PDB-6ks2: Structure of anti-Ghrelin receptor antibody

ID or keywords:

Entry

Database: PDB / ID: 6ks2

Title

Structure of anti-Ghrelin receptor antibody

Components

Fab7881 Heavy Chain (FabH)
Fab7881 Light Chain (FabL)

Keywords

IMMUNE SYSTEM / antibody

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.753 Å

Authors

Shiimura, Y. / Horita, S. / Asada, H. / Hirata, K. / Iwata, S. / Kojima, M.

Funding support

Japan, 1items

Citation

Journal: Nat Commun / Year: 2020
Title: Structure of an antagonist-bound ghrelin receptor reveals possible ghrelin recognition mode.
Authors: Shiimura, Y. / Horita, S. / Hamamoto, A. / Asada, H. / Hirata, K. / Tanaka, M. / Mori, K. / Uemura, T. / Kobayashi, T. / Iwata, S. / Kojima, M.

History

Deposition	Aug 23, 2019	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 12, 2020	Provider: repository / Type: Initial release
Revision 1.1	Aug 26, 2020	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2	Sep 2, 2020	Group: 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
Revision 1.3	Nov 22, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6ks2.cif.gz	360.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6ks2.ent.gz	294 KB	Display	PDB format
PDBx/mmJSON format	6ks2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6ks2_validation.pdf.gz	461.9 KB	Display	wwPDB validaton report
Full document	6ks2_full_validation.pdf.gz	470.5 KB	Display
Data in XML	6ks2_validation.xml.gz	38.1 KB	Display
Data in CIF	6ks2_validation.cif.gz	56.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ks/6ks2 ftp://data.pdbj.org/pub/pdb/validation_reports/ks/6ks2	HTTPS FTP

-
Related structure data

Related structure data	6ko5C 1q9kS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6tco-1 2or9-1 1aif-2 5i15-d 5b6f-2 4kuz-d 1mrd-d 6tcp-3 4x7s-d 2aj3-2 6tcq-d 2vl5-2 6be3-d 1mju-d 1bfo-1 1ai1-d 2bmk-2 6tco-2 4g6a-1 5mv3-3 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details)

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Fab7881 Light Chain (FabL)

B: Fab7881 Heavy Chain (FabH)

C: Fab7881 Light Chain (FabL)

D: Fab7881 Heavy Chain (FabH)

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

1

A: Fab7881 Light Chain (FabL)

B: Fab7881 Heavy Chain (FabH)

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

2

C: Fab7881 Light Chain (FabL)

D: Fab7881 Heavy Chain (FabH)

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

Unit cell

Length a, b, c (Å)	42.239, 107.916, 189.892
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Antibody	Fab7881 Light Chain (FabL) Mass: 24278.994 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody	Fab7881 Heavy Chain (FabH) Mass: 23331.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 620 / 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: 2.28 Å³/Da / Density % sol: 46 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100mM BICINE pH 9.0, 100mM Sodium Chloride, 30%(v/v) PEG550MME

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.74→47.473 Å / Num. obs: 169522 / % possible obs: 99.08 % / Redundancy: 3.53 % / B_iso Wilson estimate: 28.39 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.101 / R_pim(I) all: 0.062 / Net I/σ(I): 6.7
Reflection shell	Resolution: 1.74→1.81 Å / Redundancy: 3.54 % / R_merge(I) obs: 1.196 / Num. unique obs: 16885 / CC_1/2: 0.498 / R_pim(I) all: 0.74 / % possible all: 98.66

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX	dev_2210	refinement
PDB_EXTRACT	3.25	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1Q9K

1q9k

Resolution: 1.753→47.473 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.71

	R_factor	Num. reflection	% reflection
R_free	0.2328	4345	4.96 %
R_work	0.1922	-	-
obs	0.1942	87517	99.2 %

Solvent computation

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

Displacement parameters

B_iso max: 100.77 Å² / B_iso mean: 40.0923 Å² / B_iso min: 14.96 Å²

Refinement step

Cycle: final / Resolution: 1.753→47.473 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6570	0	0	620	7190
B_iso mean	-	-	-	42.35	-
Num. residues	-	-	-	-	872

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	6855
X-RAY DIFFRACTION	f_angle_d	1.215	9400
X-RAY DIFFRACTION	f_chiral_restr	0.071	1094
X-RAY DIFFRACTION	f_plane_restr	0.008	1185
X-RAY DIFFRACTION	f_dihedral_angle_d	14.757	4159

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
1.7535-1.7734	0.336	129	0.2963	2492	90
1.7734-1.7943	0.3575	125	0.3023	2717	100
1.7943-1.8162	0.3452	146	0.3005	2745	99
1.8162-1.8391	0.337	153	0.2893	2720	97
1.8391-1.8633	0.3582	139	0.2764	2693	100
1.8633-1.8889	0.3247	163	0.2789	2748	100
1.8889-1.9159	0.3053	146	0.2766	2733	98
1.9159-1.9445	0.337	142	0.2838	2713	99
1.9445-1.9748	0.3353	155	0.2827	2717	100
1.9748-2.0072	0.3675	134	0.2986	2793	99
2.0072-2.0418	0.3445	157	0.2778	2719	99
2.0418-2.079	0.2851	136	0.2508	2770	100
2.079-2.1189	0.2716	145	0.2224	2741	99
2.1189-2.1622	0.2809	135	0.2156	2751	100
2.1622-2.2092	0.2678	154	0.2121	2778	100
2.2092-2.2606	0.2674	131	0.2077	2753	99
2.2606-2.3171	0.2784	157	0.2047	2790	100
2.3171-2.3798	0.2578	156	0.2068	2728	99
2.3798-2.4498	0.2569	133	0.2015	2813	100
2.4498-2.5289	0.2622	158	0.2039	2762	100
2.5289-2.6192	0.2431	140	0.204	2789	100
2.6192-2.7241	0.2539	128	0.1936	2798	100
2.7241-2.8481	0.2752	139	0.1978	2831	100
2.8481-2.9982	0.217	144	0.1987	2816	100
2.9982-3.186	0.2259	140	0.1904	2778	99
3.186-3.4319	0.2022	151	0.1814	2806	100
3.4319-3.7772	0.2064	137	0.1625	2874	100
3.7772-4.3234	0.1695	156	0.1499	2850	100
4.3234-5.4458	0.1685	151	0.1292	2910	100
5.4458-47.473	0.1776	165	0.1622	3044	100

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	0.4565	-0.1445	-0.0195	2.4872	0.2521	3.6264	-0.0182	-0.2087	-0.0778	1.3646	0.0008	-0.204	0.6287	-0.1759	0.0072	0.9233	0.0189	-0.0899	0.3494	0.0078	0.2844	-13.7588	-3.0361	13.1983
2	1.5763	-0.1852	-1.655	2.8177	2.732	6.4721	0.0979	-0.1225	0.0172	0.4778	0.08	-0.178	0.2431	0.2379	-0.1104	0.2953	-0.0179	-0.0055	0.2094	-0.0127	0.2478	-12.1521	-17.4583	-20.9815
3	2.035	0.241	-1.8056	2.8378	0.2269	7.5357	0.075	-0.036	-0.2923	0.6018	0.0421	0.1472	1.3465	0.4307	-0.0057	0.4316	0.035	0.0052	0.2156	-0.0119	0.2803	-12.955	-26.7506	-24.3134
4	0.1705	0.4835	0.6385	5.1307	0.6233	4.1583	0.0364	0.3966	0.1011	-0.5304	0.1514	-0.3736	-0.906	-0.067	-0.1621	0.4436	-0.014	0.0216	0.2669	-0.0224	0.2758	-13.2812	13.3765	-9.378
5	5.0033	-2.0395	-0.9936	5.5924	2.3996	5.7087	-0.1344	-0.2244	-0.0453	0.2555	0.0809	0.3313	-0.5007	-0.345	0.0191	0.3934	0.0404	-0.021	0.2425	0.0169	0.2859	-17.1419	16.3037	1.6505
6	3.8433	0.1182	-0.4105	6.4684	3.1848	5.356	0.0094	-0.0902	0.4168	0.2483	0.3405	-1.0258	-0.5099	0.4875	-0.3574	0.4123	-0.0603	-0.0851	0.3148	-0.0351	0.3715	-7.0012	16.3689	3.7349
7	1.5672	2.4212	0.8797	3.7914	0.8207	4.6785	0.011	0.0453	0.3361	-0.3629	0.3515	-0.9381	-0.9212	0.225	-0.2378	0.5125	-0.0753	-0.0011	0.2618	-0.0124	0.3786	-8.7189	17.6209	-5.3309
8	1.1752	-0.4401	1.239	5.5373	2.1857	5.5312	-0.1215	-0.1159	0.008	0.2925	0.319	-0.2079	-0.1407	-0.0113	-0.1757	0.2733	0.0097	-0.0134	0.1698	0.0168	0.2814	-14.9892	9.3602	-3.1676
9	8.8371	1.8521	-0.1845	2.6966	0.8643	8.8585	-0.0838	0.1853	-0.7779	-0.0276	0.5218	0.1084	0.7586	-0.6412	-0.3268	0.2907	-0.0572	-0.0217	0.3779	-0.0362	0.3938	-24.0391	-16.2386	-25.7299
10	3.5779	2.9052	0.563	8.7524	2.2844	3.6448	-0.0563	-0.115	-0.0846	-0.1718	-0.1797	0.4567	0.0826	-0.4269	0.176	0.2139	-0.0021	0.0161	0.2416	-0.0198	0.2603	-20.1166	-5.3858	-17.9769
11	1.0755	-1.2634	1.9889	6.8464	1.3847	6.2703	0.0414	0.2492	-0.3532	0.3898	-0.1099	-0.4165	0.4873	-0.2	0.1239	0.3152	-0.0398	0.0199	0.2633	-0.0023	0.2637	-17.0795	-8.2973	-14.3169
12	3.5608	1.8508	-0.029	6.519	-0.1103	3.5949	-0.0812	0.0848	-0.3317	-0.1275	-0.0717	0.563	0.2029	-0.8084	0.0767	0.2592	-0.0562	0.0319	0.4137	-0.1088	0.3007	-25.3051	-8.6003	-19.0213
13	1.6289	-1.0711	-0.6676	6.4269	2.8751	1.7967	-0.006	0.1445	-0.0532	-0.8419	-0.2079	0.663	-0.3608	-0.3594	0.2435	0.3805	0.0477	-0.0941	0.5073	-0.0761	0.3884	-26.8738	-5.3785	-25.2922
14	2.4746	0.0421	-0.3752	4.6403	-0.7875	3.0943	0.0928	-0.0571	-0.1349	0.2446	-0.0756	0.1097	0.2783	-0.0552	-0.0008	0.2834	-0.0342	0.0542	0.2605	0.0336	0.2625	-24.1898	19.7777	-28.0731
15	1.6095	-1.6771	-1.3152	2.2187	1.7008	1.216	-0.128	-0.0826	-0.1725	0.2084	0.039	0.0426	0.2023	0.037	0.0887	0.3123	0.0238	0.0725	0.2084	0.0163	0.3023	1.6525	8.1784	-48.6536
16	9.8286	0.9563	0.5843	0.6836	-0.7054	0.3431	0.1028	0.805	-0.2486	-0.0017	0.0397	-0.0799	0.0489	0.1413	-0.0178	0.1358	-0.0028	0.0194	0.2701	-0.025	0.2845	-8.8302	38.8205	-44.1295
17	5.7205	-0.2277	0.4025	0.898	0.169	2.0437	-0.0496	-0.0432	0.077	0.0646	0.058	0.1184	0.0505	-0.0016	0.0212	0.1148	0.003	0.0145	0.1739	-0.0077	0.2931	-18.3609	38.137	-38.6775
18	1.3463	0.4567	0.1167	3.0886	-0.0356	4.1939	-0.1128	-0.3461	0.0636	0.2951	0.1192	0.1116	-0.3227	-0.1372	0.0096	0.1128	0.0153	0.041	0.196	-0.0057	0.2281	-16.2231	42.6535	-31.1801
19	2.7599	-0.7003	1.2614	2.6872	0.0858	2.7132	-0.1716	-0.2409	0.076	0.1609	0.2131	-0.1363	-0.2379	0.0411	0.017	0.119	-0.0188	0.035	0.2075	0.0033	0.2749	-9.6273	43.148	-37.9755
20	3.5744	-0.4028	-0.9997	1.1494	0.1195	0.9417	-0.0379	-0.0335	0.0865	0.0876	0.0803	0.3047	-0.0311	-0.1928	0.021	0.1428	0.0102	0.0322	0.219	0.0202	0.3562	-23.35	33.3639	-36.587
21	0.7605	-0.8977	-0.4445	0.7583	0.1515	1.1325	-0.0918	-0.1231	-0.0117	-0.0819	0.0792	-0.0039	0.1049	0.0779	-0.0089	0.1284	-0.0229	0.0293	0.1548	-0.0128	0.2881	-4.1083	30.4925	-47.467
22	3.178	1.5618	0.8986	7.028	3.7408	4.5905	0.0044	0.3857	-0.5182	0.093	-0.0765	-0.1686	0.9184	-0.2102	-0.0542	0.4238	-0.0114	0.0736	0.2094	-0.025	0.2859	-1.6006	10.3862	-60.6341
23	2.1668	1.9785	0.9189	6.2149	4.1737	4.9202	0.0164	0.1873	0.0381	-0.1372	-0.2973	0.3153	0.1804	-0.4157	0.4995	0.205	-0.0139	0.0008	0.241	-0.0305	0.3383	-6.0373	24.6714	-52.7907
24	1.9561	1.6566	0.9178	6.2284	3.5184	4.9604	-0.0151	-0.0306	-0.0961	0.3026	-0.1611	0.1471	0.6045	-0.2182	0.193	0.3043	0.0093	0.0692	0.2037	-0.0104	0.2933	-3.6855	16.7772	-51.3676
25	4.5602	0.4871	1.4527	0.088	-0.1143	4.4801	-0.3461	0.3188	0.1697	-0.8707	-0.1896	0.8439	0.2528	-0.22	0.4272	0.4299	-0.0042	-0.0212	0.2291	-0.0475	0.2483	-7.9081	18.4473	-62.7813
26	4.1947	3.34	2.6618	6.6464	6.8338	9.8228	-0.2554	0.1296	-0.0526	-1.286	-0.0125	0.2074	-0.4057	0.124	0.2437	0.4701	-0.0116	0.0286	0.2484	0.0477	0.2386	-2.5041	21.3779	-64.6603

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 1 through 118 )	A	1 - 118
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 119 through 193 )	A	119 - 193
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 194 through 219 )	A	194 - 219
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1 through 17 )	B	1 - 17
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 18 through 40 )	B	18 - 40
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 41 through 73 )	B	41 - 73
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 74 through 91 )	B	74 - 91
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 92 through 124 )	B	92 - 124
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 125 through 139 )	B	125 - 139
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 140 through 162 )	B	140 - 162
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 163 through 178 )	B	163 - 178
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 179 through 207 )	B	179 - 207
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 208 through 218 )	B	208 - 218
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1 through 96 )	C	1 - 96
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 97 through 219 )	C	97 - 219
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1 through 17 )	D	1 - 17
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 18 through 43 )	D	18 - 43
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 44 through 73 )	D	44 - 73
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 74 through 91 )	D	74 - 91
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 92 through 105 )	D	92 - 105
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 106 through 129 )	D	106 - 129
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 130 through 150 )	D	130 - 150
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 151 through 162 )	D	151 - 162
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 163 through 189 )	D	163 - 189
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 190 through 207 )	D	190 - 207
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 208 through 218 )	D	208 - 218

-
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