PDB-6uca: Crystal structure of human ZCCHC4 in complex with SAH

ID or keywords:

Entry

Database: PDB / ID: 6uca

Title

Crystal structure of human ZCCHC4 in complex with SAH

Components

rRNA N6-adenosine-methyltransferase ZCCHC4

Keywords

TRANSFERASE / 28s RNA m6A methyltransferase

Function / homology

Function and homology information

rRNA (adenine-N6-)-methyltransferase activity /

S-adenosyl-L-methionine binding / rRNA methylation /

Transferases; Transferring one-carbon groups; Methyltransferases / positive regulation of translation /

nucleic acid binding /

nucleolus / zinc ion binding /

cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.103 Å

Authors

Lu, J.W. / Ren, W.D. / Huang, M.J. / Gao, L. / Li, D.X. / Wang, G.G. / Song, J.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2019
Title: Structure and regulation of ZCCHC4 in m6A-methylation of 28S rRNA.
Authors: Ren, W. / Lu, J. / Huang, M. / Gao, L. / Li, D. / Wang, G.G. / Song, J.

History

Deposition	Sep 15, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 16, 2019	Provider: repository / Type: Initial release
Revision 1.1	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Apr 29, 2020	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3	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	6uca.cif.gz	968.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6uca.ent.gz	802.6 KB	Display	PDB format
PDBx/mmJSON format	6uca.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Similar structure data	1kcl-d 4uf6-1 4moa-d 1b0z-d 2pgi-d 4jcl-d 7c2h-d 6aij-d 1c7q-d 1tcm-2 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) 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

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: rRNA N6-adenosine-methyltransferase ZCCHC4

B: rRNA N6-adenosine-methyltransferase ZCCHC4

C: rRNA N6-adenosine-methyltransferase ZCCHC4

D: rRNA N6-adenosine-methyltransferase ZCCHC4

E: rRNA N6-adenosine-methyltransferase ZCCHC4

F: rRNA N6-adenosine-methyltransferase ZCCHC4

hetero molecules

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

1

A: rRNA N6-adenosine-methyltransferase ZCCHC4

hetero molecules

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

2

B: rRNA N6-adenosine-methyltransferase ZCCHC4

hetero molecules

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

3

C: rRNA N6-adenosine-methyltransferase ZCCHC4

hetero molecules

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

4

D: rRNA N6-adenosine-methyltransferase ZCCHC4

hetero molecules

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

5

E: rRNA N6-adenosine-methyltransferase ZCCHC4

hetero molecules

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

6

F: rRNA N6-adenosine-methyltransferase ZCCHC4

hetero molecules

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

Unit cell

Length a, b, c (Å)	136.567, 290.380, 83.529
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	rRNA N6-adenosine-methyltransferase ZCCHC4 / Zinc finger CCHC domain-containing protein 4 Mass: 50814.344 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ZCCHC4 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9H5U6, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	... ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.94 Å³/Da / Density % sol: 58.22 %
Crystal grow	Temperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: 0.03 M citric acid, 0.07 M Bis-Tris propane, pH 7.6, 11-12% PEG3350, 10% glycerol, 5 mM TCEP, pH 7.0

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.2 / Wavelength: 1.283 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 29, 2019

Radiation

Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.283 Å / Relative weight: 1

Reflection

Resolution: 3.1→50 Å / Num. obs: 60780 / % possible obs: 99.8 % / Redundancy: 5.7 % / R_merge(I) obs: 0.126 / R_pim(I) all: 0.057 / R_rim(I) all: 0.139 / Χ²: 1.049 / Net I/σ(I): 6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
3.1-3.21	5.5	0.752	5987	0.919	0.349	0.831	0.512	99.9
3.21-3.34	5.8	0.562	5996	0.943	0.252	0.618	0.548	99.8
3.34-3.49	5.9	0.41	5988	0.965	0.182	0.45	0.636	99.9
3.49-3.68	5.8	0.309	6011	0.971	0.139	0.34	0.761	99.8
3.68-3.91	5.5	0.199	6017	0.984	0.093	0.221	0.917	99.7
3.91-4.21	5.8	0.156	6059	0.99	0.071	0.172	1.043	99.9
4.21-4.63	5.9	0.122	6075	0.992	0.055	0.134	1.326	99.9
4.63-5.3	5.5	0.105	6088	0.992	0.049	0.116	1.448	99.9
5.3-6.67	5.9	0.098	6187	0.992	0.044	0.108	1.416	100
6.67-50	5.4	0.066	6431	0.996	0.03	0.073	1.853	99.7

-
Processing

Software

Name	Version	Classification
PHENIX	1.15.2_3472	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
CRANK2		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.103→47.683 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.82 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2813	3795	3.3 %
R_work	0.249	111100	-
obs	0.25	60686	98.96 %

Solvent computation

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

Displacement parameters

B_iso max: 390.44 Å² / B_iso mean: 105.472 Å² / B_iso min: 28.5 Å²

Refinement step

Cycle: final / Resolution: 3.103→47.683 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18478	0	156	0	18634
B_iso mean	-	-	76.97	-	-
Num. residues	-	-	-	-	2445

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
3.103-3.1422	0.3786	131	0.3682	3764	91
3.1422-3.1835	0.328	139	0.3425	4133	99
3.1835-3.2271	0.3755	144	0.3194	4114	99
3.2271-3.2732	0.2631	136	0.2927	4092	99
3.2732-3.3221	0.2949	147	0.2954	4202	100
3.3221-3.374	0.3253	136	0.2959	4079	99
3.374-3.4293	0.3697	139	0.2879	4131	100
3.4293-3.4884	0.3097	146	0.2923	4224	99
3.4884-3.5518	0.3392	139	0.3043	4041	100
3.5518-3.6201	0.3222	144	0.2817	4170	99
3.6201-3.6939	0.2822	142	0.2793	4099	99
3.6939-3.7742	0.2881	139	0.2537	4130	99
3.7742-3.862	0.2858	140	0.2425	4092	99
3.862-3.9585	0.2766	140	0.2439	4146	100
3.9585-4.0655	0.3255	139	0.2466	4141	100
4.0655-4.1851	0.2695	139	0.2331	4158	99
4.1851-4.3201	0.2931	142	0.2221	4122	99
4.3201-4.4744	0.2351	140	0.2191	4143	100
4.4744-4.6534	0.2713	143	0.2123	4147	100
4.6534-4.8649	0.2502	141	0.2176	4151	100
4.8649-5.1212	0.2892	144	0.2221	4075	99
5.1212-5.4416	0.2617	131	0.2378	4138	100
5.4416-5.861	0.2611	143	0.245	4144	100
5.861-6.4496	0.3003	147	0.2731	4176	99
6.4496-7.3799	0.364	133	0.2692	4095	99
7.3799-9.2866	0.2791	142	0.2288	4162	99
9.2866-47.683	0.1994	149	0.2172	4031	98

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	1.6528	-0.3813	-0.0365	1.4058	0.0201	3.4776	-0.4036	0.4689	-0.8595	-0.5667	-0.0975	0.6182	0.9713	-1.7899	0.5199	0.8936	-0.4077	0.1724	1.414	-0.3006	0.8122	131.1475	71.5498	33.0607
2	2.6462	0.2572	0.2141	4.5556	0.8936	4.7795	-0.1317	-0.489	-0.1116	0.5468	0.0433	-0.4611	-0.0057	-0.3938	0.2216	0.3052	0.1291	-0.0912	0.584	0.0413	0.2935	149.7276	82.8401	58.235
3	6.0501	-1.7306	-1.7595	5.1473	-0.8095	9.1706	0.0912	0.1908	0.1531	-0.208	-0.1424	-0.8398	-0.2966	0.0302	0.0783	0.2374	0.0027	0.06	0.295	-0.0354	0.4315	156.9032	82.895	40.32
4	3.8811	-1.4227	-0.7164	4.7084	2.0606	2.792	-0.294	0.1584	-1.1089	-0.4009	-0.0467	-0.9582	0.8085	0.0602	0.3344	0.7938	-0.0769	0.4152	0.6088	-0.1375	0.8717	164.0722	63.6438	30.4996
5	5.0023	-0.6077	-2.0158	1.9743	2.2121	3.0514	0.179	1.8974	1.0703	-0.6257	-0.3233	0.262	-0.7141	-0.4413	0.082	1.4172	0.25	0.3005	1.5853	0.5698	1.3079	48.2162	27.6669	-11.9431
6	1.0447	-0.0249	0.3719	1.9141	-0.3282	0.7519	0.663	0.3563	1.6603	-0.5422	-0.0533	-0.0002	-0.3532	0.2656	-0.2887	1.09	0.3704	0.9262	-0.2085	0.3406	3.0322	54.4578	33.154	7.3399
7	0.7416	-0.8916	0.9505	1.2914	-0.605	2.4462	-0.0111	1.0317	1.6172	-0.8948	0.0588	-0.4014	-0.5203	0.4405	0.0431	1.5232	0.267	1.0141	1.1025	0.9859	2.5246	69.6799	33.9876	-7.36
8	7.3777	-1.7582	1.6167	1.6509	-1.6272	1.6204	1.2215	0.6482	1.2998	-0.5536	-0.4865	-0.2551	0.3526	0.1596	-0.6529	1.0834	0.196	0.384	0.6136	0.0379	0.9232	77.1456	12.3701	5.1787
9	9.2976	-0.8418	-0.3917	2.2693	0.943	0.393	-0.7342	-1.5286	-0.5787	0.8993	0.5956	-0.0468	0.3499	0.3651	0.1176	3.3169	-0.3798	0.1689	1.1418	0.0696	0.8245	90.0624	20.6915	59.0569
10	5.8828	-1.3973	-0.6613	6.1497	0.432	3.5899	-0.0674	-0.1356	0.3944	0.832	-0.4563	-0.5962	0.7012	-0.3392	0.3857	0.7086	-0.2194	0.1472	0.4237	-0.1003	0.6459	94.445	38.4955	32.4449
11	3.5319	0.0138	-1.5375	0.9232	0.3958	3.2957	0.1695	-0.0263	0.0153	0.6631	-0.3228	0.7478	0.3124	-0.7041	0.0894	1.0151	-0.521	0.6096	0.9135	-0.3641	0.8151	75.909	34.3921	36.1908
12	1.1238	0.2076	-0.6844	0.6817	0.5873	2.2268	0.179	-0.1968	-0.024	0.8243	-0.0856	0.4626	0.3077	-0.345	0.2019	1.8629	-0.7115	0.8618	1.0038	-0.1892	0.7764	73.01	33.1193	50.2663
13	3.6044	1.1436	-0.5697	1.8739	-1.7053	1.6149	0.2501	0.166	-0.565	0.4272	-0.2525	0.5515	0.6388	-1.1992	0.0532	1.614	-0.9727	0.9639	1.3198	-0.5134	1.7923	58.741	20.7645	37.4595
14	0.4925	0.0813	0.15	0.1384	-0.0614	0.1008	1.4482	-0.7665	0.6198	-1.507	0.252	-0.5117	1.8673	0.7312	-1.649	2.6259	0.1554	-0.2535	1.1644	-0.6225	3.0625	58.9792	-4.0467	42.2636
15	2.6189	0.0469	0.6898	2.0511	-1.1215	4.4852	-0.3113	0.3001	-0.0144	0.0255	-0.197	-0.1558	0.5631	0.7806	0.4698	0.5113	0.0697	0.1291	0.5495	0.0298	0.427	129.4194	78.5324	-3.7116
16	5.2757	1.1249	0.2887	4.1604	-0.3795	8.6735	-0.2398	-0.5025	0.2442	0.5664	-0.0188	0.5279	-0.3607	-0.0883	0.1808	0.4417	0.055	0.1914	0.465	0.0573	0.3	119.6884	84.7466	5.4352
17	2.2998	1.4379	-0.3953	5.1341	-3.189	2.9798	-0.2883	0.1379	-0.8679	-0.2913	0.0999	0.0394	0.5052	-0.2538	0.1233	0.7851	-0.0513	0.3954	0.6709	0.0626	0.8372	107.7787	60.9322	9.9316
18	6.7938	5.284	0.8051	5.6319	0.4764	5.2235	0.9489	-0.7769	0.488	0.4795	-0.0538	-0.6757	-0.4965	0.5909	-0.9397	0.9695	-0.0847	0.2855	0.7183	-0.1696	2.1157	127.3551	27.197	31.6175
19	5.0306	0.9251	0.5356	1.1315	1.5058	3.221	0.8335	-0.3213	-0.2956	0.5633	-0.4815	-0.6366	0.3694	-0.041	-0.4126	1.1203	-0.1235	0.1006	0.3861	-0.0476	1.0148	99.4232	13.9257	26.0902
20	2.9345	-0.6423	0.592	0.6201	-0.2519	5.098	-0.0424	0.7043	-0.5897	-1.2625	-0.1321	-1.2589	0.9909	-0.0799	-0.0264	1.7472	-0.0843	0.4418	0.5788	-0.1205	1.2267	107.2564	14.6566	4.8229
21	3.7542	-0.3864	0.5736	0.0724	-0.0813	4.3596	0.1363	0.4553	-0.5483	-1.094	-0.0511	-1.4011	0.9541	0.5913	0.0328	1.4258	0.153	0.3714	0.5537	-0.0689	1.9826	119.008	13.4819	13.1822
22	1.6345	0.9653	1.2018	0.8634	-0.18	3.53	-0.1423	0.4999	0.27	-0.9931	-0.1324	-1.3061	-0.1683	0.4802	0.3078	1.5414	-0.0257	0.5203	0.587	0.0051	1.7015	115.923	29.9637	5.005
23	1.6558	-1.4006	0.2707	2.6387	1.8094	2.8846	0.2525	0.4751	0.7417	0.4149	0.1467	-0.1403	0.5711	-0.3245	-0.5631	1.6186	-0.2357	0.478	0.6879	0.0012	1.2087	111.7325	27.3839	-1.743
24	1.1144	1.2217	-0.4738	4.4472	1.1002	2.6639	0.5804	0.3239	1.0522	-0.5967	0.4922	-0.4282	-0.5995	-0.1714	-0.9944	1.8013	0.0874	0.8863	0.8751	0.1673	1.8757	118.0088	42.8397	-6.6704
25	6.738	-0.8064	0.4514	0.5028	-1.1224	2.8482	1.2291	0.6445	0.7129	-1.9634	-0.4968	0.3783	-0.6371	-0.9107	-0.7151	1.383	0.5083	-0.0705	0.9402	0.1189	2.3209	9.8021	30.2397	8.8924
26	5.3068	-2.9049	-0.8387	5.0767	0.896	1.1593	0.7253	0.6637	0.7567	-1.1011	-0.7141	0.7906	-0.1498	-0.258	-0.1482	0.8588	0.0802	0.0215	0.4102	0.1315	1.254	33.9104	14.0689	12.1324
27	2.8161	1.1763	0.0429	0.8684	1.1143	3.3941	0.1108	-0.3597	0.1793	0.8297	-0.2268	1.4685	0.4124	-0.2903	0.1053	0.9715	-0.1097	0.4585	0.5258	-0.0022	2.1348	18.1796	16.108	28.9701
28	3.2679	-2.6142	-2.053	2.5681	2.0089	1.6027	-0.0339	-0.8436	0.2594	0.9479	0.1048	0.9451	0.041	0.2702	-0.1119	1.2745	-0.1836	0.6438	0.8885	-0.1303	1.5239	18.659	36.4967	45.1516

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 28 through 97 )	A	28 - 97
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 98 through 176 )	A	98 - 176
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 177 through 283 )	A	177 - 283
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 284 through 440 )	A	284 - 440
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 28 through 116 )	B	28 - 116
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 117 through 252 )	B	117 - 252
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 253 through 311 )	B	253 - 311
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 312 through 438 )	B	312 - 438
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 36 through 98 )	C	36 - 98
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 99 through 159 )	C	99 - 159
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 160 through 241 )	C	160 - 241
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 242 through 297 )	C	242 - 297
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 298 through 415 )	C	298 - 415
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 416 through 442 )	C	416 - 442
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 25 through 200 )	D	25 - 200
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 201 through 311 )	D	201 - 311
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 312 through 440 )	D	312 - 440
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 28 through 97 )	E	28 - 97
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 98 through 176 )	E	98 - 176
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 177 through 213 )	E	177 - 213
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 214 through 311 )	E	214 - 311
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 312 through 347 )	E	312 - 347
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 348 through 372 )	E	348 - 372
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 373 through 439 )	E	373 - 439
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 28 through 84 )	F	28 - 84
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 85 through 176 )	F	85 - 176
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 177 through 344 )	F	177 - 344
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 345 through 439 )	F	345 - 439

-
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