PDB-6o63: Crystal Structure of Arabidopsis thaliana Spermidine Synthase iso...

ID or keywords:

Entry

Database: PDB / ID: 6o63

Title

Crystal Structure of Arabidopsis thaliana Spermidine Synthase isoform 1 (AtSPDS1)

Components

Spermidine synthase 1

Keywords

TRANSFERASE / Polyamine metabolism / Putrescine Biosynthesis /

dc-SAM / MTA

Function / homology

Function and homology information

spermidine synthase /

spermidine synthase activity / spermidine biosynthetic process /

cytosol
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Sekula, B. / Dauter, Z.

Funding support

United States, 1items

Citation

Journal: Front Plant Sci / Year: 2019
Title: Spermidine Synthase (SPDS) Undergoes Concerted Structural Rearrangements Upon Ligand Binding - A Case Study of the Two SPDS Isoforms FromArabidopsis thaliana.
Authors: Sekula, B. / Dauter, Z.

History

Deposition	Mar 5, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 5, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6o63.cif.gz	467 KB	Display	PDBx/mmCIF format
PDB format	pdb6o63.ent.gz	385 KB	Display	PDB format
PDBx/mmJSON format	6o63.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o6/6o63 ftp://data.pdbj.org/pub/pdb/validation_reports/o6/6o63	HTTPS FTP

-
Related structure data

Related structure data	6o64C 6o65C C: citing same article (ref.)
Similar structure data	6o64-1 6o64-4 6o64-2 5xb6-1 2d0j-2 3rw9-d 3ma7-2 5xb6-3 3bwb-d 5xb6-6 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Spermidine synthase 1

B: Spermidine synthase 1

C: Spermidine synthase 1

D: Spermidine synthase 1

hetero molecules

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

1

A: Spermidine synthase 1

B: Spermidine synthase 1

hetero molecules

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

2

C: Spermidine synthase 1

D: Spermidine synthase 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	89.536, 76.338, 90.192
Angle α, β, γ (deg.)	90.00, 104.68, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Spermidine synthase 1 / / SPDSY 1 / Putrescine aminopropyltransferase 1 Mass: 36862.645 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Tissue: Leaves / Gene: SPDSYN1, At1g23820, F5O8.38 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Tissue (production host): Leaves / References: UniProt: Q9ZUB3, spermidine synthase
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 986 / 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: 2.02 Å³/Da / Density % sol: 39.17 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M ammonium sulfate, 0.1 M BIS-TRIS, 25% PEG 3350, cryoprotection 25% glycerol

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 1, 2018
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.8→44.6 Å / Num. obs: 95958 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / CC_1/2: 0.999 / R_merge(I) obs: 0.055 / Net I/σ(I): 14.1
Reflection shell	Resolution: 1.8→1.86 Å / Redundancy: 4 % / R_merge(I) obs: 0.547 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4794 / CC_1/2: 0.787 / % possible all: 78.5

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0238	refinement
PHASER	2.8.2	phasing
STARANISO		data scaling
XDS	version Jan 2018	data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→43.46 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.922 / SU B: 6.238 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22209	1083	1.1 %	RANDOM
R_work	0.16524	-	-	-
obs	0.16583	94875	87.89 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 24.503 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.21 Å²	0 Å²	-0.16 Å²
2-	-	0.5 Å²	-0 Å²
3-	-	-	-0.19 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→43.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8798	0	62	986	9846

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	9161
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	8490
X-RAY DIFFRACTION	r_angle_refined_deg	1.796	1.632	12448
X-RAY DIFFRACTION	r_angle_other_deg	1.463	1.571	19813
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.817	5	1159
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.273	24.034	414
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.21	15	1498
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	9.671	15	28
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	1184
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.02	10165
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1800
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.142	1.004	4587
X-RAY DIFFRACTION	r_mcbond_other	1.142	1.003	4586
X-RAY DIFFRACTION	r_mcangle_it	1.855	1.491	5726
X-RAY DIFFRACTION	r_mcangle_other	1.855	1.491	5727
X-RAY DIFFRACTION	r_scbond_it	1.448	1.164	4574
X-RAY DIFFRACTION	r_scbond_other	1.424	1.158	4567
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.274	1.652	6698
X-RAY DIFFRACTION	r_long_range_B_refined	5.98	13.303	10533
X-RAY DIFFRACTION	r_long_range_B_other	5.979	13.306	10534
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.799→1.846 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.255	47	-
R_work	0.231	3472	-
obs	-	-	43.94 %

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	0.2939	-0.1385	0.0913	0.1064	0.0708	0.4003	0.0103	0.0339	-0.0184	-0.0122	-0.0228	0.0373	-0.0084	0.0646	0.0125	0.2073	-0.0113	-0.0022	0.1282	0.0061	0.1761	19.2433	9.2111	-11.9714
2	0.4995	-0.2994	-0.1992	0.2063	0.0646	1.5803	0.021	-0.0003	-0.0178	-0.0397	-0.0166	0.073	-0.0339	-0.075	-0.0044	0.1779	0.01	-0.0137	0.1298	-0.0013	0.1954	1.0162	19.6404	-1.1519
3	0.4474	-0.2034	-0.2337	1.5489	0.6867	0.3662	-0.0261	0.1534	-0.1899	-0.0947	-0.0359	0.0828	-0.0389	-0.0971	0.062	0.1634	0.0143	-0.017	0.1506	-0.0044	0.192	1.6706	12.3805	-13.019
4	0.9886	-0.3516	-0.093	0.1423	-0.0351	0.3313	0.0348	-0.0165	0.1173	-0.0228	-0.0059	-0.043	-0.0651	0.0368	-0.0288	0.2204	-0.0224	0.0019	0.0858	0.0017	0.2099	14.1493	26.4911	-0.4985
5	0.711	-0.5019	0.375	0.4732	-0.3108	0.3867	-0.0253	-0.1862	-0.087	-0.0032	0.0646	-0.0217	-0.0244	-0.1116	-0.0393	0.1585	0.0007	0.0181	0.1663	-0.0131	0.1733	6.362	15.5647	11.1075
6	3.2213	1.2977	0.112	0.543	-0.0742	0.8975	-0.0355	-0.0797	0.0123	0.023	-0.0226	0.0021	-0.1157	0.0286	0.0581	0.1992	-0.0097	-0.0155	0.1357	-0.0116	0.1796	22.5759	18.2177	12.2995
7	1.5957	0.9129	-0.5019	0.5568	-0.448	1.0669	0.1026	0.0622	-0.0682	0.0429	-0.0187	0.0004	0.03	0.1614	-0.0838	0.1572	0.0352	0.0121	0.1948	-0.0082	0.1683	35.3081	2.9107	-10.8676
8	0.3707	-0.6257	0.234	1.0888	-0.3659	1.164	0.0069	0.0531	-0.0533	-0.0008	-0.0678	0.1608	0.0114	0.4874	0.0609	0.0612	0.0333	0.0321	0.2929	0.0231	0.1815	44.7002	0.8347	-3.6394
9	0.5822	-0.201	0.3128	0.0716	-0.1341	1.1118	-0.0033	-0.008	-0.0127	0.0107	-0.0145	-0.0043	-0.0412	0.1488	0.0179	0.1417	-0.0198	0.0011	0.1915	0.0154	0.1766	35.48	5.3678	9.0951
10	0.7823	-0.6746	-0.399	0.6957	0.558	1.3459	-0.0008	-0.0499	0.0165	0.0299	-0.0464	-0.0607	0.0491	0.1501	0.0472	0.0662	0.0237	-0.0268	0.2625	0.0196	0.161	41.899	0.5248	19.8544
11	1.7186	0.0542	1.3544	0.0056	0.0515	1.2047	-0.0444	0.3598	0.0943	0.0129	-0.0165	-0.0014	0.03	0.5093	0.0609	0.0516	0.0295	0.0081	0.4731	0.059	0.1024	50.5232	2.2486	6.5971
12	0.6609	0.087	-0.3092	0.0173	-0.0408	0.1471	-0.0505	-0.1893	-0.0945	-0.0316	-0.011	-0.012	0.0355	0.1115	0.0615	0.1244	0.0711	-0.0101	0.2734	0.0686	0.1698	42.7472	-8.0608	19.388
13	0.3035	-0.119	0.235	0.0561	-0.1289	0.6844	0.0548	-0.057	-0.0586	-0.0554	0.0164	0.0382	0.0758	0.0589	-0.0712	0.1844	0.0131	-0.0156	0.1474	0.0367	0.1918	27.5366	-6.5228	12.4198
14	0.4058	0.2808	-0.028	1.1298	-1.1104	1.5631	-0.0409	-0.1569	0.0962	-0.0291	-0.0148	0.0231	0.0022	0.1015	0.0556	0.1205	0.0014	0.0044	0.2251	0.0116	0.1583	30.0173	7.4305	22.7604
15	1.2933	0.7736	0.7585	0.5138	0.5784	0.8798	-0.0213	-0.1319	-0.0268	-0.0201	-0.0174	0.0396	-0.004	0.0061	0.0387	0.1727	-0.0041	0.0045	0.1526	0.0357	0.1974	17.6217	3.4517	13.4941
16	0.3198	0.0471	-0.1002	0.0158	0.0428	0.678	-0.0073	-0.0178	-0.0804	0.01	-0.0127	0.0027	-0.053	0.0889	0.02	0.1751	-0.0135	0.0097	0.1716	-0.0003	0.1615	6.2241	10.7371	50.665
17	1.86	1.0464	0.1465	0.6151	-0.0685	1.394	-0.0202	-0.2412	-0.251	-0.014	-0.1848	-0.1248	-0.0039	0.239	0.205	0.0995	0.0375	-0.0158	0.1833	0.0254	0.2494	15.611	4.8808	54.9534
18	0.3336	0.0412	0.001	0.0134	0.0483	0.6941	0.0436	-0.0468	-0.0713	-0.0096	-0.0042	0.0139	-0.2268	0.1012	-0.0394	0.2402	-0.0695	0.0191	0.1463	-0.0231	0.1474	11.3173	24.385	44.2953
19	1.2801	0.9101	0.0014	0.7016	0.1009	0.8372	0.0234	0.0734	-0.0436	0.0017	0.0633	0.0447	-0.0654	0.2433	-0.0868	0.1388	-0.0408	0.017	0.1993	-0.0263	0.1976	13.4463	13.9646	30.9644
20	1.4796	-1.965	0.125	3.0013	0.327	0.636	-0.0478	0.0448	-0.0957	-0.172	0.0541	0.1091	-0.2967	0.1579	-0.0064	0.2249	-0.0263	0.0239	0.1359	-0.0022	0.1549	0.4893	22.296	30.893
21	0.3966	-0.3018	-0.1991	1.1735	1.2051	2.1636	0.0256	0.0106	-0.1126	0.0115	-0.0523	0.0267	-0.0683	-0.194	0.0267	0.1686	0.0061	0.0184	0.1703	-0.0203	0.161	-16.3687	8.4858	51.5723
22	1.6576	0.638	1.055	0.4778	0.0913	1.1411	0.0447	-0.1165	-0.0106	0.1707	0.0552	0.0214	-0.1636	-0.268	-0.0999	0.1518	0.0577	0.0608	0.2302	-0.0233	0.1455	-26.3475	16.5814	47.0251
23	0.5732	-0.1226	-0.0422	0.0319	-0.0769	1.3529	-0.0104	0.0521	0.0177	0.0036	0.0042	-0.0044	-0.1139	-0.2156	0.0062	0.1793	0.036	0.0148	0.1717	-0.0187	0.1612	-17.0239	16.5306	32.8634
24	2.5889	1.066	-1.0628	0.5856	-0.2477	0.7464	-0.0398	0.0163	0.0949	-0.0985	-0.0073	0.1053	-0.0682	-0.1222	0.0471	0.0859	0.066	-0.0182	0.2775	0.0278	0.1146	-24.8222	16.4457	21.8466
25	2.1997	-1.6023	1.4001	1.6741	-0.6812	1.1189	-0.056	-0.1207	0.0293	-0.0656	0.0714	-0.1216	-0.1411	-0.1247	-0.0155	0.1034	0.0767	0.0509	0.2477	-0.0312	0.1533	-32.2372	19.9829	35.7731
26	0.2436	0.1962	0.0549	0.1894	0.0675	0.0663	-0.0299	0.0493	-0.0284	0.0237	0.0259	-0.0281	0.0064	-0.0893	0.004	0.122	0.001	0.0086	0.2649	-0.0131	0.1335	-23.3434	4.8374	24.672
27	0.1636	-0.039	0.3302	0.345	0.4596	1.6165	-0.0177	-0.0043	-0.0259	0.02	0.026	0.0028	0.0461	-0.079	-0.0083	0.1673	-0.0205	0.0186	0.1663	-0.038	0.174	-11.0927	3.8097	28.493
28	1.3433	0.32	0.1469	0.3104	0.7611	2.3714	0.0576	0.2247	0.0735	-0.0019	0.0253	-0.0497	-0.1133	-0.1576	-0.0828	0.2074	0.0494	-0.0066	0.149	-0.0189	0.1614	-10.5674	16.6929	19.2557
29	0.6734	-0.8853	-0.2138	2.9699	-1.1027	1.1385	-0.0262	0.0738	0.0013	-0.028	-0.0616	-0.1712	0.0183	-0.0417	0.0878	0.1534	-0.0117	0.0143	0.1556	-0.0356	0.1954	-1.7371	7.21	27.6686

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	31 - 117
2	X-RAY DIFFRACTION	2	A	118 - 153
3	X-RAY DIFFRACTION	3	A	154 - 175
4	X-RAY DIFFRACTION	4	A	176 - 281
5	X-RAY DIFFRACTION	5	A	282 - 311
6	X-RAY DIFFRACTION	6	A	312 - 334
7	X-RAY DIFFRACTION	7	B	31 - 67
8	X-RAY DIFFRACTION	8	B	68 - 92
9	X-RAY DIFFRACTION	9	B	93 - 117
10	X-RAY DIFFRACTION	10	B	118 - 153
11	X-RAY DIFFRACTION	11	B	154 - 172
12	X-RAY DIFFRACTION	12	B	173 - 201
13	X-RAY DIFFRACTION	13	B	202 - 281
14	X-RAY DIFFRACTION	14	B	282 - 311
15	X-RAY DIFFRACTION	15	B	312 - 334
16	X-RAY DIFFRACTION	16	C	31 - 153
17	X-RAY DIFFRACTION	17	C	154 - 175
18	X-RAY DIFFRACTION	18	C	176 - 281
19	X-RAY DIFFRACTION	19	C	282 - 311
20	X-RAY DIFFRACTION	20	C	312 - 334
21	X-RAY DIFFRACTION	21	D	31 - 60
22	X-RAY DIFFRACTION	22	D	61 - 92
23	X-RAY DIFFRACTION	23	D	93 - 117
24	X-RAY DIFFRACTION	24	D	118 - 153
25	X-RAY DIFFRACTION	25	D	154 - 172
26	X-RAY DIFFRACTION	26	D	173 - 241
27	X-RAY DIFFRACTION	27	D	242 - 281
28	X-RAY DIFFRACTION	28	D	282 - 311
29	X-RAY DIFFRACTION	29	D	312 - 334

-
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