PDB-4ani: Structural basis for the intermolecular communication between Dna...

ID or keywords:

Entry

Database: PDB / ID: 4ani

Title

Structural basis for the intermolecular communication between DnaK and GrpE in the DnaK chaperone system from Geobacillus kaustophilus HTA426

Components

CHAPERONE PROTEIN DNAK
PROTEIN GRPE

Keywords

CHAPERONE / CHAPERONE CYCLE / COMPLEMENTARY ASSAY

Function / homology

Function and homology information

adenyl-nucleotide exchange factor activity / ATP-dependent protein folding chaperone / unfolded protein binding /

protein folding / protein-folding chaperone binding / protein homodimerization activity /

ATP binding /

cytoplasm
Similarity search - Function

Biological species

GEOBACILLUS KAUSTOPHILUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 4.094 Å

Authors

Wu, C.-C. / Naveen, V. / Chien, C.-H. / Chang, Y.-W. / Hsiao, C.-D.

Citation

Journal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of Dnak Protein Complexed with Nucleotide Exchange Factor Grpe in Dnak Chaperone System: Insight Into Intermolecular Communication.
Authors: Wu, C.-C. / Naveen, V. / Chien, C.-H. / Chang, Y.-W. / Hsiao, C.-D.

History

Deposition	Mar 19, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 23, 2012	Provider: repository / Type: Initial release
Revision 1.1	Aug 1, 2012	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ani.cif.gz	983.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4ani.ent.gz	848.6 KB	Display	PDB format
PDBx/mmJSON format	4ani.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/an/4ani ftp://data.pdbj.org/pub/pdb/validation_reports/an/4ani	HTTPS FTP

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Related structure data

Related structure data	2v7y
Similar structure data	23582 6pa7-d 5b66-d 6dhf-d 6jlo-d 5ws5-d 8706 6jln-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (15)

Deposited unit

A: PROTEIN GRPE

B: PROTEIN GRPE

C: CHAPERONE PROTEIN DNAK

D: CHAPERONE PROTEIN DNAK

E: PROTEIN GRPE

F: PROTEIN GRPE

G: CHAPERONE PROTEIN DNAK

H: CHAPERONE PROTEIN DNAK

317 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	279.975, 279.975, 278.820
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	98
Space group name H-M	I4₁22

#1: Protein	PROTEIN GRPE / GKGRPE / HSP-70 COFACTOR Mass: 24071.840 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GEOBACILLUS KAUSTOPHILUS (bacteria) / Strain: HTA426 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5KWZ6
#2: Protein	CHAPERONE PROTEIN DNAK / / GKGRPE / HSP70 / HEAT SHOCK 70 KDA PROTEIN / HEAT SHOCK PROTEIN 70 Mass: 55125.156 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-509 Source method: isolated from a genetically manipulated source Source: (gene. exp.) GEOBACILLUS KAUSTOPHILUS (bacteria) / Strain: HTA426 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q5KWZ7

#1: Protein

PROTEIN GRPE / GKGRPE / HSP-70 COFACTOR

Mass: 24071.840 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

GEOBACILLUS KAUSTOPHILUS (bacteria) / Strain: HTA426 / Production host:

ESCHERICHIA COLI (E. coli) / References: UniProt: Q5KWZ6

#2: Protein

CHAPERONE PROTEIN DNAK /

/ GKGRPE / HSP70 / HEAT SHOCK 70 KDA PROTEIN / HEAT SHOCK PROTEIN 70

Mass: 55125.156 Da / Num. of mol.: 4 / Fragment: RESIDUES 1-509
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

GEOBACILLUS KAUSTOPHILUS (bacteria) / Strain: HTA426 / Production host:

ESCHERICHIA COLI (E. coli) / References: UniProt: Q5KWZ7

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 4.31 Å³/Da / Density % sol: 71 % / Description: NONE

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Data collection

Diffraction

Mean temperature: 273 K

Diffraction source

Source:

SYNCHROTRON / Site:

NSRRC

/ Beamline: BL13B1 / Wavelength: 1.02249, 1.03964

Detector

Type: ADSC QUANTUM 315 / Detector: CCD

Radiation

Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.02249	1
2	1.03964	1

Reflection

Resolution: 4.09→26.22 Å / Num. obs: 41248 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 8.5 % / B_iso Wilson estimate: 143.41 Å² / R_merge(I) obs: 0.09 / Net I/σ(I): 32.3

Reflection shell

Resolution: 4.1→4.35 Å / Redundancy: 8.7 % / R_merge(I) obs: 0.49 / Mean I/σ(I) obs: 2.8 / % possible all: 94.5

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE: 1.7_650)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MAD
Starting model: NONE

Resolution: 4.094→26.221 Å / SU ML: 0.73 / σ(F): 1.34 / Phase error: 35.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3474	2083	5.1 %
R_work	0.2737	-	-
obs	0.2773	41248	94.78 %

Solvent computation

Shrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 152.677 Å² / k_sol: 0.286 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-14.9513 Å²	0 Å²	0 Å²
2-	-	-14.9513 Å²	0 Å²
3-	-	-	29.9025 Å²

Refinement step

Cycle: LAST / Resolution: 4.094→26.221 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18889	0	0	0	18889

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.022	19872
X-RAY DIFFRACTION	f_angle_d	1.84	25867
X-RAY DIFFRACTION	f_dihedral_angle_d	20.859	6944
X-RAY DIFFRACTION	f_chiral_restr	0.118	3038
X-RAY DIFFRACTION	f_plane_restr	0.008	3464

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 (%)
4.0943-4.1892	0.4585	139	0.352	2545	X-RAY DIFFRACTION	94
4.1892-4.2935	0.3854	143	0.3403	2588	X-RAY DIFFRACTION	95
4.2935-4.4091	0.3652	134	0.319	2616	X-RAY DIFFRACTION	96
4.4091-4.5382	0.3615	148	0.3016	2595	X-RAY DIFFRACTION	96
4.5382-4.6838	0.331	156	0.2697	2581	X-RAY DIFFRACTION	96
4.6838-4.8502	0.328	139	0.2644	2613	X-RAY DIFFRACTION	96
4.8502-5.0431	0.3199	133	0.2354	2622	X-RAY DIFFRACTION	95
5.0431-5.2709	0.338	136	0.2505	2621	X-RAY DIFFRACTION	95
5.2709-5.5463	0.3704	127	0.2855	2594	X-RAY DIFFRACTION	95
5.5463-5.8901	0.4181	136	0.3342	2617	X-RAY DIFFRACTION	95
5.8901-6.3389	0.4505	129	0.3318	2628	X-RAY DIFFRACTION	95
6.3389-6.966	0.3844	149	0.3362	2601	X-RAY DIFFRACTION	95
6.966-7.9493	0.3401	149	0.2583	2615	X-RAY DIFFRACTION	94
7.9493-9.9242	0.3102	130	0.2101	2623	X-RAY DIFFRACTION	93
9.9242-26.2216	0.2976	135	0.253	2706	X-RAY DIFFRACTION	92

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	0.5745	-0.2557	0.3169	0.2924	0.5727	0.6481	-1.0358	-1.4455	-0.1733	-0.5493	0.6489	-0.3395	1.0893	-1.0616	0	1.6327	0.1494	0.2083	1.7971	0.3782	2.1265	118.1024	14.9909	37.0856
2	3.6553	1.4076	1.5263	2.9498	-1.0609	2.2317	0.2727	0.9533	0.1142	-0.0452	0.0781	1.2502	0.8671	-1.2601	0	1.5991	-0.1485	-0.0732	2.06	0.3858	1.4256	80.8674	42.7172	18.0552
3	-0.8109	1.2748	-0.4195	2.4743	-1.9557	2.1703	-0.7307	0.0534	0.5039	0.6147	-0.1985	-0.9643	-0.1751	0.4803	0	1.6044	0.1803	0.0259	1.5718	-0.0626	0.9886	111.5213	36.5687	31.6358
4	2.712	0.5839	0.5252	1.1506	1.9262	0.6421	-0.0937	-0.5734	1.155	0.6367	0.501	0.0715	-0.7406	-0.168	0	1.8707	0.1528	0.1942	1.4828	0.2484	1.4809	100.3274	68.0066	24.5381
5	5.3247	-1.7589	-0.0643	4.6562	-2.6276	5.2319	0.3127	0.313	-0.0749	-0.3174	0.0851	1.2417	1.2307	-0.7187	0	1.7289	-0.0772	0.101	1.523	0.3092	1.1932	88.8044	17.5236	36.8531
6	6.3112	-1.9772	-1.2717	2.8261	-0.4007	2.056	-0.1828	0.0064	0.3007	0.1752	0.1376	-0.4071	0.0356	-0.0477	0	1.5413	0.0071	0.4115	1.4487	0.0349	1.3859	86.6067	37.2918	50.3629
7	5.4736	2.0491	-0.8315	2.9211	0.192	1.6033	0.1887	-0.7236	0.5837	0.9287	0.1325	-0.6458	-0.4415	0.4301	0	1.4688	0.2799	-0.02	1.4845	-0.1388	1.37	135.153	39.8742	35.9684
8	5.1344	-1.7891	-2.4097	1.5266	-1.887	6.7688	0.0145	-0.2444	1.0692	0.7597	-0.1067	1.0691	-0.1327	0.8806	0	1.5436	-0.0715	0.1262	1.5596	0.153	1.0566	123.4631	68.5923	7.7478
9	3.9233	1.468	-2.4867	2.8559	-0.2961	3.547	0.59	1.1753	0.8232	-0.3204	-0.2253	-0.0473	0.7392	0.5067	0	1.899	0.1138	-0.2391	1.5952	0.1452	1.3094	128.0927	62.198	-8.1802
10	1.0862	-2.2058	-1.2271	4.1511	-0.4474	4.659	0.2779	-0.355	-0.126	-0.7154	0.4662	0.7837	0.0472	-0.055	0	1.6803	-0.246	-0.3331	1.5445	0.3122	1.6503	100.545	65.5348	-6.3603
11	-1.4838	-1.0535	1.0659	1.4126	0.0485	0.6575	-0.3566	0.4621	-1.1815	-0.7887	0.2743	0.4176	0.0454	0.5145	0	2.2241	-0.0795	0.1807	1.7204	0.3879	1.8026	127.3256	49.2766	-7.3735
12	0.3872	0.231	0.4257	0.2841	0.2707	1.6884	-0.8538	0.2949	0.2355	-0.2794	-0.1028	-2.3488	0.0986	-0.2771	0	1.4522	-0.0339	0.2672	1.3259	-0.0961	2.2046	154.7627	19.9799	16.2265
13	0.2996	0.4387	0.3432	0.6636	2.4678	0.6334	0.2098	-0.5726	0.2379	0.1737	0.8271	-0.5031	2.2248	0.9341	0	1.8018	0.5518	-0.3279	1.6391	-0.0877	2.6263	160.5062	11.1708	23.3304
14	2.4	-0.0231	1.4043	3.8303	-0.5585	0.9067	-0.4074	0.2222	0.2324	-0.1344	-0.0367	-0.4489	1.2351	0.8287	0	1.904	0.1818	0.2888	1.6615	-0.5625	2.4414	158.7271	16.3806	14.975
15	1.9318	-1.3021	-1.6675	1.0487	-0.0658	0.9101	0.5315	1.3576	0.9132	-0.1845	0.6779	-0.9206	0.8416	1.3395	0	2.3242	0.4437	0.3835	1.699	-0.0118	3.5811	162.1991	2.1205	-11.2905
16	-0.0178	0.0629	-0.0026	-0.0003	0.0372	-0.0477	-1.6925	0.3743	0.2236	-1.0236	-2.7461	1.0594	0.5739	0.1635	0	1.9837	0.3751	0.2342	3.0916	-0.5413	2.371	192.3919	21.5423	5.7937
17	-0.0326	0.1907	0.3801	-0.0899	-0.276	-0.0316	0.0699	-1.0833	0.3618	0.3354	-1.0816	1.3764	-0.9176	0.166	0	2.7266	-0.2125	-0.3886	2.7827	-0.9323	3.9514	214.6928	27.5467	10.4715
18	-0.0472	-0.1679	-0.055	0.0088	-0.109	0.5107	-1.2617	1.2616	2.1437	0.5009	-1.4719	-1.1351	2.1268	-0.9396	0	1.5353	1.0415	0.9684	2.5444	-0.3698	4.699	201.864	22.6707	14.9754
19	-0.0178	-0.0485	0.1036	0.0002	0.0734	0.066	0.2355	1.169	-0.4049	0.0842	0.2262	-0.0201	0.7	-0.004	0.0001	5.5662	2.0016	-2.4921	2.6177	-1.6539	5.3271	207.4294	2.9926	8.0831
20	0.0631	0.1971	0.0469	0.1057	0.0079	0.0733	0.4084	-0.9254	0.7833	1.7661	-0.1351	0.6955	-3.014	0.6433	0	2.8506	0.767	-1.1092	2.1381	-1.4752	9.8905	204.9894	10.3525	11.9668
21	-0.0696	-0.1718	0.2453	-0.0859	0.131	-0.1912	-1.0774	0.9761	0.5257	-0.9671	-0.345	-0.4581	-1.6581	0.8936	0.0001	0.3001	2.8305	-0.7572	4.2199	-2.2	6.2774	207.6929	7.4518	7.8145
22	0.6746	-0.3607	-1.7519	0.2804	-0.2513	0.6826	-0.4766	-1.2288	0.4004	0.0135	0.3219	0.3917	0.0092	0.0493	0	2.5251	0.3075	0.5981	2.0498	0.0263	2.5801	162.0148	12.3968	-11.977
23	0.0176	0.2663	0.4615	0.6257	0.4819	-0.126	-0.7006	1.0707	0.4811	-2.7134	0.3308	0.5596	2.0696	-1.1165	0	1.6988	-0.182	0.6026	3.5539	0.8001	4.402	205.0512	32.0678	4.5062
24	-0.1401	0.2339	0.0435	0.0979	0.2388	-0.1921	1.1024	0.7265	-0.4724	-0.4417	-2.3199	-2.9288	0.4969	-0.0954	0	2.329	-0.0398	0.0518	2.5804	-0.3239	3.2618	198.289	47.6267	2.3471
25	-0.0267	-1.3639	-1.9758	-0.5967	0.5892	2.0543	1.54	-0.5504	-0.7131	1.4844	2.6017	-3.5212	1.1586	2.4842	0	2.385	0.5441	-0.5172	2.9866	-1.9787	6.881	194.0952	-5.488	-3.4175
26	1.177	-2.8837	1.5437	3.8779	0.1116	1.2473	0.383	1.6875	-2.0064	0.2033	0.7067	-2.6339	0.5306	0.9843	0	2.7673	-0.0467	1.297	2.6842	-0.7282	4.4809	200.5586	5.3548	-16.9548
27	-1.0706	0.1958	-1.2265	-2.1766	0.6163	-1.2789	0.0553	0.4333	0.058	-0.2982	0.298	-1.0286	-0.507	0.3645	0	3.5351	-0.1391	1.5596	3.0067	-0.3563	3.6911	192.7778	9.4326	-26.2631
28	4.4282	-0.2616	0.4917	1.1573	-2.2977	5.4311	-0.1884	0.6213	0.5795	-2.0144	0.3362	-1.3106	-0.7266	0.7468	0	2.6081	-0.0479	1.0417	1.7062	0.2001	2.4923	156.1133	37.5407	-9.4871
29	0.8945	-1.0411	-1.4693	3.7651	0.7615	8.0744	0.4128	0.271	0.2147	0.0078	0.6378	-3.4616	-0.6335	0.0133	0	1.8451	0.0479	0.4476	2.019	-0.308	3.9356	176.2825	56.7612	21.8912
30	0.0235	0.692	0.7499	3.7413	2.5942	1.8795	1.104	-0.0181	-0.1268	-0.3135	5.5664	-15.4837	-0.6162	2.7703	0	2.472	-0.2167	0.3967	4.1545	-6.2477	22.0111	198.9585	50.1101	31.9625
31	6.3088	1.6662	2.8277	4.6264	1.7	4.2259	0.1528	-0.0496	-0.2155	0.0986	0.1561	-0.7724	0.2494	-0.3112	0	1.5165	0.1357	0.1105	1.063	0.3152	1.6361	140.7377	27.9147	15.0888

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESSEQ 58:106)
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESSEQ 107:213)
3	X-RAY DIFFRACTION	3	CHAIN B AND (RESSEQ 60:135)
4	X-RAY DIFFRACTION	4	CHAIN B AND (RESSEQ 136:213)
5	X-RAY DIFFRACTION	5	CHAIN C AND (RESSEQ 1:134)
6	X-RAY DIFFRACTION	6	CHAIN C AND (RESSEQ 135:338)
7	X-RAY DIFFRACTION	7	CHAIN C AND (RESSEQ 339:509)
8	X-RAY DIFFRACTION	8	CHAIN D AND (RESSEQ 1:105)
9	X-RAY DIFFRACTION	9	CHAIN D AND (RESSEQ 106:181)
10	X-RAY DIFFRACTION	10	CHAIN D AND (RESSEQ 182:315)
11	X-RAY DIFFRACTION	11	CHAIN D AND (RESSEQ 316:367)
12	X-RAY DIFFRACTION	12	CHAIN D AND (RESSEQ 368:395)
13	X-RAY DIFFRACTION	13	CHAIN D AND (RESSEQ 396:440)
14	X-RAY DIFFRACTION	14	CHAIN D AND (RESSEQ 441:509)
15	X-RAY DIFFRACTION	15	CHAIN E AND (RESSEQ 58:102)
16	X-RAY DIFFRACTION	16	CHAIN E AND (RESSEQ 103:113)
17	X-RAY DIFFRACTION	17	CHAIN E AND (RESSEQ 114:144)
18	X-RAY DIFFRACTION	18	CHAIN E AND (RESSEQ 145:168)
19	X-RAY DIFFRACTION	19	CHAIN E AND (RESSEQ 169:186)
20	X-RAY DIFFRACTION	20	CHAIN E AND (RESSEQ 187:202)
21	X-RAY DIFFRACTION	21	CHAIN E AND (RESSEQ 203:213)
22	X-RAY DIFFRACTION	22	CHAIN F AND (RESSEQ 60:105)
23	X-RAY DIFFRACTION	23	CHAIN F AND (RESSEQ 106:158)
24	X-RAY DIFFRACTION	24	CHAIN F AND (RESSEQ 159:210)
25	X-RAY DIFFRACTION	25	CHAIN G AND (RESSEQ 1:105)
26	X-RAY DIFFRACTION	26	CHAIN G AND (RESSEQ 106:271)
27	X-RAY DIFFRACTION	27	CHAIN G AND (RESSEQ 272:367)
28	X-RAY DIFFRACTION	28	CHAIN G AND (RESSEQ 368:509)
29	X-RAY DIFFRACTION	29	CHAIN H AND (RESSEQ 1:181)
30	X-RAY DIFFRACTION	30	CHAIN H AND (RESSEQ 182:302)
31	X-RAY DIFFRACTION	31	CHAIN H AND (RESSEQ 303:509)

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About Yorodumi

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Yorodumi