PDB-4dmi: Crystal Structure of a Pentameric Capsid Protein Isolated from Me...

ID or keywords:

Entry

Database: PDB / ID: 4dmi

Title

Crystal Structure of a Pentameric Capsid Protein Isolated from Metagenomic Phage Sequences (CASP)

Components

Capsid Protein

Capsid

Keywords

VIRAL PROTEIN /

Capsid Protein

Function / homology

Double Stranded RNA Binding Domain - #10 / Jelly Rolls - #1010 / Double Stranded RNA Binding Domain / Other non-globular / Special / Jelly Rolls /

Sandwich / Mainly Beta

Function and homology information

Biological species

unidentified (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.5 Å

Authors

Craig, T.K. / Abendroth, J. / Lorimer, D. / Burgin Jr, A.B. / Segall, A. / Rohwer, F.

Citation

Journal: To be Published
Title: Crystal Structure of a Pentameric Capsid Protein Isolated from Metagenomic Phage Sequences
Authors: Craig, T.K. / Abendroth, J. / Lorimer, D. / Burgin Jr, A.B. / Segall, A. / Rohwer, F.

History

Deposition	Feb 7, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 29, 2012	Provider: repository / Type: Initial release
Revision 1.1	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4dmi.cif.gz	342.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4dmi.ent.gz	279.5 KB	Display	PDB format
PDBx/mmJSON format	4dmi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Similar structure data	1c4p-d 22630 5gvk-1 5nok-2 6ewq-2 3hwo-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Capsid Protein

B: Capsid Protein

C: Capsid Protein

D: Capsid Protein

E: Capsid Protein

hetero molecules

93.4 kDa, 5 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)	57.570, 147.870, 57.850
Angle α, β, γ (deg.)	90.00, 112.05, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Capsid Protein / Capsid Mass: 18626.734 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Details: Metagenomic Sample / Source: (gene. exp.) unidentified (others) / Plasmid: VCID5936 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1145 / 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: 2.45 Å³/Da / Density % sol: 49.81 %
Crystal grow	pH: 7.4 Details: 20% w/v PEG 3350, 0.2M Potassium Formate, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 100K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2011
Radiation	Monochromator: SI(220) ASYMMETRIC CUT SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9774 Å / Relative weight: 1
Reflection	Resolution: 1.5→43.41 Å / Num. obs: 139069 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / B_iso Wilson estimate: 19.9 Å² / R_merge(I) obs: 0.066 / Net I/σ(I): 16.53
Reflection shell	Resolution: 1.5→1.54 Å / R_merge(I) obs: 0.413 / Mean I/σ(I) obs: 3.94 / % possible all: 93.1

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.5 Å	28.58 Å
Translation	2.5 Å	28.58 Å

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.4.0	phasing
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.1	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.5→43.41 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.17 / σ(F): 1.37 / Phase error: 16.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.182	6957	5 %
R_work	0.158	-	-
obs	0.16	139061	97.5 %
all	-	146018	-

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 39.12 Å² / k_sol: 0.34 e/Å³

Refinement step

Cycle: LAST / Resolution: 1.5→43.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6128	0	16	1145	7289

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6488
X-RAY DIFFRACTION	f_angle_d	1.102	8874
X-RAY DIFFRACTION	f_dihedral_angle_d	11.24	2359
X-RAY DIFFRACTION	f_chiral_restr	0.075	1132
X-RAY DIFFRACTION	f_plane_restr	0.004	1173

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 (%)
1.5-1.5171	0.2844	213	0.2433	4139	X-RAY DIFFRACTION	92
1.5171-1.5349	0.259	223	0.2135	4197	X-RAY DIFFRACTION	94
1.5349-1.5536	0.239	221	0.2091	4255	X-RAY DIFFRACTION	94
1.5536-1.5733	0.2313	227	0.192	4309	X-RAY DIFFRACTION	95
1.5733-1.594	0.2262	230	0.1866	4278	X-RAY DIFFRACTION	96
1.594-1.6158	0.2139	237	0.1878	4362	X-RAY DIFFRACTION	96
1.6158-1.6389	0.231	219	0.1819	4335	X-RAY DIFFRACTION	97
1.6389-1.6634	0.1958	235	0.1759	4368	X-RAY DIFFRACTION	97
1.6634-1.6894	0.2142	232	0.1695	4409	X-RAY DIFFRACTION	97
1.6894-1.7171	0.2083	228	0.1671	4339	X-RAY DIFFRACTION	97
1.7171-1.7467	0.1891	232	0.1648	4439	X-RAY DIFFRACTION	97
1.7467-1.7784	0.1965	228	0.1632	4357	X-RAY DIFFRACTION	98
1.7784-1.8126	0.1857	232	0.1504	4406	X-RAY DIFFRACTION	97
1.8126-1.8496	0.1718	234	0.1502	4438	X-RAY DIFFRACTION	98
1.8496-1.8899	0.157	233	0.1518	4381	X-RAY DIFFRACTION	98
1.8899-1.9338	0.1663	229	0.1574	4452	X-RAY DIFFRACTION	98
1.9338-1.9822	0.1681	232	0.1515	4428	X-RAY DIFFRACTION	98
1.9822-2.0358	0.1554	235	0.1515	4416	X-RAY DIFFRACTION	98
2.0358-2.0957	0.1752	232	0.1561	4415	X-RAY DIFFRACTION	98
2.0957-2.1633	0.1934	235	0.161	4448	X-RAY DIFFRACTION	98
2.1633-2.2406	0.1849	238	0.1581	4482	X-RAY DIFFRACTION	98
2.2406-2.3303	0.1665	236	0.1562	4425	X-RAY DIFFRACTION	99
2.3303-2.4364	0.163	235	0.1462	4468	X-RAY DIFFRACTION	99
2.4364-2.5648	0.1754	238	0.1532	4478	X-RAY DIFFRACTION	99
2.5648-2.7255	0.1737	232	0.1605	4506	X-RAY DIFFRACTION	99
2.7255-2.9359	0.1778	244	0.1527	4495	X-RAY DIFFRACTION	99
2.9359-3.2313	0.1786	234	0.1516	4502	X-RAY DIFFRACTION	99
3.2313-3.6986	0.1756	234	0.1475	4488	X-RAY DIFFRACTION	100
3.6986-4.659	0.1735	240	0.1376	4545	X-RAY DIFFRACTION	100
4.659-43.425	0.1708	239	0.1649	4544	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	2.2431	-0.0189	-2.0306	3.0015	4.3096	8.0778	0.1587	-0.2494	0.4694	0.2958	0.1193	-0.3023	-0.4632	0.4089	-0.3341	0.475	0.0134	-0.1726	0.2045	-0.0603	0.4527	5.135	36.471	25.46
2	3.4517	-0.4049	-0.9855	1.3858	0.8694	3.2574	-0.018	-0.0571	0.2156	0.317	-0.064	0.0523	-0.2737	-0.0092	0.0717	0.2551	0.0321	-0.022	0.069	-0.0121	0.279	6.034	36.385	13.003
3	1.5244	-0.4054	0.6603	0.6624	-0.7493	0.9781	0.0616	-0.1163	0.2551	-0.1137	0.0494	-0.0851	-0.2107	0.0706	-0.0947	0.1208	-0.0343	0.0214	0.057	-0.0314	0.104	23.993	12.2964	-0.9446
4	0.9	0.0625	-0.2825	1.0171	0.3266	0.678	0.0568	-0.3071	0.0925	0.006	0.013	-0.0911	-0.0282	0.2258	-0.0652	0.0499	-0.0261	-0.0075	0.1431	-0.0481	0.0867	33.0499	-1.6085	8.9403
5	1.3752	-1.0431	0.2103	2.6948	-0.1912	0.972	0.1523	-0.1875	0.1748	-0.0905	-0.1465	-0.0235	-0.2234	0.3181	-0.0272	0.1171	-0.0957	0.0414	0.01	-0.0954	0.092	30.3876	8.4053	3.0719
6	0.8915	0.1163	-0.1482	5.4408	-0.2616	1.8994	-0.1742	0.0305	-0.1694	-0.192	-0.0037	0.4929	0.0336	-0.2856	0.0757	0.2237	0.1121	-0.1268	-0.0197	-0.0941	0.5913	-8.1091	32.7406	-1.3562
7	1.6942	0.233	0.374	2.1963	-0.3046	1.4053	0.0431	-0.0944	-0.0702	0.2958	-0.0444	0.6033	0.0017	-0.1591	-0.0196	0.2813	0.0577	-0.0233	0.067	-0.0453	0.3824	-2.0378	35.3677	5.9041
8	0.4578	-1.5277	0.486	5.3174	-1.6426	0.5176	-0.0459	-0.1828	0.5071	0.4295	0.2499	0.2925	-0.7381	-0.3376	-0.143	0.2448	0.0496	0.0431	0.2058	-0.0294	0.2197	8.142	15.6203	21.1986
9	0.7572	-0.0197	-0.0923	0.3969	0.2211	1.0972	-0.0007	-0.1528	-0.0862	0.0468	-0.021	0.0576	0.0886	-0.1507	0.0253	0.0512	-0.0124	0.0001	0.1035	0.0195	0.0683	3.8113	-11.343	16.0327
10	5.5865	-2.0312	-0.8852	1.6471	0.3068	1.5723	-0.0943	-0.4531	0.0631	0.211	0.015	0.2241	-0.1475	-0.134	0.0445	0.8137	0.0955	-0.0512	0.3475	-0.0816	0.3174	16.988	40.084	12.026
11	0.1651	0.3559	0.5926	0.7464	1.2565	2.066	-0.1013	0.0973	0.0699	-0.1713	0.1444	-0.094	-0.2276	0.3242	-0.0542	0.6344	-0.0214	-0.1651	0.3379	-0.171	0.3045	14.91	42.768	6.155
12	0.8373	0.1863	-0.2045	3.9311	3.5882	4.9688	-0.0102	-0.1894	0.1133	0.4843	0.0656	0.0346	0.0016	0.0165	-0.0428	0.2993	0.0625	0.0062	0.1355	-0.0572	0.3282	-0.7196	30.8773	9.7175
13	1.4543	-0.5684	-0.5161	0.9351	0.5392	1.1175	0.0165	0.0257	0.1443	-0.0947	-0.0187	0.036	-0.1968	-0.0248	0.0077	0.098	0.0076	-0.0074	0.0385	0.0098	0.0781	6.4652	7.3785	-6.344
14	0.6061	-0.0835	-0.0905	1.023	0.17	0.8516	0.0404	0.048	0.0368	-0.0931	0.0165	-0.0827	-0.1622	0.1488	-0.041	0.0827	-0.018	0.0192	0.0639	-0.0053	0.0595	23.8577	-1.1002	-8.9865
15	1.5312	-0.6053	-0.0991	1.1719	0.0808	0.6017	0.0892	0.1272	0.0697	-0.08	-0.1312	0.1105	-0.1735	-0.0318	0.0281	0.1292	0.0049	0.0063	0.0328	0.0114	0.0561	13.6257	5.6663	-10.1339
16	5.719	4.3838	1.3299	7.6091	1.9445	3.062	-0.1786	0.3156	0.2719	-0.561	0.0678	-0.0473	-0.4725	0.1401	0.1006	0.3568	0.0105	-0.0674	0.1275	0.0461	0.2991	9.2227	36.0552	-5.3417
17	3.3828	2.2064	0.2441	3.0908	1.0763	2.1928	-0.1614	0.3869	0.4248	-0.1903	0.0987	0.2751	-0.4657	0.1786	0.0794	0.3194	0.0924	-0.0862	0.0777	-0.0144	0.3445	3.9848	38.8317	0.7366
18	0.1536	-0.899	-0.0179	5.3524	0.0705	0.0083	0.1077	-0.0291	0.5958	0.1022	-0.0099	0.3148	-0.4185	-0.0551	-0.0834	0.2165	0.0416	0.0285	0.1482	-0.0241	0.2953	-2.4787	16.5628	13.5459
19	0.9696	-0.0725	-0.1079	0.2573	0.127	0.7817	-0.0097	0.0687	-0.0637	-0.0468	-0.0327	0.0614	-0.0066	-0.1166	0.0379	0.0618	0.0001	-0.0154	0.0539	-0.0054	0.0576	2.0809	-6.6112	-3.3018
20	1.0726	-0.3374	0.4359	1.5912	-1.718	1.8749	-0.1599	-0.3077	-0.0171	0.3799	0.2135	0.2775	-0.1334	-0.2114	-0.0318	0.4315	0.0826	0.1526	0.357	0.0281	0.5245	-10.3282	32.8541	15.7773
21	0.0759	-0.2592	0.1084	1.4844	0.1364	0.3815	-0.2347	-0.3192	0.1471	0.5873	0.1676	0.1109	-0.1201	-0.0553	0.0281	0.3654	0.062	-0.0144	0.1596	-0.0428	0.2582	7.3144	30.5443	12.171
22	0.9118	0.0164	-0.1309	0.6662	0.1865	0.6454	0.0357	-0.3555	-0.0172	0.0691	0.0194	-0.0591	0.008	0.0854	-0.0444	0.0684	-0.005	-0.0031	0.1815	-0.0072	0.0355	22.1992	-5.0581	22.0216

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 3:19)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 20:48)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 49:72)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 73:152)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 153:176)
6	X-RAY DIFFRACTION	6	chain 'B' and (resseq 1:19)
7	X-RAY DIFFRACTION	7	chain 'B' and (resseq 20:44)
8	X-RAY DIFFRACTION	8	chain 'B' and (resseq 45:58)
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 59:176)
10	X-RAY DIFFRACTION	10	chain 'C' and (resseq 3:19)
11	X-RAY DIFFRACTION	11	chain 'C' and (resseq 20:35)
12	X-RAY DIFFRACTION	12	chain 'C' and (resseq 36:48)
13	X-RAY DIFFRACTION	13	chain 'C' and (resseq 49:72)
14	X-RAY DIFFRACTION	14	chain 'C' and (resseq 73:152)
15	X-RAY DIFFRACTION	15	chain 'C' and (resseq 153:176)
16	X-RAY DIFFRACTION	16	chain 'D' and (resseq 4:19)
17	X-RAY DIFFRACTION	17	chain 'D' and (resseq 20:42)
18	X-RAY DIFFRACTION	18	chain 'D' and (resseq 43:58)
19	X-RAY DIFFRACTION	19	chain 'D' and (resseq 59:176)
20	X-RAY DIFFRACTION	20	chain 'E' and (resseq 1:19)
21	X-RAY DIFFRACTION	21	chain 'E' and (resseq 20:54)
22	X-RAY DIFFRACTION	22	chain 'E' and (resseq 55:176)

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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