PDB-9t7m: Crystallographic structure of Clostridioides difficile CspA prote...

ID or keywords:

Entry

Database: PDB / ID: 9t7m

Title

Crystallographic structure of Clostridioides difficile CspA protein in complex with Taurocholate at 2.9 angstrom resolution

Components

Subtilisin-like serine germination related protease

Keywords

SIGNALING PROTEIN / Pseudo Protease / Clostridium / spore germination

Function / homology

Function and homology information

subtilisin / serine-type endopeptidase activity / proteolysis / :
Similarity search - Function

Biological species

Clostridioides difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Alcorlo, M. / Mayor-Luna, C. / Hermoso, J.

Funding support

Spain, 1items

Citation

Journal: To be published
Title: Crystallographic structure of Clostridioides difficile CspA protein in complex with Taurocholate at 2.9 angstrom resolution
Authors: Alcorlo, M. / Mayor-Luna, C. / Hermoso, J.

History

Deposition	Nov 11, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 17, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9t7m.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb9t7m.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	9t7m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t7/9t7m ftp://data.pdbj.org/pub/pdb/validation_reports/t7/9t7m	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#184 - Apr 2015 Glucagon similarity (7) #142 - Oct 2011 PDB Pioneers similarity (8)

Deposited unit

E: Subtilisin-like serine germination related protease

A: Subtilisin-like serine germination related protease

B: Subtilisin-like serine germination related protease

C: Subtilisin-like serine germination related protease

D: Subtilisin-like serine germination related protease

F: Subtilisin-like serine germination related protease

hetero molecules

364 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

E: Subtilisin-like serine germination related protease

C: Subtilisin-like serine germination related protease

hetero molecules

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

2

A: Subtilisin-like serine germination related protease

hetero molecules

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

3

B: Subtilisin-like serine germination related protease

D: Subtilisin-like serine germination related protease

hetero molecules

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

4

F: Subtilisin-like serine germination related protease

hetero molecules

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

Unit cell

Length a, b, c (Å)	141.239, 158.629, 188.364
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	Subtilisin-like serine germination related protease Mass: 60007.977 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: cspBA, SAMEA1402399_00499 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0AB74Q767, subtilisin
#2: Chemical	ChemComp-TCH / TAUROCHOLIC ACID Mass: 515.703 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂₆H₄₅NO₇S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.94 Å³/Da / Density % sol: 58.11 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Na Sulfate and 20 % PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 17, 2025
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.9→49.52 Å / Num. obs: 94280 / % possible obs: 100 % / Redundancy: 13.4 % / CC_1/2: 0.996 / Net I/σ(I): 14.2
Reflection shell	Resolution: 2.9→2.95 Å / Num. unique obs: 4617 / CC_1/2: 0.812

-
Processing

Software

Name	Version	Classification
PHENIX	(1.21.2_5419: ???)	refinement
PDB_EXTRACT		data extraction
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.9→28.87 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.35 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2406	4707	5 %
R_work	0.2051	-	-
obs	0.2069	94107	99.98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.9→28.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	25211	0	280	0	25491

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	26013
X-RAY DIFFRACTION	f_angle_d	0.535	35403
X-RAY DIFFRACTION	f_dihedral_angle_d	16.098	9925
X-RAY DIFFRACTION	f_chiral_restr	0.045	4035
X-RAY DIFFRACTION	f_plane_restr	0.005	4556

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 (%)
2.9-2.93	0.3691	159	0.3111	2921	X-RAY DIFFRACTION	100
2.93-2.97	0.3548	160	0.2905	2921	X-RAY DIFFRACTION	100
2.97-3	0.3124	150	0.2964	2986	X-RAY DIFFRACTION	100
3-3.04	0.3098	172	0.2711	2914	X-RAY DIFFRACTION	100
3.04-3.08	0.3344	156	0.2683	2961	X-RAY DIFFRACTION	100
3.08-3.12	0.28	176	0.261	2944	X-RAY DIFFRACTION	100
3.12-3.17	0.3074	145	0.2509	2925	X-RAY DIFFRACTION	100
3.17-3.22	0.2768	168	0.2553	2949	X-RAY DIFFRACTION	100
3.22-3.27	0.3048	150	0.2503	2985	X-RAY DIFFRACTION	100
3.27-3.32	0.3007	147	0.2557	2943	X-RAY DIFFRACTION	100
3.32-3.38	0.2765	156	0.2324	2976	X-RAY DIFFRACTION	100
3.38-3.44	0.3085	157	0.2407	2931	X-RAY DIFFRACTION	100
3.44-3.5	0.2544	157	0.2278	2958	X-RAY DIFFRACTION	100
3.5-3.57	0.2464	151	0.2269	2957	X-RAY DIFFRACTION	100
3.57-3.65	0.2543	161	0.2223	2958	X-RAY DIFFRACTION	100
3.65-3.74	0.2743	168	0.2177	2967	X-RAY DIFFRACTION	100
3.74-3.83	0.2482	167	0.2156	2956	X-RAY DIFFRACTION	100
3.83-3.93	0.2606	135	0.2055	3003	X-RAY DIFFRACTION	100
3.93-4.05	0.2348	151	0.1894	2966	X-RAY DIFFRACTION	100
4.05-4.18	0.2202	159	0.1913	2975	X-RAY DIFFRACTION	100
4.18-4.33	0.218	147	0.1737	2971	X-RAY DIFFRACTION	100
4.33-4.5	0.1798	129	0.1625	3026	X-RAY DIFFRACTION	100
4.5-4.71	0.2069	170	0.1584	2978	X-RAY DIFFRACTION	100
4.71-4.95	0.2016	184	0.1602	2953	X-RAY DIFFRACTION	100
4.95-5.26	0.2023	153	0.1772	3019	X-RAY DIFFRACTION	100
5.26-5.66	0.1952	154	0.1908	3024	X-RAY DIFFRACTION	100
5.66-6.23	0.2588	163	0.2084	2997	X-RAY DIFFRACTION	100
6.23-7.12	0.2415	156	0.2066	3058	X-RAY DIFFRACTION	100
7.12-8.92	0.1826	146	0.1693	3095	X-RAY DIFFRACTION	100
8.92-28.87	0.1705	160	0.1622	3183	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	2.6146	-0.3999	0.1857	1.4664	0.4042	1.7598	-0.0464	-0.2001	0.251	0.1192	0.0083	-0.1717	-0.0965	0.0874	0.0286	0.3049	0.0159	-0.0465	0.2083	0.032	0.1865	-29.1404	-6.7445	29.9416
2	1.6361	-0.0928	-1.2025	0.9075	-0.5093	2.7726	-0.0479	-0.4854	0.2641	0.3741	0.1583	-0.3817	-0.0967	1.0205	-0.1762	0.3365	-0.0043	-0.0687	0.4274	-0.0304	0.3783	-18.0233	-15.5848	36.1815
3	1.4693	0.1049	0.5207	0.8257	-0.052	0.8415	0.0128	0.108	-0.0597	0.0179	-0.0886	-0.3099	0.0214	0.2753	0.0635	0.2872	0.0315	-0.0314	0.3043	0.0616	0.3245	-10.0447	-17.4898	27.5849
4	1.3883	-0.5136	0.3598	1.9613	-0.6665	1.61	-0.0472	-0.0923	0.0136	-0.0596	0.0799	0.0454	0.0327	-0.0209	-0.0567	0.2486	0.0032	-0.0052	0.1986	-0.0462	0.2034	-44.2732	-27.0489	-4.4953
5	1.5292	-0.2828	-0.1613	0.8926	0.0473	0.5278	-0.0483	0.0402	-0.0177	-0.2073	0.0955	-0.2142	0.0232	0.1042	-0.0383	0.3442	-0.0141	0.0361	0.2126	-0.042	0.2179	-30.5049	-32.4261	-17.9837
6	2.7668	-0.0976	0.1118	0.6729	-0.3612	2.5118	0.0574	0.1128	0.0214	-0.1823	-0.0644	-0.5237	0.2034	0.6809	0.0722	0.4436	-0.0181	0.0616	0.6803	0.1033	0.4747	-54.783	-18.1134	41.8566
7	1.027	-0.1416	0.1606	1.6313	0.0723	1.6237	-0.0105	0.3316	0.3603	-0.2177	-0.0985	0.0827	-0.286	-0.0474	0.0859	0.4502	0.0505	0.0041	0.474	0.1495	0.4287	-82.5922	-8.8103	39.254
8	1.1057	-0.6344	-0.1757	2.1586	1.2202	1.848	-0.0222	0.3824	0.1003	0.562	0.1544	-0.6062	0.1335	0.5251	-0.0718	0.3472	-0.0037	-0.0624	0.404	0.0281	0.3874	-77.1296	-19.126	52.5037
9	0.6736	0.0613	-0.1499	1.6787	0.0831	1.9865	0.1042	0.4209	-0.3391	-0.2806	-0.0719	-0.2166	0.3391	0.181	-0.0238	0.4294	0.1474	0.0037	0.5891	-0.0947	0.416	-65.8263	-44.139	44.6227
10	1.1824	-0.7281	0.1157	1.4211	0.0617	1.0532	0.022	0.2497	-0.0032	0.1271	-0.0782	0.154	0.031	-0.0168	0.055	0.3026	-0.0054	0.0496	0.375	0.0154	0.309	-83.978	-25.3217	50.901
11	4.4793	-0.1035	0.2628	0.7353	0.8831	3.2535	-0.2612	-0.1648	0.4146	0.0868	-0.1931	0.3303	0.3217	-0.1736	0.2964	0.4122	-0.0045	0.0067	0.4356	0.0777	0.5489	-28.2293	-15.8565	67.6769
12	2.3392	0.2968	0.2265	1.3524	-0.2082	1.9537	-0.0703	-0.1383	0.2654	0.2414	0.0382	-0.217	-0.2091	0.0396	0.0084	0.4267	0.0018	-0.1814	0.2841	0.0205	0.5114	0.547	-8.82	70.4459
13	0.6229	0.9329	-0.2765	1.7586	-0.2805	0.7384	0.1845	-0.1338	-0.0893	-0.3756	0.0494	0.469	0.051	-0.1567	-0.2245	0.458	0.0344	-0.1434	0.3354	0.0357	0.558	-4.6066	-17.036	55.9966
14	0.5711	-0.0878	0.0328	1.6898	-0.4188	1.723	0.1456	-0.2914	-0.4054	0.1082	0.068	0.1153	0.2741	-0.3506	-0.199	0.5407	-0.0929	-0.1832	0.4533	0.1681	0.5716	-18.2546	-40.7627	59.593
15	1.3496	0.6992	0.0698	1.0643	-0.0988	1.3744	0.0071	-0.0118	-0.0856	-0.0224	0.0363	-0.2095	0.0724	0.2071	-0.0206	0.3112	0.0157	-0.1148	0.3248	0.0307	0.5176	4.7091	-20.3906	55.9439
16	2.5219	0.2639	0.1333	2.0952	-0.7578	1.4049	-0.0012	0.6446	1.5832	-0.5086	0.2292	-0.135	-0.6357	-0.2784	-0.2501	0.7162	-0.0617	0.027	0.6351	0.1468	0.9449	-67.7805	2.3912	74.145
17	2.2133	-0.2852	-0.2587	1.7128	0.233	1.813	0.0247	-0.3483	0.2955	0.3191	-0.0279	-0.2577	-0.0798	0.5264	0.0165	0.4165	-0.0847	-0.0472	0.5726	-0.0473	0.372	-48.6375	-20.4558	81.9854
18	1.8346	-0.304	-1.7614	0.6597	-0.263	3.3071	0.0639	0.5328	0.1517	0.081	-0.0934	-0.2548	-0.588	-0.5238	-0.0768	0.3924	-0.0186	-0.0191	0.4902	0.0786	0.3646	-64.4093	-22.8407	72.7709
19	1.2019	-0.3012	-0.1508	1.6067	0.3935	1.6224	-0.0557	-0.3321	-0.0636	0.5405	-0.0728	0.1373	0.2189	-0.0877	0.0574	0.4977	-0.0627	0.0942	0.3871	-0.0444	0.3436	-86.0759	-19.158	86.6677
20	0.5808	-0.1077	-0.8726	0.2175	-0.0019	2.6526	-0.0349	0.0099	0.3578	0.275	0.0147	0.2521	-0.3292	-0.4016	0.0153	0.6141	0.0436	0.1156	0.4867	-0.0831	0.4773	-88.8173	-9.8389	82.6101
21	2.0181	-0.6129	-0.1881	0.7283	0.2412	1.4342	-0.0052	-0.2571	-0.0726	0.2804	-0.0334	0.0956	-0.001	0.0921	0.0126	0.453	-0.0441	0.0392	0.2958	0.0323	0.3132	-73.1771	-25.2671	84.031
22	2.7163	0.038	0.3002	1.63	-0.0873	1.0081	-0.0147	0.0809	-0.4762	0.1088	-0.1236	-0.1924	0.1355	0.4105	0.1069	0.3918	0.0204	0.051	0.4741	0.0237	0.3139	-56.4773	-36.0525	69.1273
23	1.3397	-0.9284	-0.2524	0.9695	0.0551	1.3161	-0.0661	-1.0508	0.4359	0.5449	0.2356	0.2159	-0.0546	-0.0175	0.0305	0.901	-0.0387	-0.1139	1.2402	-0.0853	0.6426	-29.3448	48.3911	89.6568
24	0.7108	0.2035	0.6244	1.6448	-0.3876	0.7769	0.092	-0.3729	-1.0431	-0.0628	-0.0316	-0.4097	0.2413	0.091	-0.0834	0.5196	-0.0432	-0.1654	0.529	0.1574	0.8821	-4.968	27.2169	69.0223
25	0.7984	0.0452	0.1586	0.9922	-0.2644	0.7421	0.2497	-0.8494	-0.4887	0.3809	-0.04	-0.4489	0.3889	-0.1242	-0.172	0.6448	-0.1549	-0.3133	0.8457	0.2761	0.7954	-5.538	29.3943	82.6373
26	1.4647	-0.2399	0.0961	0.7964	-0.2519	0.5909	0.2324	-0.5508	-0.1663	0.1553	-0.0478	-0.1358	0.0619	-0.1729	-0.169	0.4903	-0.102	-0.0989	0.503	0.0919	0.47	-15.8807	41.4479	73.0654
27	0.8634	0.0504	-0.018	0.7594	0.1139	0.9177	0.1987	-0.4419	-0.3249	0.0692	-0.0151	0.1103	0.2441	-0.2073	-0.0743	0.5475	-0.1185	-0.1274	0.6999	0.1707	0.4456	-43.7564	35.1274	66.5704
28	1.9749	0.8343	0.1917	0.9014	-0.0475	0.7017	0.0218	-0.9965	-0.163	0.6117	0.2511	0.6474	0.0919	-1.2543	-0.1553	0.6239	-0.2369	0.0056	1.1739	0.2412	0.6898	-50.545	36.3564	77.0373
29	0.8106	0.1339	-0.0619	0.3714	-0.1008	1.0984	0.1665	-0.5169	-0.4301	0.593	-0.0111	-0.1051	-0.0619	-0.2188	-0.1877	0.5615	-0.1352	-0.1265	0.7476	0.2076	0.5108	-40.9072	35.9475	69.1063
30	1.7315	-0.0829	-0.0168	0.3551	0.0882	1.3688	0.2033	-0.0831	-0.5117	0.0198	-0.0257	-0.211	0.2785	-0.1869	-0.1772	0.4426	-0.0799	-0.1555	0.3899	0.1076	0.583	-15.4829	32.9588	63.2668
31	1.9105	0.0417	0.5162	1.0145	0.0844	0.9983	-0.119	0.1817	-0.511	-0.1019	0.2817	-0.2193	0.1862	0.1092	-0.1279	0.4274	-0.066	-0.0923	0.459	-0.0586	0.5515	-9.969	38.0471	52.8193

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'E' and (resid 587 through 833 )
2	X-RAY DIFFRACTION	2	chain 'E' and (resid 834 through 862 )
3	X-RAY DIFFRACTION	3	chain 'E' and (resid 863 through 1132 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 587 through 797 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 798 through 1134 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 587 through 635 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 636 through 833 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 834 through 862 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 863 through 939 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 940 through 1132 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 587 through 635 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 636 through 833 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 834 through 862 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 863 through 970 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 971 through 1133 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 587 through 645 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 646 through 833 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 834 through 862 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 863 through 894 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 895 through 947 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 948 through 1062 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 1063 through 1133 )
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 587 through 645 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 646 through 703 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 704 through 797 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 798 through 862 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 863 through 905 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 906 through 939 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 940 through 989 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 990 through 1092 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 1093 through 1134 )

-
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