PDB-6p8j: Structure of P. aeruginosa ATCC27853 CdnD D62N/D64N mutant bound ...

ID or keywords:

Entry

Database: PDB / ID: 6p8j

Title

Structure of P. aeruginosa ATCC27853 CdnD D62N/D64N mutant bound to ATP

Components

Nucleotidyltransferase

Keywords

SIGNALING PROTEIN / second-messenger signaling / cGAS / CD-NTase

Function / homology

Function and homology information

diadenylate cyclase / diadenylate cyclase activity / nucleotide metabolic process / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / ATP binding / metal ion binding
Similarity search - Function

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.47 Å

Authors

Ye, Q. / Corbett, K.D.

Citation

Journal: Mol.Cell / Year: 2020
Title: HORMA Domain Proteins and a Trip13-like ATPase Regulate Bacterial cGAS-like Enzymes to Mediate Bacteriophage Immunity.
Authors: Ye, Q. / Lau, R.K. / Mathews, I.T. / Birkholz, E.A. / Watrous, J.D. / Azimi, C.S. / Pogliano, J. / Jain, M. / Corbett, K.D.

History

Deposition	Jun 7, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 25, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 22, 2020	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Mar 4, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3	Oct 11, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Download

PDBx/mmCIF format	6p8j.cif.gz	723.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6p8j.ent.gz	609 KB	Display	PDB format
PDBx/mmJSON format	6p8j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6p8j_validation.pdf.gz	508.7 KB	Display	wwPDB validaton report
Full document	6p8j_full_validation.pdf.gz	510.7 KB	Display
Data in XML	6p8j_validation.xml.gz	2.3 KB	Display
Data in CIF	6p8j_validation.cif.gz	21.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p8/6p8j ftp://data.pdbj.org/pub/pdb/validation_reports/p8/6p8j	HTTPS FTP

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Related structure data

Related structure data	6p80C 6p82SC 6p8oC 6p8pC 6p8rC 6p8sC 6p8uC 6p8vC 6pb3C 6u7bC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1jpd-d 2gqg-2 6p82-2 1e7q-d 5l10-1 2wek-1 1e6u-d 4xgq-2 1qi3-d 4ddd-d 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
Experimental dataset #1	Data set type: diffraction image data / Details: raw diffraction data / Metadata reference: 10.15785/SBGRID/671

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

C: Nucleotidyltransferase

A: Nucleotidyltransferase

B: Nucleotidyltransferase

D: Nucleotidyltransferase

hetero molecules

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

1

C: Nucleotidyltransferase

hetero molecules

defined by author
Evidence: gel filtration
34.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Nucleotidyltransferase

hetero molecules

defined by author
34.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

B: Nucleotidyltransferase

hetero molecules

defined by author
34.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Nucleotidyltransferase

hetero molecules

defined by author
34.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	46.484, 152.166, 88.255
Angle α, β, γ (deg.)	90.00, 90.12, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Nucleotidyltransferase / Nucleotidyltransferase domain protein Mass: 34202.422 Da / Num. of mol.: 4 / Mutation: D62N, D64N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: DY979_07585, EGY23_20895, IPC669_24880, PA5486_02902, PAERUG_E15_London_28_01_14_04351, PAMH19_6112 Production host: Escherichia coli (E. coli) / References: UniProt: A0A080VY32, UniProt: P0DTF7*PLUS
#2: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1444 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.29 Å³/Da / Density % sol: 46.31 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris pH 8.5, 0.2 M sodium formate, and 20-22% PEG 6000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.47→100 Å / Num. obs: 201994 / % possible obs: 97.4 % / Redundancy: 3.4 % / CC_1/2: 0.996 / R_merge(I) obs: 0.088 / R_rim(I) all: 0.104 / Net I/σ(I): 9.7
Reflection shell	Resolution: 1.47→1.56 Å / Redundancy: 3.1 % / R_merge(I) obs: 0.948 / Mean I/σ(I) obs: 0.97 / Num. unique obs: 31103 / CC_1/2: 0.356 / R_rim(I) all: 1.143 / % possible all: 92.7

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6P82

6p82

Resolution: 1.47→88.26 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.95

	R_factor	Num. reflection	% reflection
R_free	0.229	10054	4.98 %
R_work	0.195	-	-
obs	0.197	201964	97.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.47→88.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9612	0	132	1444	11188

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	10057
X-RAY DIFFRACTION	f_angle_d	1.116	13635
X-RAY DIFFRACTION	f_dihedral_angle_d	18.865	3727
X-RAY DIFFRACTION	f_chiral_restr	0.073	1409
X-RAY DIFFRACTION	f_plane_restr	0.007	1784

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 (%)
1.47-1.4863	0.3733	268	0.3334	5233	X-RAY DIFFRACTION	80
1.4863-1.5038	0.3371	306	0.3164	6326	X-RAY DIFFRACTION	96
1.5038-1.5221	0.3415	346	0.3003	6276	X-RAY DIFFRACTION	97
1.5221-1.5414	0.3238	326	0.2916	6355	X-RAY DIFFRACTION	96
1.5414-1.5617	0.3388	330	0.2955	6289	X-RAY DIFFRACTION	96
1.5617-1.5831	0.3645	316	0.3278	6362	X-RAY DIFFRACTION	97
1.5831-1.6057	0.3339	357	0.3148	6430	X-RAY DIFFRACTION	97
1.6057-1.6297	0.3441	306	0.2918	6369	X-RAY DIFFRACTION	98
1.6297-1.6551	0.3077	312	0.2704	6472	X-RAY DIFFRACTION	98
1.6551-1.6823	0.3065	371	0.2607	6372	X-RAY DIFFRACTION	99
1.6823-1.7113	0.3028	370	0.2424	6442	X-RAY DIFFRACTION	98
1.7113-1.7424	0.2486	329	0.2189	6484	X-RAY DIFFRACTION	99
1.7424-1.7759	0.2771	374	0.2197	6469	X-RAY DIFFRACTION	98
1.7759-1.8122	0.2598	345	0.2173	6441	X-RAY DIFFRACTION	99
1.8122-1.8516	0.2486	315	0.2137	6506	X-RAY DIFFRACTION	98
1.8516-1.8947	0.2765	324	0.2165	6440	X-RAY DIFFRACTION	98
1.8947-1.942	0.2625	376	0.2191	6461	X-RAY DIFFRACTION	98
1.942-1.9946	0.2668	319	0.2137	6420	X-RAY DIFFRACTION	98
1.9946-2.0533	0.2475	346	0.2067	6427	X-RAY DIFFRACTION	98
2.0533-2.1195	0.25	303	0.1903	6487	X-RAY DIFFRACTION	97
2.1195-2.1953	0.2162	404	0.1786	6375	X-RAY DIFFRACTION	99
2.1953-2.2832	0.2263	330	0.1715	6525	X-RAY DIFFRACTION	99
2.2832-2.3871	0.2031	346	0.1683	6492	X-RAY DIFFRACTION	99
2.3871-2.513	0.2137	298	0.1698	6567	X-RAY DIFFRACTION	99
2.513-2.6704	0.2062	354	0.1754	6539	X-RAY DIFFRACTION	99
2.6704-2.8766	0.2094	348	0.1738	6470	X-RAY DIFFRACTION	99
2.8766-3.1661	0.2074	293	0.177	6522	X-RAY DIFFRACTION	98
3.1661-3.6243	0.207	352	0.1753	6443	X-RAY DIFFRACTION	98
3.6243-4.5662	0.1738	313	0.1617	6353	X-RAY DIFFRACTION	96
4.5662-88.4143	0.192	377	0.185	6563	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	0.9179	1.0348	-1.0773	3.0673	-2.4622	3.3532	0.1173	-0.0396	0.012	0.4018	0.0989	0.1046	-0.3443	-0.0352	-0.0738	0.1632	-0.0253	0.0033	0.1923	-0.0026	0.1853	47.8197	20.5267	-30.4915
2	0.5726	0.2158	0.0323	0.4958	-0.1045	1.6079	0.0257	-0.0156	0.0011	-0.0042	-0.0159	-0.0641	0.0079	0.1595	-0.0005	0.1498	0.0022	0.001	0.1674	-0.003	0.1697	54.1698	19.6663	-44.0371
3	0.8572	-0.1886	0.3805	1.6207	-0.822	2.7577	0.0064	0.0299	0.1102	-0.172	-0.0509	-0.1215	-0.0255	0.206	0.0299	0.1742	-0.0045	0.0085	0.164	-0.0338	0.164	54.7117	20.4649	-59.1212
4	2.0137	-1.3314	1.9714	2.5818	-2.5694	3.3658	0.0433	-0.1471	-0.1484	0.0052	0.1577	0.2084	0.1186	-0.2824	-0.3332	0.191	0.0005	0.0099	0.1928	-0.0084	0.1859	56.5132	43.7331	-59.133
5	0.8699	-0.2859	0.2793	1.4539	-0.6452	1.3977	0.0665	0.0476	0.0841	-0.0261	-0.0081	0.0287	-0.114	-0.0281	-0.1502	0.1507	-0.0068	-0.005	0.152	-0.0126	0.1804	61.59	53.0674	-70.3639
6	0.4522	-0.2756	-0.0038	0.5808	-0.0085	1.5573	0.0138	0.0711	-0.0055	-0.0074	-0.0001	-0.0308	0.0133	0.1087	-0.0305	0.1363	0.0031	-0.0007	0.1777	-0.0034	0.1562	77.4608	44.6552	-59.5375
7	1.0016	-0.3898	-0.113	1.6208	-0.8837	2.4754	0.0154	-0.0691	-0.1388	0.1339	-0.0482	-0.0859	0.0518	0.2246	0.0013	0.1687	-0.0019	-0.0048	0.1689	-0.0225	0.1592	77.964	44.2226	-44.3981
8	0.2907	0.9597	0.7819	2.121	2.0392	2.464	-0.0528	0.0977	-0.0328	-0.1225	0.2182	-0.1882	-0.1389	0.3115	-0.2229	0.1566	0.0151	-0.008	0.1994	0.0026	0.2048	74.1565	-28.5982	-71.1873
9	0.5783	0.7687	0.7408	1.1515	0.8603	0.9866	-0.0224	0.0452	0.0354	-0.0293	0.0709	0.0105	-0.0126	0.0957	-0.0055	0.1514	0.0017	0.0076	0.1648	0.0119	0.1536	60.9111	-30.3701	-82.0231
10	1.6391	-0.8013	0.9879	2.3994	-0.214	1.1016	0.0213	-0.0058	-0.1463	0.0754	0.0079	0.1086	0.0357	0.0521	-0.0391	0.143	-0.0058	0.0175	0.1629	0.0248	0.1527	55.3843	-41.1446	-77.5434
11	1.5653	0.306	0.7031	1.2514	0.8468	2.2278	0.1014	-0.0025	-0.0386	0.0724	-0.0194	-0.0265	0.1232	0.2887	-0.048	0.154	-0.0104	0.0263	0.1873	0.0132	0.1514	64.0276	-32.7075	-74.4552
12	1.7599	1.9491	1.2227	2.3849	1.6449	1.9696	-0.2092	0.3189	0.075	-0.125	0.2567	0.0743	-0.2177	0.1879	0.1243	0.166	0.0161	-0.0114	0.1601	0.017	0.2094	58.6986	-17.3899	-77.9306
13	0.9077	-0.0851	0.8024	0.7979	-0.2346	1.4592	-0.0024	-0.0531	0.0241	0.008	-0.0221	0.0412	-0.0917	-0.1181	0.0128	0.166	0.0109	0.0038	0.16	-0.0041	0.1696	61.7293	-17.3087	-57.6882
14	0.0789	0.1439	-0.3526	0.9667	-1.0145	2.3904	-0.0028	0.0635	0.0089	-0.0103	0.1072	0.122	0.0381	-0.2131	-0.0759	0.1547	-0.0004	-0.0157	0.1828	-0.0078	0.1909	45.3347	16.8409	-88.5176
15	1.5765	0.264	-0.33	1.3134	-0.062	1.4735	0.0294	-0.0835	0.0839	0.0716	0.0186	0.04	-0.0247	-0.1482	-0.0508	0.1017	0.0005	-0.0197	0.1258	-0.0013	0.1094	56.6396	25.3992	-92.9342
16	0.6871	0.9466	-0.9035	1.1687	-1.1509	1.4936	-0.2265	0.042	-0.115	-0.3603	0.0811	-0.1364	0.3029	-0.0858	0.0686	0.2302	0.0025	0.0302	0.1699	-0.0094	0.2193	59.5203	7.8488	-95.3881
17	1.1255	-0.0733	-0.4606	0.5514	0.1563	1.6858	-0.0162	-0.0566	-0.0631	-0.0373	-0.0058	-0.0285	0.1787	0.0798	0.0063	0.1653	0.016	-0.0056	0.1384	0.0026	0.1723	54.7933	5.8272	-72.8338
18	1.3219	0.7627	-1.302	1.5697	-1.699	3.113	0.019	0.0901	0.0325	0.0019	0.0728	0.1096	-0.1046	-0.1945	-0.272	0.1452	0.0174	-0.0074	0.1544	-0.0182	0.1835	34.5187	19.6178	-41.5464
19	0.9197	0.1632	0.2325	1.381	-1.09	2.827	0.0551	-0.0077	-0.1027	-0.0579	-0.0061	0.0134	0.1665	-0.0387	-0.1975	0.1391	0.0053	-0.0063	0.1514	-0.0062	0.1961	35.9953	7.5403	-33.3421

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'B' AND (RESID 146 THROUGH 170 )
2	X-RAY DIFFRACTION	2	CHAIN 'B' AND (RESID 171 THROUGH 252 )
3	X-RAY DIFFRACTION	3	CHAIN 'B' AND (RESID 253 THROUGH 300 )
4	X-RAY DIFFRACTION	4	CHAIN 'D' AND (RESID 1 THROUGH 39 )
5	X-RAY DIFFRACTION	5	CHAIN 'D' AND (RESID 40 THROUGH 168 )
6	X-RAY DIFFRACTION	6	CHAIN 'D' AND (RESID 169 THROUGH 252 )
7	X-RAY DIFFRACTION	7	CHAIN 'D' AND (RESID 253 THROUGH 300 )
8	X-RAY DIFFRACTION	8	CHAIN 'C' AND (RESID 1 THROUGH 39 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 40 THROUGH 80 )
10	X-RAY DIFFRACTION	10	CHAIN 'C' AND (RESID 81 THROUGH 107 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 108 THROUGH 145 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 146 THROUGH 170 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 171 THROUGH 300 )
14	X-RAY DIFFRACTION	14	CHAIN 'A' AND (RESID 1 THROUGH 62 )
15	X-RAY DIFFRACTION	15	CHAIN 'A' AND (RESID 63 THROUGH 136 )
16	X-RAY DIFFRACTION	16	CHAIN 'A' AND (RESID 137 THROUGH 170 )
17	X-RAY DIFFRACTION	17	CHAIN 'A' AND (RESID 171 THROUGH 300 )
18	X-RAY DIFFRACTION	18	CHAIN 'B' AND (RESID 1 THROUGH 62 )
19	X-RAY DIFFRACTION	19	CHAIN 'B' AND (RESID 63 THROUGH 145 )

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