PDB-6bo7: Crystal structure of Plasmodium vivax hypoxanthine guanine phosph...

ID or keywords:

Entry

Database: PDB / ID: 6bo7

Title

Crystal structure of Plasmodium vivax hypoxanthine guanine phosphoribosyltransferase in complex with [3R,4R]-4-guanin-9-yl-3-((S)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine

Components

Hypoxanthine phosphoribosyltransferase

Hypoxanthine-guanine phosphoribosyltransferase

Keywords

TRANSFERASE/INHIBITOR / Inhibitor /

Complex /

Phosphonate /

Phosphoribosyltransferase /

TRANSFERASE / TRANSFERASE-INHIBITOR complex

Function / homology

Function and homology information

hypoxanthine phosphoribosyltransferase / guanine phosphoribosyltransferase activity /

hypoxanthine phosphoribosyltransferase activity / IMP salvage / purine ribonucleoside salvage /

nucleotide binding /

metal ion binding /

cytoplasm
Similarity search - Function

Biological species

Plasmodium vivax (malaria parasite P. vivax)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.856 Å

Authors

Guddat, L.W. / Keough, D.T. / Rejman, D.

Funding support

Australia, 1items

Citation

Journal: ACS Chem. Biol. / Year: 2018
Title: Design of Plasmodium vivax Hypoxanthine-Guanine Phosphoribosyltransferase Inhibitors as Potential Antimalarial Therapeutics.
Authors: Keough, D.T. / Rejman, D. / Pohl, R. / Zbornikova, E. / Hockova, D. / Croll, T. / Edstein, M.D. / Birrell, G.W. / Chavchich, M. / Naesens, L.M.J. / Pierens, G.K. / Brereton, I.M. / Guddat, L.W.

History

Deposition	Nov 18, 2017	Deposition site: RCSB / Processing site: RCSB
Supersession	Dec 13, 2017	ID: 5HHU
Revision 1.0	Dec 13, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2018	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2	Jan 8, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_conn Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6bo7.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb6bo7.ent.gz	930.5 KB	Display	PDB format
PDBx/mmJSON format	6bo7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bo/6bo7 ftp://data.pdbj.org/pub/pdb/validation_reports/bo/6bo7	HTTPS FTP

-
Related structure data

Related structure data	5hiaC 6bnjC C: citing same article (ref.)
Similar structure data	3ozf-d 1qk4-d 3ozg-2 1cjb-2 1dbr-d 5zrn-d 1fsg-1 6dgi-d 5eu9-1 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

5hiaC

6bnjC

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (5)

Deposited unit

A: Hypoxanthine phosphoribosyltransferase

B: Hypoxanthine phosphoribosyltransferase

C: Hypoxanthine phosphoribosyltransferase

D: Hypoxanthine phosphoribosyltransferase

E: Hypoxanthine phosphoribosyltransferase

F: Hypoxanthine phosphoribosyltransferase

G: Hypoxanthine phosphoribosyltransferase

H: Hypoxanthine phosphoribosyltransferase

I: Hypoxanthine phosphoribosyltransferase

J: Hypoxanthine phosphoribosyltransferase

K: Hypoxanthine phosphoribosyltransferase

L: Hypoxanthine phosphoribosyltransferase

hetero molecules

339 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Hypoxanthine phosphoribosyltransferase

B: Hypoxanthine phosphoribosyltransferase

C: Hypoxanthine phosphoribosyltransferase

D: Hypoxanthine phosphoribosyltransferase

hetero molecules

defined by author&software
Evidence: Subunits a, b, c, and d are one tetramer e, f, g, and h a second and i, j, k and l are the third tetramer in the asymmetric unit
113 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Hypoxanthine phosphoribosyltransferase

F: Hypoxanthine phosphoribosyltransferase

I: Hypoxanthine phosphoribosyltransferase

J: Hypoxanthine phosphoribosyltransferase

hetero molecules

defined by author&software
113 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

G: Hypoxanthine phosphoribosyltransferase

H: Hypoxanthine phosphoribosyltransferase

K: Hypoxanthine phosphoribosyltransferase

L: Hypoxanthine phosphoribosyltransferase

hetero molecules

defined by author&software
113 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	55.784, 219.854, 254.139
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	Hypoxanthine phosphoribosyltransferase / Hypoxanthine-guanine phosphoribosyltransferase Mass: 27706.842 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium vivax (malaria parasite P. vivax) Gene: PVC01_080017300, PVP01_0812500, PVT01_080017400 / Production host: Escherichia coli (E. coli) References: UniProt: A0A1G4HBT9, UniProt: A5K7E9*PLUS, hypoxanthine phosphoribosyltransferase
#2: Chemical	... ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-YPG / [3-[(3~{R},4~{R})-3-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-[(2~{S})-2-oxidanyl-2-phosphono-ethoxy]pyrrolidin-1-y l]-3-oxidanylidene-propyl]phosphonic acid / [3R,4R]-4-guanin-9-yl-3-((S)-2-hydroxy-2-phosphonoethyl)oxy-1-N-(phosphonopropionyl)pyrrolidine Mass: 496.306 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₁₄H₂₂N₆O₁₀P₂

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.56 Å³/Da / Density % sol: 51.96 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.3 M potassium thiocyanate, 0.1 M Bis-tris propane, pH 8.5.

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9 Å
Detector	Type: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 10, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9 Å / Relative weight: 1
Reflection	Resolution: 2.85→39.168 Å / Num. obs: 73747 / % possible obs: 99.7 % / Redundancy: 5.2 % / Net I/σ(I): 20.6
Reflection shell	Resolution: 2.85→2.9 Å / Redundancy: 4.9 % / Num. unique obs: 3627 / % possible all: 99.6

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.856→39.168 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2563	1999	2.72 %
R_work	0.2304	-	-
obs	0.2311	73367	99.23 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.856→39.168 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21466	0	411	0	21877

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	22375
X-RAY DIFFRACTION	f_angle_d	0.835	30277
X-RAY DIFFRACTION	f_dihedral_angle_d	11.696	8307
X-RAY DIFFRACTION	f_chiral_restr	0.035	3329
X-RAY DIFFRACTION	f_plane_restr	0.004	3748

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 (%)
2.8562-2.9276	0.4233	139	0.3642	4979	X-RAY DIFFRACTION	97
2.9276-3.0068	0.3623	140	0.3377	4963	X-RAY DIFFRACTION	99
3.0068-3.0952	0.3283	143	0.3158	5123	X-RAY DIFFRACTION	100
3.0952-3.1951	0.3216	140	0.299	4995	X-RAY DIFFRACTION	100
3.1951-3.3092	0.318	143	0.2916	5084	X-RAY DIFFRACTION	100
3.3092-3.4416	0.3661	141	0.287	5042	X-RAY DIFFRACTION	99
3.4416-3.5982	0.3051	139	0.3056	4966	X-RAY DIFFRACTION	98
3.5982-3.7877	0.3674	140	0.2944	5034	X-RAY DIFFRACTION	98
3.7877-4.0248	0.2057	143	0.2191	5092	X-RAY DIFFRACTION	99
4.0248-4.3352	0.2042	143	0.1886	5102	X-RAY DIFFRACTION	100
4.3352-4.7708	0.189	143	0.1584	5121	X-RAY DIFFRACTION	100
4.7708-5.4595	0.1849	145	0.172	5183	X-RAY DIFFRACTION	100
5.4595-6.8724	0.224	147	0.208	5259	X-RAY DIFFRACTION	100
6.8724-39.1716	0.224	153	0.1902	5425	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	0.9242	0.7257	0.2405	2.0075	-0.5938	0.7422	-0.1077	-0.1705	0.1588	-0.0213	-0.1812	0.2021	0.6665	-0.4726	-0.0917	0.5352	-0.0657	0.0436	0.5954	-0.0758	0.4235	-27.543	36.5832	-120.732
2	3.1027	-0.6228	0.5875	1.6123	-0.4621	0.1851	-0.0824	0.6597	0.4954	-0.4131	0.0443	-0.288	-0.3416	0.3164	0.0043	0.2877	0.0392	0.0075	0.4701	-0.0204	0.2622	1.6899	47.7253	-122.0471
3	1.5294	0.1204	-0.2587	2.8258	0.2446	1.8506	0.0319	-0.1751	0.0932	0.5256	0.0221	0.7181	-0.0304	-0.3905	-0.0616	0.3699	0.0028	0.0717	0.4077	-0.0349	0.3259	-20.442	40.2965	-110.2217
4	1.1256	0.4172	-0.6037	2.8896	0.1538	3.201	0.3207	-0.7092	-0.106	0.4931	-0.5428	0.4922	-0.2897	-0.2679	0.0417	0.4937	0.1238	0.2017	0.3885	-0.059	0.626	-22.0015	43.933	-103.1568
5	3.5966	-0.9438	0.4242	3.5924	0.1925	0.1125	0.6534	-1.129	-0.8337	0.6619	-0.2629	0.0537	0.9739	-0.3813	0.2871	0.8535	0.1372	-0.1726	0.3742	0.1755	0.5746	-13.7943	25.203	-104.8758
6	2.7548	0.5244	0.4822	1.222	-0.1972	1.6522	-0.0394	0.1485	-0.5191	0.2183	-0.005	-0.0215	0.419	0.0771	0.0443	0.3801	0.0503	0.0379	0.3791	-0.0945	0.2918	-10.5306	31.6176	-117.2546
7	0.3572	-0.2189	-0.4793	0.1689	0.1707	0.7834	-0.1574	0.9611	-0.2273	-0.2838	0.2104	-0.5206	-0.8026	0.3077	-0.0382	0.177	-0.0948	0.0311	0.6742	-0.0465	0.6725	8.4652	67.9983	-123.1288
8	7	3.5079	-2.9333	2.2182	-0.8806	1.8919	-0.7703	0.6469	-0.3542	-1.0745	0.4693	0.9951	0.1506	-0.65	-0.25	0.5074	-0.0361	-0.0297	0.669	0.0068	0.4777	-16.5502	54.5692	-127.8864
9	1.6859	0.4987	0.607	1.7165	0.148	1.995	0.2913	0.0337	-0.2387	0.2658	-0.2013	-0.2136	-0.194	0.1752	-0.0336	0.2599	0.0186	-0.0452	0.3769	-0.0006	0.299	-11.5904	59.1787	-117.2287
10	0.8888	1.1437	-0.8874	2.4077	-0.9609	1.7359	0.3462	-0.2133	-0.3831	0.6753	-0.0968	-0.2328	-0.201	0.8311	0.0511	0.5102	0.0002	-0.1226	0.5341	0.016	0.4769	2.5218	67.1232	-106.434
11	6.1658	-1.0076	-1.9177	3.9361	-1.5177	4.9508	0.9351	0.0223	2.0071	-0.1797	0.8552	0.0764	-1.1897	-0.3965	1.0161	0.5765	-0.1675	-0.2347	0.4051	-0.2404	0.3581	-5.508	81.9827	-109.1702
12	3.3845	0.3396	0.4325	1.6202	-0.3137	2.8805	-0.2714	-0.8679	1.1011	0.0039	-0.1492	0.0812	-1.3557	-0.9519	-0.0009	0.4045	-0.0818	0.0051	0.4532	0.0395	0.3527	0.5173	77.9651	-115.0709
13	0.838	0.4734	-0.2703	1.2663	-0.5642	1.1941	0.079	0.1321	0.5291	-0.0549	-0.0174	-0.2159	-0.5556	0.3297	-0.0063	0.4073	0.0092	-0.0378	0.5785	0.1016	0.4196	-0.5502	77.4419	-122.301
14	3.7191	-0.9943	-0.4161	2.2323	-0.3835	1.6429	0.0411	0.0728	0.3834	-0.2906	0.1806	0.2998	0.0541	-0.0865	-0.0657	0.3692	0.0711	-0.0524	0.3478	0.1132	0.3614	-20.9376	67.5154	-121.6207
15	1.4536	0.0323	0.5441	1.8389	-0.2183	1.584	-0.2046	0.0067	0.1251	1.0256	0.0967	0.1977	0.5183	0.106	0.0106	0.9953	0.2676	-0.1224	0.4488	-0.0583	0.1777	-6.7857	45.7472	-84.6641
16	1.4045	0.0914	-0.4358	1.9284	0.4204	2.1448	-0.078	0.0183	0.203	0.2371	0.2335	-0.2371	0.0885	0.1695	-0.0193	0.5047	0.1496	-0.0714	0.4198	-0.0347	0.2533	-2.7512	44.0057	-95.7669
17	2.8292	-0.085	0.0156	3.3004	-0.6742	3.2844	-0.6032	0.1818	0.3666	0.7364	-0.0988	-0.5348	0.1102	0.8438	-0.6423	0.3973	0.1569	-0.1958	0.4088	-0.0161	0.3812	3.9618	36.0699	-103.2428
18	3.1601	2.1145	-0.3179	2.5138	-1.1459	0.7888	-0.7341	0.5779	-1.6169	0.3854	0.5552	-1.838	0.8567	-0.1642	-0.1996	0.9126	0.5257	-0.3273	0.1116	0.3107	-0.1464	1.0622	27.7953	-91.3113
19	0.0488	-0.0644	0.1066	0.108	-0.0113	0.2155	-0.0899	0.0003	-0.6777	0.5387	-0.0925	-0.0623	0.6165	1.0264	-1.2546	1.3279	0.672	-0.3431	0.7162	0.1131	0.3223	-1.2345	35.8958	-79.5563
20	1.8796	-0.2552	0.358	2.6249	0.783	1.3029	-0.2703	-0.2599	-0.3748	0.8081	0.0887	0.7406	-0.0919	-0.5251	-0.0485	0.8449	0.2013	0.2011	0.4796	0.0961	0.3716	-20.021	39.1213	-86.5484
21	2.6089	-1.0758	-0.1834	2.7724	-0.2773	0.3439	0.1494	-1.076	-0.0579	0.6475	0.2794	0.3131	-0.383	-0.4839	0.0879	0.7447	0.0629	0.1544	0.5558	0.0298	0.5068	-23.997	69.6052	-84.7126
22	4.4691	1.9967	-0.2352	3.5433	-1.8875	2.2763	-0.0845	-0.0582	0.3536	0.4766	0.348	-0.5655	-0.5274	0.4295	-0.0338	0.7964	0.2082	-0.3129	0.5815	-0.2839	0.3224	2.5343	58.6142	-87.5714
23	0.859	-1.0321	0.0028	1.9003	-0.5009	1.9585	0.3667	0.1669	-0.6146	0.3359	0.0964	0.3176	0.2179	0.1646	-0.029	0.5382	0.1613	-0.037	0.3851	-0.0019	0.254	-11.9572	61.6622	-91.581
24	2.7384	0.719	-1.0741	1.7626	-0.64	2.2062	0.3602	0.2113	-0.2388	-0.1467	-0.1028	0.1661	-0.2536	-0.0498	-0.0362	0.5849	0.0989	0.0689	0.3967	-0.0176	0.4324	-22.8391	72.6123	-101.458
25	1.2997	0.4961	0.0573	3.3493	-0.3895	1.7032	0.0126	0.2276	0.0269	0.2638	-0.0364	0.029	0.1514	-0.042	-0.0457	0.2968	0.0332	0.0051	0.3321	0.0069	0.4083	-18.3117	62.6106	-103.194
26	1.8216	0.0126	-0.2617	3.5166	-0.2995	2.2559	0.0788	0.1409	0.236	0.7974	-0.3054	0.3776	0.4391	0.0783	0.0152	0.4664	-0.0492	0.0115	0.4797	0.0252	0.4444	-23.1905	71.5479	-106.188
27	2.0583	-0.0038	0.9601	1.1588	-0.4079	1.0962	0.094	0.388	0.7731	-0.3093	-0.4275	0.5617	-0.4948	0.0919	0.0398	0.7376	0.1095	-0.0096	0.331	0.1428	0.4886	-21.2988	82.8194	-101.3405
28	1.6882	-1.0143	2.1036	1.3535	-1.8731	3.1953	0.1907	-0.1406	0.5803	0.2417	-0.0603	-0.394	-0.2054	0.1462	0.0132	0.8189	0.0898	0.0495	0.4893	-0.0342	0.393	-18.3829	83.2561	-90.9181
29	0.6787	0.1928	-0.202	1.1516	0.8686	0.7634	-0.2751	-0.5458	0.4289	0.7241	0.3213	0.3601	-0.3944	-0.3282	0.0234	0.7686	0.1195	0.0309	0.4413	-0.0928	0.4401	-20.2275	75.9422	-88.0985
30	1.6126	-0.4797	-1.324	1.5466	-0.802	1.8873	-0.2658	0.0444	0.4289	0.444	0.1863	-0.5117	0.2525	0.3918	-0.0289	0.5672	0.0524	-0.1676	0.5759	-0.0645	0.4359	0.5704	70.9449	-89.0214
31	1.6317	-0.3256	0.6934	1.028	-0.7454	1.7956	0.2332	-0.3475	-0.7698	-0.1103	0.0008	0.2764	-0.488	-0.5544	0.1705	0.5515	0.2792	0.0053	0.615	-0.0066	0.4021	-14.6641	1.9713	-90.8918
32	2.8164	0.5761	0.3889	1.8083	-1.1011	2.5387	-0.0252	-0.6073	-0.162	-0.2364	-0.0102	-0.4112	-0.7638	0.3059	-0.0013	0.5589	-0.0983	-0.09	0.4346	0.007	0.4868	12.5171	-2.0404	-85.053
33	1.6207	-0.3472	0.2268	1.3473	0.1851	3.1422	0.0723	0.1445	-0.5811	0.1111	0.1246	0.2477	-0.0715	-0.4953	-0.0036	0.268	0.0765	0.0027	0.5109	-0.0247	0.4904	-10.6426	-9.9406	-96.2497
34	0.6376	0.1204	-1.0312	4.784	-2.9394	4.4873	0.0053	0.2812	-0.7718	-0.1832	-0.3212	-0.2312	0.7188	-0.8061	-0.0021	0.4585	-0.123	-0.01	0.4737	-0.0877	0.467	-6.8108	-15.9672	-96.276
35	2.8201	0.1683	1.2393	1.0604	1.1883	2.2165	-0.198	-0.0579	-0.7974	-0.4413	0.3002	0.2111	0.1825	0.0686	-0.0796	0.5439	0.1997	-0.0156	0.719	-0.0326	0.6373	-12.4211	-12.8259	-107.1778
36	1.8927	-0.1264	-0.4639	1.575	0.134	0.9645	-0.1424	0.3984	0.1974	-0.2618	0.0708	0.2999	-0.7662	-0.5502	0.0928	0.6076	0.1902	-0.1425	0.5531	-0.0689	0.4647	-11.419	2.8356	-102.0643
37	3.2324	0.5929	-1.0219	1.4386	-0.212	2.5373	-0.132	0.1685	0.2513	0.2249	0.2138	-0.2078	-0.838	0.2411	0.0117	0.5808	-0.0984	-0.097	0.3608	0.0188	0.409	9.8804	2.6798	-94.6375
38	3.3616	-0.5411	0.7438	1.6295	-0.4342	1.7022	-0.4993	-1.0151	1.0127	0.2871	0.4913	-0.7561	-0.4194	0.4652	0.0944	0.5196	-0.1108	-0.0168	0.5058	-0.0111	0.4987	18.8868	-11.2022	-67.7053
39	4.324	0.9289	-0.1909	2.4512	-0.5493	2.2227	-0.7222	-0.355	0.7941	-0.1624	0.1582	0.4939	-0.6888	-0.898	-0.1354	0.3823	0.1604	0.058	0.5681	-0.0675	0.4456	-10.2635	-10.0081	-75.6075
40	1.3946	-0.9939	0.8864	2.8489	-0.1979	1.8859	0.2126	0.3174	-0.1442	-0.2476	-0.1275	0.047	-0.2384	0.5041	0.0862	0.3281	-0.0385	-0.0143	0.3665	0.0548	0.3493	14.2275	-19.8694	-75.9278
41	0.77	0.5911	-0.6234	2.1055	-1.0874	5.1636	0.3144	0.6181	-0.3001	-0.0593	-0.1867	0.0588	0.6359	-0.0219	0.1794	0.4031	0.0115	0.0728	0.4614	0.096	0.4106	11.5859	-23.2265	-81.8482
42	4.2286	0.9251	-0.9874	2.2694	-0.094	5.1631	-0.2972	0.9549	-0.4827	-0.0732	0.2313	-0.0503	0.5422	-0.2587	-0.0549	0.3347	0.0438	0.054	0.3545	0.0194	0.4236	17.1648	-29.619	-75.3588
43	2.2608	1.7345	1.0329	3.3299	-0.5769	1.3897	-0.9739	0.0496	-0.8892	-0.4649	0.668	0.0325	1.0657	-0.2853	0.2132	0.8876	-0.0495	-0.1098	0.3127	0.1819	0.7775	11.8622	-34.4899	-60.7992
44	1.4358	0.4438	-0.6494	2.2188	1.0886	2.4441	-0.1711	-0.2325	-0.3089	0.3533	-0.0313	-0.0288	0.2308	-0.3204	0.0935	0.4634	0.091	0.0011	0.3199	0.0418	0.3308	13.8514	-23	-64.8844
45	0.7058	0.0449	-0.2282	0.0003	-0.0477	0.8886	-0.1104	-0.6517	-0.4154	0.2293	0.1629	0.1413	0.4407	0.5005	0.0582	0.5047	0.0081	0.0317	0.5049	0.1112	0.2829	14.5222	-22.9206	-60.6523
46	0.1163	0.0253	0.3133	0.1818	-0.0762	0.7496	0.0012	-0.6048	0.2462	0.4418	-0.0254	-0.0493	-0.3802	0.2174	0.0386	0.6861	0.0276	-0.0698	0.6097	-0.1811	0.3904	10.0064	-11.3631	-61.0796
47	4.0159	1.5414	-0.483	2.5812	-0.0278	1.7903	-0.1328	-0.4203	0.206	1.0717	-0.2554	0.2276	-0.2342	-0.5829	0.0531	0.4618	0.0395	0.1468	0.4786	-0.0038	0.4112	-3.8606	-16.6948	-67.2309
48	1.8414	0.3801	0.0855	1.1845	0.2921	0.4551	0.0683	0.4707	-0.3953	0.078	0.3859	0.0048	-0.4425	-0.7927	0.0445	0.4512	0.007	0.1958	0.684	0.0226	0.5306	-12.1737	-17.6355	-68.1687
49	2.6524	-1.2628	0.4943	1.8827	0.0878	2.0072	0.0548	-0.1165	0.35	0.0586	-0.1236	-0.3186	-0.1084	-0.1056	0.0051	0.2704	0.0179	0.047	0.3513	-0.0314	0.4905	-26.2031	24.9757	-21.4434
50	4.3841	0.7514	-0.6853	2.4285	-0.7105	3.3561	0.9781	0.1558	-0.0879	0.2198	-0.305	-0.4186	-0.1869	-0.0708	-0.0019	0.3521	-0.0586	0.0671	0.3859	-0.0664	0.5209	-20.4028	9.601	-18.6861
51	6.2392	0.0391	2.208	1.2301	-1.0785	1.7549	-0.1222	-1.0355	-0.562	-0.2493	0.0722	0.8505	0.2024	-1.4173	0.0703	1.1893	-0.0396	-0.1896	1.1988	-0.1139	0.9372	-29.9976	7.3314	-5.6369
52	1.9771	-0.6372	-0.1765	1.8976	0.9314	1.6937	-0.1073	-0.1982	0.0994	0.3701	-0.028	0.1485	-0.0625	-0.237	-0.0939	0.2917	0.0493	0.0673	0.4709	-0.0844	0.399	-32.2214	24.0119	-11.4177
53	0.66	-0.4983	0.2303	0.578	-0.214	0.7699	0.0819	0.4443	0.4643	-0.1023	0.0646	0.1188	-0.3664	0.713	0.1219	0.6203	0.1083	0.0682	0.4633	0.0749	0.758	-38.2602	47.0417	-42.1837
54	3.309	0.5472	0.1562	1.1676	-1.1667	2.4557	-0.2631	-0.5913	0.3126	0.9258	0.1791	-0.5093	-0.966	0.5983	-0.0874	0.437	-0.001	0.0476	0.4081	-0.0462	0.6823	-15.2573	36.35	-29.5132
55	1.1657	-0.0931	0.8687	0.7763	0.2216	2.4072	0.594	0.3395	-0.0607	-0.3422	-0.3718	0.1893	0.1289	-0.3667	-0.028	0.5569	0.233	0.0124	0.4595	0.0718	0.5499	-36.101	34.123	-46.4112
56	1.2666	0.8713	-1.38	1.6283	-0.5997	1.6747	0.2349	0.0098	-0.0843	-0.6342	-0.0079	0.2171	0.0209	0.1054	-0.0158	0.6395	0.181	-0.0363	0.5344	0.0193	0.4626	-35.0213	28.8172	-50.6328
57	3.132	-1.8914	-1.2894	1.9017	-0.4648	2.5275	-0.1554	0.6937	-0.1389	-0.1409	0.1448	-1.2076	-0.3094	0.6479	-0.0674	1.035	0.005	0.0805	0.8489	0.1377	0.8322	-26.5703	40.3416	-64.3823
58	0.7197	-0.3806	0.39	3.151	1.3664	4.2612	0.2684	0.9638	0.4339	-0.4266	0.228	-0.6947	-0.0951	0.8815	0.7584	0.7179	0.2005	0.0796	0.4529	0.2074	0.572	-31.3298	45.4761	-56.4772
59	1.5708	0.3548	-0.1671	0.1941	-0.0359	0.1537	0.7736	-0.0441	0.5095	0.0856	-0.1675	0.1147	-0.395	-0.1998	0.1255	0.7024	0.2593	0.1343	0.3183	0.1319	0.7976	-32.6182	47.4297	-47.2602
60	2.943	-0.2369	-0.5374	1.1374	-0.189	0.6805	-0.2962	0.1315	0.3884	-0.1727	0.3195	-0.6517	-0.0306	0.2453	-0.0276	0.5211	-0.0393	0.1337	0.3431	-0.0119	0.7054	-14.1767	40.8971	-39.5039
61	1.6401	0.0483	0.7155	2.0301	1.2017	2.8381	0.0595	0.0776	-0.0514	0.0075	-0.092	-0.0829	0.2497	0.0479	0.0511	0.2628	-0.0503	0.0309	0.2926	-0.0265	0.4092	7.4014	-24.4725	-105.3841
62	2.6205	-0.5996	0.2722	0.6342	0.7268	1.2925	0.9849	-0.252	-0.3523	-0.9325	0.0163	-0.421	0.1805	0.5689	0.2036	0.9298	-0.0942	-0.093	0.9228	-0.143	0.7801	21.081	-9.3482	-96.0204
63	4.4462	1.3633	4.0718	0.939	1.3256	7.863	0.8462	-0.0598	0.1173	-0.7001	0.3491	1.2705	-0.0649	0.593	0.3765	0.5547	0.0573	-0.1627	0.2232	0.2278	0.7419	5.1843	-7.5298	-115.7721
64	1.3999	0.4604	-0.2103	1.6484	0.2015	2.2086	-0.0576	0.3604	-0.0019	-0.434	0.0038	-0.0376	-0.12	-0.104	0.0324	0.3683	-0.0385	0.0511	0.4233	-0.1037	0.3394	3.9702	-21.9819	-115.9074
65	4.3144	0.8292	-1.5592	1.3471	-0.6977	1.917	-0.1174	0.6109	-1.0434	-0.1316	0.1699	-0.1792	0.5602	-0.4888	0.525	0.7167	-0.269	0.111	0.3797	-0.0895	0.5842	-7.8362	-47.8157	-88.5723
66	2.3545	-0.976	-0.1148	0.8768	-0.9375	2.0297	-0.1455	0.8376	-0.706	-0.5823	0.3377	-0.933	0.6924	0.3786	0.0386	0.4282	0.0713	0.1113	0.4006	-0.1022	0.5728	17.0259	-36.2379	-95.8379
67	1.2703	0.6479	-0.4027	0.7751	-0.2242	2.4493	0.0697	0.0427	0.0233	0.3034	-0.0313	0.333	0.2279	-0.3711	0.0131	0.5105	-0.1938	0.1324	0.4186	-0.0819	0.6083	-6.6408	-35.2744	-83.2063
68	1.3838	-0.1028	-0.4566	1.8092	-0.2291	1.8925	0.1678	0.2375	-0.0538	-0.1389	-0.1815	0.6323	-0.146	-0.4193	0.0333	0.3596	-0.065	0.0902	0.5459	0.0394	0.4873	-9.064	-27.6331	-81.2381
69	3.7166	-4.25	2.0457	7.7034	-1.1596	3.8391	0.229	-0.2589	0.0661	1.01	0.0019	-0.5833	1.1172	0.2014	0.1962	0.8741	-0.1216	0.2279	0.5557	0.029	0.5317	0.7267	-39.8845	-67.9451
70	2.1901	-0.1351	-1.5874	2.4628	1.3503	4.7418	0.3205	-0.56	-0.3379	0.3492	0.3821	0.1135	0.303	0.6112	0.3371	0.6787	-0.199	0.3131	0.307	0.0486	0.7129	-5.073	-43.3114	-74.2067
71	1.3132	-0.4235	1.0359	0.7096	-0.1786	0.8168	0.0514	-0.4818	-0.4337	0.3397	0.0095	0.5564	0.9127	-0.2032	0.1132	0.6678	-0.1823	0.1796	0.4358	-0.0044	0.7935	-3.2768	-49.2563	-78.1066
72	2.9808	0.1122	0.471	0.8981	-0.1606	1.1252	0.0891	-0.3922	-0.3714	-0.2177	-0.1216	-0.4648	0.0058	0.272	0.0464	0.4766	0.0748	0.0794	0.4486	0.0453	0.6336	16.2712	-41.4846	-86.2151
73	2.3786	-0.2564	-1.7836	1.3669	-0.4954	2.3711	0.1441	0.9469	0.1385	-0.4727	0.1059	-0.1403	0.0006	0.1171	0.0703	0.5594	0.1725	0.1319	0.5865	-0.0509	0.5474	-11.2319	7.9768	-56.2415
74	2.0677	0.3247	0.8546	1.2612	-1.2784	2.2119	0.1372	0.1381	-0.2231	-0.8828	0.1969	0.5812	-0.0255	-0.5871	-0.016	0.6216	0.0721	-0.11	0.5736	-0.0648	0.4553	-39.1395	9.0822	-52.2717
75	2.1639	0.4801	-1.3488	2.628	0.0237	1.7088	0.4679	-0.167	0.1362	-0.2547	-0.4525	-0.297	-0.2109	0.5009	0.0406	0.46	0.0441	0.1354	0.4413	0.0408	0.4438	-14.3096	18.6486	-48.3639
76	1.8336	-0.5516	-0.1689	4.4175	-0.9144	6.2073	0.1175	-0.4568	0.2312	0.0715	-0.1317	0.0849	-0.0396	-0.2432	0.0542	0.4435	0.0745	0.0822	0.483	0.0972	0.575	-18.5214	22.0742	-44.8724
77	3.7552	2.8798	-3.3166	2.3442	-2.3419	3.1464	0.7286	-0.5617	0.6677	-0.434	-0.1906	-0.4571	-0.5537	1.6951	-0.0226	0.9996	0.1817	0.0053	1.1507	-0.1153	0.8776	-7.4491	24.5921	-36.9655
78	1.9551	0.4662	1.4054	1.3668	1.2126	6.6594	-0.2597	0.39	0.8547	-0.5915	0.1209	0.1043	-0.8642	-0.3282	-0.1658	0.8161	0.1011	0.1424	0.6143	0.4225	0.8847	-16.0207	30.5642	-60.903
79	1.4195	-0.3348	0.2116	0.8333	-0.0735	0.9794	0.3623	0.8195	0.3013	-0.6413	-0.2816	-0.2056	-0.2273	0.2312	0.0042	0.8013	0.158	0.248	0.6475	0.1485	0.5037	-11.0141	21.5467	-61.8254
80	0.2051	0.1346	-0.2709	0.1874	-0.002	1.1111	-0.0263	0.6243	-0.2842	-0.8747	-0.3057	-0.8167	0.0272	-0.1034	-0.0237	0.6605	0.1547	0.2041	0.6868	-0.0772	0.5194	-15.493	9.1228	-63.199
81	2.1355	-0.5663	0.2331	1.3241	-0.4933	1.7561	0.1394	0.3407	-0.188	-0.455	0.0663	0.414	0.0308	-0.4978	0.0061	0.6468	0.1526	-0.0756	0.693	-0.0631	0.4591	-34.7357	14.9444	-60.5271
82	2.9086	0.6351	-0.177	3.0917	-0.6018	2.1167	-0.073	0.1784	-0.0563	-0.2886	-0.0039	0.1388	0.2344	-0.1578	0.0138	0.4021	0.0544	-0.0056	0.3079	-0.0675	0.3715	-32.303	2.5965	-38.1756
83	2.1033	1.2844	-1.2095	2.0301	0.2539	2.3998	0.0861	0.2341	0.4364	0.179	-0.0517	0.1241	-0.3047	-0.5592	-0.0698	0.2804	0.0699	0.0981	0.5248	0.0227	0.4973	-41.6323	12.9737	-29.143
84	3.8864	0.1241	-1.1669	1.5051	1.9676	3.0813	0.3125	0.1876	-0.2746	0.2506	0.0397	1.0056	-0.0854	0.4445	-0.2679	0.5099	0.0599	0.0425	0.6235	0.0183	0.7352	-44.2608	11.1697	-21.6938
85	3.2551	-1.5084	-0.529	3.0221	0.3828	1.6394	0.4393	-0.7826	0.0036	0.1302	0.0061	-0.0382	0.3908	-0.5766	0.0463	0.2944	-0.1272	0.0761	0.5937	-0.0262	0.5864	-45.3541	2.6131	-22.5686
86	1.8015	0.0324	0.6052	1.5436	0.2447	2.5493	0.2577	-0.1778	-0.4231	0.1242	-0.1892	0.1694	0.3224	-0.0503	0.0303	0.3853	-0.0357	0.0524	0.3178	0.0263	0.5118	-33.3088	-3.3502	-27.634

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 18 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 19 through 46 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 47 through 79 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 80 through 105 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 106 through 132 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 133 through 228 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -1 through 18 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 19 through 29 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 30 through 64 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 65 through 105 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 106 through 132 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 133 through 150 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 151 through 190 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 191 through 228 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 1 through 36 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 37 through 96 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 97 through 114 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 115 through 176 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 177 through 190 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 191 through 228 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 2 through 21 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 22 through 36 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 37 through 64 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 65 through 79 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 80 through 96 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 97 through 114 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 115 through 144 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 145 through 162 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 163 through 190 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 191 through 228 )
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 2 through 21 )
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 22 through 46 )
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 47 through 79 )
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 80 through 96 )
35	X-RAY DIFFRACTION	35	chain 'E' and (resid 97 through 135 )
36	X-RAY DIFFRACTION	36	chain 'E' and (resid 136 through 190 )
37	X-RAY DIFFRACTION	37	chain 'E' and (resid 191 through 228 )
38	X-RAY DIFFRACTION	38	chain 'F' and (resid 0 through 19 )
39	X-RAY DIFFRACTION	39	chain 'F' and (resid 20 through 46 )
40	X-RAY DIFFRACTION	40	chain 'F' and (resid 47 through 79 )
41	X-RAY DIFFRACTION	41	chain 'F' and (resid 80 through 96 )
42	X-RAY DIFFRACTION	42	chain 'F' and (resid 97 through 114 )
43	X-RAY DIFFRACTION	43	chain 'F' and (resid 115 through 135 )
44	X-RAY DIFFRACTION	44	chain 'F' and (resid 136 through 150 )
45	X-RAY DIFFRACTION	45	chain 'F' and (resid 151 through 176 )
46	X-RAY DIFFRACTION	46	chain 'F' and (resid 177 through 190 )
47	X-RAY DIFFRACTION	47	chain 'F' and (resid 191 through 208 )
48	X-RAY DIFFRACTION	48	chain 'F' and (resid 209 through 228 )
49	X-RAY DIFFRACTION	49	chain 'G' and (resid 2 through 96 )
50	X-RAY DIFFRACTION	50	chain 'G' and (resid 97 through 114 )
51	X-RAY DIFFRACTION	51	chain 'G' and (resid 115 through 135 )
52	X-RAY DIFFRACTION	52	chain 'G' and (resid 136 through 228 )
53	X-RAY DIFFRACTION	53	chain 'H' and (resid 2 through 21 )
54	X-RAY DIFFRACTION	54	chain 'H' and (resid 22 through 46 )
55	X-RAY DIFFRACTION	55	chain 'H' and (resid 47 through 79 )
56	X-RAY DIFFRACTION	56	chain 'H' and (resid 80 through 114 )
57	X-RAY DIFFRACTION	57	chain 'H' and (resid 115 through 135 )
58	X-RAY DIFFRACTION	58	chain 'H' and (resid 136 through 163 )
59	X-RAY DIFFRACTION	59	chain 'H' and (resid 164 through 190 )
60	X-RAY DIFFRACTION	60	chain 'H' and (resid 191 through 228 )
61	X-RAY DIFFRACTION	61	chain 'I' and (resid 2 through 94 )
62	X-RAY DIFFRACTION	62	chain 'I' and (resid 95 through 105 )
63	X-RAY DIFFRACTION	63	chain 'I' and (resid 106 through 132 )
64	X-RAY DIFFRACTION	64	chain 'I' and (resid 133 through 228 )
65	X-RAY DIFFRACTION	65	chain 'J' and (resid 2 through 21 )
66	X-RAY DIFFRACTION	66	chain 'J' and (resid 22 through 46 )
67	X-RAY DIFFRACTION	67	chain 'J' and (resid 47 through 79 )
68	X-RAY DIFFRACTION	68	chain 'J' and (resid 80 through 105 )
69	X-RAY DIFFRACTION	69	chain 'J' and (resid 106 through 132 )
70	X-RAY DIFFRACTION	70	chain 'J' and (resid 133 through 150 )
71	X-RAY DIFFRACTION	71	chain 'J' and (resid 151 through 190 )
72	X-RAY DIFFRACTION	72	chain 'J' and (resid 191 through 228 )
73	X-RAY DIFFRACTION	73	chain 'K' and (resid 2 through 21 )
74	X-RAY DIFFRACTION	74	chain 'K' and (resid 22 through 46 )
75	X-RAY DIFFRACTION	75	chain 'K' and (resid 47 through 79 )
76	X-RAY DIFFRACTION	76	chain 'K' and (resid 80 through 94 )
77	X-RAY DIFFRACTION	77	chain 'K' and (resid 95 through 105 )
78	X-RAY DIFFRACTION	78	chain 'K' and (resid 106 through 132 )
79	X-RAY DIFFRACTION	79	chain 'K' and (resid 133 through 176 )
80	X-RAY DIFFRACTION	80	chain 'K' and (resid 177 through 190 )
81	X-RAY DIFFRACTION	81	chain 'K' and (resid 191 through 228 )
82	X-RAY DIFFRACTION	82	chain 'L' and (resid 2 through 64 )
83	X-RAY DIFFRACTION	83	chain 'L' and (resid 65 through 96 )
84	X-RAY DIFFRACTION	84	chain 'L' and (resid 97 through 131 )
85	X-RAY DIFFRACTION	85	chain 'L' and (resid 132 through 150 )
86	X-RAY DIFFRACTION	86	chain 'L' and (resid 151 through 228 )

-
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