial Bestrophin homolog from Klebsiella pneumoniae with a mutation L177T

Components

Bestrophin

Keywords

MEMBRANE PROTEIN / Bestrophin / Klebsiella pneumoniae / mutation

Function / homology

UPF0187 family / Bestrophin/UPF0187 / Bestrophin, RFP-TM, chloride channel / chloride channel activity / membrane / Ibestrophin

Function and homology information

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.14 Å

Authors

Zhang, Y. / Chen, S. / Yang, T.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	P41 GM103403	United States
Department of Energy (DOE, United States)	DE-AC02-06CH11357	United States
National Institutes of Health/National Eye Institute (NIH/NEI)	EY025290	United States

Citation

Journal: Elife / Year: 2017
Title: Patient-specific mutations impair BESTROPHIN1's essential role in mediating Ca2+-dependent Cl-currents in human RPE.
Authors: Li, Y. / Zhang, Y. / Xu, Y. / Kittredge, A. / Ward, N. / Chen, S. / Tsang, S.H. / Yang, T.

History

Deposition	Mar 1, 2017	Deposition site: PDBJ / Processing site: RCSB
Revision 1.0	Nov 1, 2017	Provider: repository / Type: Initial release
Revision 1.1	Dec 13, 2017	Group: Database references / Category: citation / Item: _citation.title
Revision 1.2	Feb 28, 2018	Group: Database references / Category: citation / Item: _citation.title
Revision 1.3	Mar 28, 2018	Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.4	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5	Nov 29, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5x87.cif.gz	551.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5x87.ent.gz	458.4 KB	Display	PDB format
PDBx/mmJSON format	5x87.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5x87_validation.pdf.gz	461.9 KB	Display	wwPDB validaton report
Full document	5x87_full_validation.pdf.gz	473 KB	Display
Data in XML	5x87_validation.xml.gz	45.1 KB	Display
Data in CIF	5x87_validation.cif.gz	60.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x8/5x87 ftp://data.pdbj.org/pub/pdb/validation_reports/x8/5x87	HTTPS FTP

-
Related structure data

Related structure data	4wd8S S: Starting model for refinement
Similar structure data	4wd7-d 6ivp-d 6iv1-d 6ivw-d 6ivo-d 6ivq-d 6ivn-d 6iv0-d 4wd8-d 6jlf-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Bestrophin

B: Bestrophin

C: Bestrophin

D: Bestrophin

E: Bestrophin

hetero molecules

170 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: homology

Unit cell

Length a, b, c (Å)	114.485, 160.573, 162.657
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Bestrophin Mass: 33819.188 Da / Num. of mol.: 5 / Mutation: L177T Source method: isolated from a genetically manipulated source Details: KpBest mutant L177T / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: W1ELP7
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.42 Å³/Da / Density % sol: 72.18 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 0.05 M zinc acetate, 6% v/v ethylene glycol, 0.1 M sodium cacodylate, pH 6.0, 6.6 % w/v PEG 8000

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 19, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 3.14→65.73 Å / Num. obs: 101018 / % possible obs: 99.88 % / Redundancy: 7.4 % / CC_1/2: 0.998 / R_merge(I) obs: 0.061 / R_pim(I) all: 0.061 / R_sym value: 0.086 / Net I/σ(I): 11.91
Reflection shell	Resolution: 3.14→3.24 Å / Redundancy: 7.6 % / R_merge(I) obs: 2.206 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 5204 / CC_1/2: 0.429 / R_pim(I) all: 0.859 / R_sym value: 2.369 / % possible all: 99.5

-
Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
PHENIX		phasing
XDS		data reduction
Aimless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4WD8

4wd8

Resolution: 3.14→65.73 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.09

	R_factor	Num. reflection	% reflection
R_free	0.2366	3805	3.77 %
R_work	0.1987	-	-
obs	0.2002	101018	99.89 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.14→65.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10622	0	15	41	10678

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	10847
X-RAY DIFFRACTION	f_angle_d	0.462	14778
X-RAY DIFFRACTION	f_dihedral_angle_d	9.933	6476
X-RAY DIFFRACTION	f_chiral_restr	0.034	1760
X-RAY DIFFRACTION	f_plane_restr	0.004	1857

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 (%)
3.14-3.1798	0.4785	144	0.3836	3562	X-RAY DIFFRACTION	99
3.1798-3.2216	0.3765	131	0.3633	3593	X-RAY DIFFRACTION	100
3.2216-3.2657	0.3569	149	0.3386	3631	X-RAY DIFFRACTION	100
3.2657-3.3124	0.3086	146	0.3098	3566	X-RAY DIFFRACTION	100
3.3124-3.3618	0.3409	138	0.2963	3630	X-RAY DIFFRACTION	100
3.3618-3.4143	0.3113	140	0.2887	3597	X-RAY DIFFRACTION	100
3.4143-3.4703	0.3064	128	0.285	3615	X-RAY DIFFRACTION	100
3.4703-3.5302	0.3093	162	0.2714	3577	X-RAY DIFFRACTION	100
3.5302-3.5943	0.2621	130	0.2614	3633	X-RAY DIFFRACTION	100
3.5943-3.6635	0.2942	137	0.2517	3574	X-RAY DIFFRACTION	100
3.6635-3.7382	0.2728	142	0.2403	3616	X-RAY DIFFRACTION	100
3.7382-3.8195	0.2701	144	0.2116	3641	X-RAY DIFFRACTION	100
3.8195-3.9084	0.2376	138	0.1887	3550	X-RAY DIFFRACTION	100
3.9084-4.0061	0.2214	132	0.1879	3633	X-RAY DIFFRACTION	100
4.0061-4.1144	0.1921	142	0.177	3610	X-RAY DIFFRACTION	100
4.1144-4.2354	0.194	146	0.1699	3602	X-RAY DIFFRACTION	100
4.2354-4.3721	0.1767	132	0.1541	3590	X-RAY DIFFRACTION	100
4.3721-4.5283	0.2126	152	0.1472	3600	X-RAY DIFFRACTION	100
4.5283-4.7096	0.1837	143	0.146	3579	X-RAY DIFFRACTION	100
4.7096-4.9239	0.2156	133	0.1379	3641	X-RAY DIFFRACTION	100
4.9239-5.1834	0.1346	147	0.1412	3591	X-RAY DIFFRACTION	100
5.1834-5.508	0.1958	139	0.1672	3603	X-RAY DIFFRACTION	100
5.508-5.933	0.2911	141	0.1989	3606	X-RAY DIFFRACTION	100
5.933-6.5296	0.2655	141	0.2043	3601	X-RAY DIFFRACTION	100
6.5296-7.4733	0.2446	144	0.1833	3593	X-RAY DIFFRACTION	100
7.4733-9.4112	0.1959	145	0.1536	3621	X-RAY DIFFRACTION	100
9.4112-65.748	0.231	139	0.2083	3558	X-RAY DIFFRACTION	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	7.3223	-1.012	-2.3198	2.9091	-2.0251	2.7211	0.0704	-1.361	1.1777	0.2703	0.6769	-1.3188	1.51	1.8288	-0.554	1.186	0.5212	-0.3131	1.2405	-0.2097	1.0241	-15.4241	-12.2319	43.2093
2	-0.8657	-0.6632	-0.3695	4.1515	7.2344	7.8956	-0.1128	-0.0587	0.0016	0.0603	0.3041	0.3124	0.0741	0.4003	-0.2927	0.7321	-0.0864	-0.0211	0.5326	-0.0795	0.6419	-21.4638	-28.9002	7.994
3	4.1812	-0.3394	1.1474	3.189	0.0554	5.0173	-0.0774	0.1796	-0.3956	-0.1175	0.1072	-0.2983	0.3994	0.3572	-0.0317	0.3549	0.0033	0.0136	0.4098	0.0282	0.4871	-10.5718	-45.3411	-5.4157
4	2.1647	1.4015	-0.971	1.3726	0.5358	4.0374	-0.5156	-0.4967	0.2577	-0.0216	0.248	0.2207	0.4292	0.7434	0.1487	0.8484	0.3043	-0.2263	0.8558	-0.1369	0.6181	-18.4056	-16.3859	31.5246
5	8.3064	-1.5643	-0.8473	2.2953	-0.581	2.4377	-0.2297	0.1316	-1.2004	1.0269	0.2204	0.9132	1.2191	-0.7559	-0.0477	0.8622	-0.0503	0.0085	0.784	0.162	0.7184	-18.7854	-44.9492	8.0407
6	1.4648	-0.2398	-1.3732	2.0399	-1.4366	2.4252	1.261	-0.2651	-0.5941	0.6315	0.1108	-0.7914	-0.8939	0.5778	-0.3649	0.9105	-0.0547	-0.539	1.0822	-0.341	1.3877	-10.3697	9.9036	30.3429
7	2.3081	-3.8072	-3.9147	4.6588	5.813	4.7662	-0.3738	-0.4974	0.0823	0.4188	0.4195	-0.0168	0.0778	0.7304	0.1998	0.7539	0.1001	0.0191	0.5813	-0.0878	0.6286	-14.548	-17.5677	2.5338
8	1.6565	-0.9571	0.2433	4.4085	1.69	5.152	0.0778	0.3072	0.3587	-0.7814	0.1272	-0.9356	-0.484	0.8554	-0.0991	0.5173	-0.0444	0.1558	0.7027	0.1019	0.6369	-3.0864	-23.2522	-17.9317
9	3.844	-0.7625	-0.7411	5.5897	2.4263	1.0228	-0.018	0.1131	-0.0907	-0.4399	0.8433	-0.8541	0.0876	0.8775	-0.9158	0.6992	-0.0008	-0.1853	0.9113	-0.3287	0.9398	-13.0478	0.5447	21.4273
10	5.7893	-3.3428	-0.7284	5.9503	-0.3482	2.4924	-0.2391	-0.7149	1.0607	0.4852	0.6936	-1.9766	-0.0865	0.5558	-0.3116	0.4604	-0.0409	-0.0151	0.8422	-0.1194	0.8911	-0.9977	-22.4675	-1.53
11	1.8729	-0.1153	1.7559	2.6477	-0.7006	5.9683	0.3189	-0.8022	0.6911	1.3837	-0.7385	1.1503	-0.427	-2.8833	0.4692	1.3231	0.1494	-0.0219	1.9334	-0.4916	1.2747	-52.0778	3.2856	29.0043
12	0.4709	-0.6584	0.4623	2.6185	3.4104	3.3486	0.0183	-0.0108	0.3276	0.1143	0.3122	-0.0992	-0.0653	-0.1185	-0.2157	0.3669	0.0077	-0.0026	0.4004	-0.0313	0.4135	-36.5971	-14.8054	-2.8552
13	5.4411	-0.5677	-1.3222	5.0693	0.0158	3.5553	-0.0346	0.1358	-0.0263	-0.3991	0.0025	0.51	-0.0298	-0.5973	-0.0144	0.4057	-0.0289	-0.0923	0.3859	0.0654	0.4185	-45.6209	-26.8367	-21.0782
14	4.4014	-0.1185	-1.6137	2.0189	-2.0092	6.4567	-0.359	-0.0309	0.3568	-0.1257	0.0157	0.5385	0.6438	0.2995	0.3892	0.6205	0.1964	-0.065	0.8077	-0.1949	0.6528	-45.5215	-2.3151	19.3028
15	6.5441	-0.7349	-3.5641	5.963	1.408	2.1554	0.7141	0.4227	0.7278	0.2161	-0.2357	0.0235	-2.5045	0.0073	-0.4957	1.0013	-0.0292	-0.0876	0.5445	0.0718	0.8983	-45.0071	-11.6011	-17.9937
16	3.565	2.1776	1.1692	3.1857	-1.5422	3.1546	-0.1898	-0.1026	1.6538	-0.7029	0.312	0.7687	-1.2073	-1.2925	-0.0396	1.3687	0.3025	-0.2731	0.7085	-0.0078	1.2871	-33.0602	19.1829	20.9478
17	1.9628	-1.3444	-2.1968	3.0174	2.0307	3.1195	-0.21	-0.1999	0.1374	-0.2114	0.1867	-0.248	0.1268	0.9257	0.3115	0.444	0.0371	-0.1078	0.5375	0.1143	0.5614	-23.6198	-9.457	-4.613
18	3.5282	-2.1994	-0.25	6.1039	2.1753	3.9025	0.2139	0.7248	0.4008	-1.0529	-0.2539	-0.0775	-1.0186	-0.1321	0.0791	0.7612	0.0203	0.0291	0.6758	0.1231	0.4984	-24.436	-12.431	-29.1173
19	0.4387	-0.8121	-0.6902	4.5572	6.5182	9.6897	-0.2723	0.6795	0.0281	-0.4547	0.1786	0.1165	0.3533	-0.1894	0.2652	0.8917	-0.0156	-0.1406	0.7656	-0.1628	0.7585	-36.3603	4.5415	7.3583
20	5.648	-1.6109	-1.2663	8.8297	2.6099	4.3884	-0.02	-0.2304	1.3282	-0.0492	-0.2749	0.32	-1.2436	-0.1305	0.1967	0.9831	0.2568	-0.1657	0.5789	-0.0828	1.0011	-26.22	10.2435	16.0627
21	2.1137	-0.3081	-0.199	2.2467	-1.6966	5.3722	-0.0057	0.0076	1.8628	0.5255	-0.4393	-1.3552	-1.0101	1.1086	0.1575	1.017	-0.157	-0.1082	1.0717	0.1501	0.9568	-15.6122	-4.116	-18.5173
22	5.0185	0.8563	-1.3019	3.5417	-1.2262	0.6911	0.0817	-0.77	-0.5457	1.909	0.1462	-0.0289	0.4571	0.6143	0.0142	1.415	-0.1086	0.2668	0.8795	0.0262	0.7923	-40.4342	-15.694	43.8865
23	1.1513	2.2305	2.714	5.9563	5.7417	4.066	-0.0199	-0.5036	0.2638	0.1402	-0.6014	0.3651	-0.2146	-1.1291	0.7312	0.678	0.073	-0.0052	0.7539	-0.2236	0.5418	-35.1966	-26.5531	5.1454
24	4.3013	1.2518	0.6619	4.6636	-1.9839	9.105	0.2247	0.0388	-0.7833	-0.0396	-0.1824	0.0831	1.509	-0.1399	-0.2953	0.6282	-0.0915	0.0769	0.5116	-0.0583	0.7526	-42.1765	-49.7436	-4.2613
25	1.706	-0.5095	-0.9137	1.5584	0.2361	7.4675	-0.0815	0.5554	-0.3123	-0.1337	0.0695	0.228	0.34	0.5806	-0.0282	0.3873	-0.0049	-0.0597	0.7899	-0.052	0.6341	-31.7692	-44.7914	-11.3953
26	3.7773	-1.4628	0.7537	4.8074	2.0268	5.4661	-0.2121	-0.0063	-0.2592	0.53	-0.0779	0.504	0.6335	-0.7106	0.1714	0.7521	-0.0264	0.0658	0.7216	-0.0986	0.5428	-37.8963	-21.667	26.8071
27	7.1535	0.0479	-0.2508	5.548	-1.423	5.7078	-0.2579	-0.6141	0.706	0.4924	0.0987	0.1842	-0.2176	-0.1896	0.2418	0.3722	0.0997	-0.0352	0.532	-0.0196	0.5213	-50.9375	-39.133	-7.4885

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 22 through 54 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 55 through 103 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 104 through 208 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 209 through 259 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 260 through 289 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 22 through 53 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 54 through 103 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 104 through 208 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 209 through 259 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 260 through 286 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 23 through 54 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 55 through 103 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 104 through 208 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 209 through 260 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 261 through 291 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 22 through 54 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 55 through 103 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 104 through 204 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 205 through 226 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 227 through 260 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 261 through 289 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 24 through 54 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 55 through 103 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 104 through 155 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 156 through 203 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 204 through 269 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 270 through 293 )

-
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://pdbjlvh1.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