PDB-6vi1: Structure of Fab4 bound to P22 TerL(1-33)

ID or keywords:

Entry

Database: PDB / ID: 6vi1

Title

Structure of Fab4 bound to P22 TerL(1-33)

Components

Synthetic Fab4 heavy chain
Synthetic Fab4 light chain
Terminase, large subunit

Keywords

IMMUNE SYSTEM / Synthetic fab / large terminase / genome-packaging / crystallization chaperone /

VIRAL PROTEIN

Function / homology

Function and homology information

viral terminase complex / viral terminase, large subunit / viral DNA genome packaging /

Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization /

Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement /

endonuclease activity /

ATP hydrolysis activity /

ATP binding /

metal ion binding
Similarity search - Function

Biological species

Homo sapiens (human)

Salmonella phage P22 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Cingolani, G. / Lokareddy, R. / Ko, Y.

Funding support

United States, 3items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM100888	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	OD017987	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	CA56036	United States

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Recognition of an alpha-helical hairpin in P22 large terminase by a synthetic antibody fragment.
Authors: Lokareddy, R.K. / Ko, Y.H. / Hong, N. / Doll, S.G. / Paduch, M. / Niederweis, M. / Kossiakoff, A.A. / Cingolani, G.

History

Deposition	Jan 11, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 2, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 9, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6vi1.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb6vi1.ent.gz	902.8 KB	Display	PDB format
PDBx/mmJSON format	6vi1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vi/6vi1 ftp://data.pdbj.org/pub/pdb/validation_reports/vi/6vi1	HTTPS FTP

-
Related structure data

Related structure data	6vi2C 6xmiC 5eu7S 6vhm PDB Unreleased entry S: Starting model for refinement C: citing same article (ref.)
Similar structure data	1op8-3 6xmi-2 1op8-1 1q9w-1 6bli-2 5jx8-d 5i0m-d 4zfo-2 6i7l-d 6vge-d 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

Related structure data

6vi2C

6xmiC

5eu7S

6vhm
PDB Unreleased entry

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

D: Synthetic Fab4 light chain

E: Synthetic Fab4 heavy chain

A: Synthetic Fab4 light chain

B: Synthetic Fab4 heavy chain

C: Synthetic Fab4 light chain

F: Synthetic Fab4 heavy chain

G: Synthetic Fab4 light chain

H: Synthetic Fab4 heavy chain

I: Synthetic Fab4 light chain

J: Synthetic Fab4 heavy chain

K: Synthetic Fab4 light chain

L: Synthetic Fab4 heavy chain

M: Terminase, large subunit

N: Terminase, large subunit

O: Terminase, large subunit

P: Terminase, large subunit

Q: Terminase, large subunit

R: Terminase, large subunit

320 kDa, 18 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

D: Synthetic Fab4 light chain

E: Synthetic Fab4 heavy chain

M: Terminase, large subunit

defined by author
Evidence: equilibrium centrifugation
53.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Synthetic Fab4 light chain

B: Synthetic Fab4 heavy chain

N: Terminase, large subunit

defined by author
53.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Synthetic Fab4 light chain

F: Synthetic Fab4 heavy chain

O: Terminase, large subunit

defined by author
53.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Synthetic Fab4 light chain

H: Synthetic Fab4 heavy chain

P: Terminase, large subunit

defined by author
53.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: Synthetic Fab4 light chain

J: Synthetic Fab4 heavy chain

Q: Terminase, large subunit

defined by author
53.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

K: Synthetic Fab4 light chain

L: Synthetic Fab4 heavy chain

R: Terminase, large subunit

defined by author
53.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	77.747, 139.334, 163.761
Angle α, β, γ (deg.)	90.000, 98.300, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 1

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ASP	ASP	GLY	GLY	chain A	A	C	1 - 214	2 - 215
2	1	ASP	ASP	GLY	GLY	chain C	C	E	1 - 214	2 - 215
3	1	ASP	ASP	GLY	GLY	chain D	D	A	1 - 214	2 - 215
4	1	ASP	ASP	GLY	GLY	chain G	G	G	1 - 214	2 - 215
5	1	ASP	ASP	GLY	GLY	chain I	I	I	1 - 214	2 - 215
6	1	ASP	ASP	GLY	GLY	chain K	K	K	1 - 214	2 - 215
1	2	GLU	GLU	PRO	PRO	(chain B and resid 220 through 449)	B	D	220 - 449	6 - 235
2	2	GLU	GLU	PRO	PRO	chain E	E	B	220 - 449	6 - 235
3	2	GLU	GLU	PRO	PRO	(chain F and resid 220 through 449)	F	F	220 - 449	6 - 235
4	2	GLU	GLU	PRO	PRO	(chain H and resid 220 through 449)	H	H	220 - 449	6 - 235
5	2	GLU	GLU	PRO	PRO	chain J	J	J	220 - 449	6 - 235
6	2	GLU	GLU	PRO	PRO	(chain L and resid 220 through 449)	L	L	220 - 449	6 - 235
1	3	MET	MET	GLU	GLU	chain M	M	M	1 - 23	1 - 23
2	3	MET	MET	GLU	GLU	chain N	N	N	1 - 23	1 - 23
3	3	MET	MET	GLU	GLU	chain O	O	O	1 - 23	1 - 23
4	3	MET	MET	GLU	GLU	chain P	P	P	1 - 23	1 - 23
5	3	MET	MET	GLU	GLU	chain Q	Q	Q	1 - 23	1 - 23
6	3	MET	MET	GLU	GLU	chain R	R	R	1 - 23	1 - 23

NCS ensembles :

ID
1
2
3

#1: Antibody	Synthetic Fab4 light chain Mass: 23286.883 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: PROTEIN SELECTED BY PHAGE DISPLAY / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody	Synthetic Fab4 heavy chain Mass: 26025.027 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Details: PROTEIN SELECTED BY PHAGE DISPLAY / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide	Terminase, large subunit / DNA-packaging protein gp2 / Gene product 2 / gp2 Mass: 3976.288 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Salmonella phage P22 (virus) References: UniProt: P26745, type II site-specific deoxyribonuclease, DNA helicase, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 836 / 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: 2.75 Å³/Da / Density % sol: 55.19 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion / pH: 6.5 Details: 100 mM KCl, 25 mM MgCl2, 50 mM Na-Cacodylate trihydrate pH 6.0, 15% (v/v) 2-propanol

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.978 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 2.4→50 Å / Num. obs: 127623 / % possible obs: 94 % / Redundancy: 2.5 % / B_iso Wilson estimate: 32.5 Å² / R_pim(I) all: 0.085 / R_sym value: 0.118 / Net I/σ(I): 11.3
Reflection shell	Resolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 12764 / CC_1/2: 0.508 / R_pim(I) all: 0.555 / R_sym value: 0.639

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
PDB_EXTRACT	3.25	data extraction
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5EU7

5eu7

Resolution: 2.4→14.98 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.03

	R_factor	Num. reflection	% reflection
R_free	0.2394	1977	1.57 %
R_work	0.1887	-	-
obs	0.1895	126104	94.02 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 191.87 Å² / B_iso mean: 51.7492 Å² / B_iso min: 16.36 Å²

Refinement step

Cycle: final / Resolution: 2.4→14.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21330	0	0	836	22166
B_iso mean	-	-	-	43	-
Num. residues	-	-	-	-	2808

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	3834	X-RAY DIFFRACTION	6.414	TORSIONAL
1	2	C	3834	X-RAY DIFFRACTION	6.414	TORSIONAL
1	3	D	3834	X-RAY DIFFRACTION	6.414	TORSIONAL
1	4	G	3834	X-RAY DIFFRACTION	6.414	TORSIONAL
1	5	I	3834	X-RAY DIFFRACTION	6.414	TORSIONAL
1	6	K	3834	X-RAY DIFFRACTION	6.414	TORSIONAL
2	1	B	4152	X-RAY DIFFRACTION	6.414	TORSIONAL
2	2	E	4152	X-RAY DIFFRACTION	6.414	TORSIONAL
2	3	F	4152	X-RAY DIFFRACTION	6.414	TORSIONAL
2	4	H	4152	X-RAY DIFFRACTION	6.414	TORSIONAL
2	5	J	4152	X-RAY DIFFRACTION	6.414	TORSIONAL
2	6	L	4152	X-RAY DIFFRACTION	6.414	TORSIONAL
3	1	M	396	X-RAY DIFFRACTION	6.414	TORSIONAL
3	2	N	396	X-RAY DIFFRACTION	6.414	TORSIONAL
3	3	O	396	X-RAY DIFFRACTION	6.414	TORSIONAL
3	4	P	396	X-RAY DIFFRACTION	6.414	TORSIONAL
3	5	Q	396	X-RAY DIFFRACTION	6.414	TORSIONAL
3	6	R	396	X-RAY DIFFRACTION	6.414	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.4-2.46	0.3167	141	0.3031	8856	8997	94
2.46-2.53	0.2961	140	0.2931	8786	8926	93
2.53-2.6	0.3743	139	0.2783	8709	8848	93
2.6-2.68	0.3233	144	0.2644	9075	9219	96
2.68-2.78	0.306	144	0.253	9008	9152	96
2.78-2.89	0.2977	143	0.2405	8983	9126	95
2.89-3.02	0.3098	142	0.2252	8893	9035	95
3.02-3.18	0.2514	136	0.212	8616	8752	92
3.18-3.37	0.2971	144	0.2027	9013	9157	95
3.37-3.63	0.2345	143	0.1747	8974	9117	95
3.63-3.99	0.2022	142	0.168	8899	9041	94
3.99-4.55	0.1793	140	0.1378	8793	8933	93
4.55-5.68	0.1744	141	0.1342	8897	9038	94
5.68-14.98	0.2059	138	0.1556	8625	8763	90

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	1.0351	0.3444	0.2341	1.7814	0.4258	1.6613	-0.0594	0.0275	-0.1517	-0.0542	0.0362	0.0031	-0.0218	0.0201	-0.0004	0.2638	0.0372	0.0252	0.3091	0.005	0.3749	-24.917	19.9669	17.5079
2	1.4979	0.498	-0.9925	1.1751	0.5882	1.7433	-0.2166	0.2859	-0.1775	-0.2903	0.1744	0.0071	-0.0302	-0.1338	0.0147	0.3924	-0.1165	-0.0211	0.5203	-0.0651	0.483	-38.1273	19.3903	-16.0945
3	0.9887	0.0213	-0.2195	1.5082	-0.3453	1.0823	-0.1627	0.2011	-0.0554	-0.2762	0.1058	0.1555	0.2912	-0.1706	-0.006	0.4338	-0.0776	-0.0148	0.5222	-0.0953	0.5428	-36.1074	16.6552	-17.3885
4	1.0806	-0.2085	1.5342	1.2518	-1.6389	4.5155	-0.2295	-0.0991	0.1895	0.2438	0.0914	0.1008	-0.8202	-0.3188	-0.0042	0.4807	0.035	-0.0015	0.3275	-0.0245	0.3974	-23.9174	40.6689	15.0599
5	0.6873	-0.3889	-0.4852	0.2101	0.025	1.2038	-0.4037	0.1978	-0.5251	-0.587	0.1462	0.2826	0.8273	-0.3866	0.0083	0.6906	-0.1424	0.0406	0.7956	-0.1098	0.672	-49.558	21.9425	-16.7139
6	0.7788	1.3486	0.308	1.7427	-0.398	0.902	-0.1155	0.1012	0.1779	0.0036	0.1002	0.4612	-0.1666	-0.3374	0.0003	0.3289	0.0123	0.0315	0.5722	-0.0167	0.594	-43.5145	30.7116	-8.6619
7	0.9004	1.2016	-0.0309	1.1693	-0.1329	1.0922	-0.1199	-0.1025	-0.0083	0.2428	0.0401	0.0906	0.2225	0.1785	0.0085	0.3148	-0.0076	0.0148	0.339	0.0175	0.3905	14.6707	-4.4387	26.2641
8	0.862	-0.2731	-0.3717	1.2441	0.139	1.9071	0.0237	-0.0576	-0.0119	0.0283	-0.0201	0.0287	0.0379	0.0266	-0.0002	0.2934	-0.0273	0.0127	0.3037	-0.0063	0.3448	9.0441	-9.881	28.7426
9	0.7327	-0.0139	-0.1049	0.3873	-0.0573	0.3455	-0.0508	0.1653	-0.7998	-0.245	0.1757	0.5481	-0.1503	-0.3415	-0.0147	0.7615	0.0087	-0.1652	0.5864	-0.0676	0.5316	-8.0791	-11.6101	-10.1069
10	0.9489	-0.2264	-0.0301	0.151	-0.1654	0.4367	-0.167	-0.1751	0.2192	-0.118	-0.1102	-0.1444	-0.2508	-0.095	0.0201	0.6365	-0.0619	0.0019	0.3943	0.0102	0.5394	4.9163	-8.0806	-3.4906
11	1.7573	-0.4344	0.2185	0.7747	0.6248	0.6888	0.2295	-0.3684	0.3211	-0.2551	-0.1362	0.285	0.3003	-0.4569	-0.0066	0.7559	-0.1737	0.0631	0.4608	-0.0744	0.5242	3.9916	-7.5932	0.0148
12	0.3358	0.1081	0.2475	0.2882	0.0453	0.1105	0.1325	-0.3459	0.1015	-0.1695	0.0202	0.3319	-0.1876	-0.4361	-0.0001	0.671	-0.0444	-0.0439	0.4712	-0.0253	0.4872	-4.5917	-4.8795	-8.1775
13	0.0687	-0.143	-0.0199	0.1916	0.0811	0.2538	0.3027	0.2487	0.2674	-0.126	-0.266	0.0584	-0.3076	0.2583	0.011	0.8655	-0.0887	-0.0309	0.4276	0.0971	0.5206	3.0873	-5.5221	-13.6685
14	0.2137	0.0136	-0.4093	0.9174	-0.0172	0.7827	0.4742	0.2125	0.155	-0.2162	-0.3143	0.0706	-0.186	0.4185	-0.0007	0.7803	-0.0396	0.0393	0.6302	0.0129	0.4676	7.5047	-10.7371	-12.5241
15	0.8883	0.4468	-0.2611	0.3058	0.3433	1.2843	0.035	0.016	-0.1928	0.1616	-0.0238	0.5891	0.0613	-0.1218	-0.0093	0.3599	-0.0013	-0.0314	0.3664	-0.0045	0.6436	-15.746	-6.8641	25.1261
16	2.9672	-0.9605	0.1639	0.9538	0.4988	1.8247	0.1335	-0.253	-0.0766	0.2002	0.015	0.4546	0.0799	-0.3098	-0.0032	0.3336	-0.0255	0.0863	0.3566	-0.0139	0.4869	-11.6699	-3.5691	33.4655
17	0.5876	0.4484	-0.5395	0.5693	0.1001	0.8484	0.1578	-0.0787	-0.5749	0.0012	-0.1056	-0.1262	0.5823	0.5071	-0.0169	0.5713	-0.0484	0.0764	0.5191	0.0541	0.4143	5.5625	-11.75	49.6198
18	0.8096	0.2356	-0.0102	1.4656	-0.2939	1.6344	-0.1318	0.0984	0.0798	-0.3758	-0.0428	0.036	0.2455	-0.4138	-0.0087	0.43	-0.0219	0.0363	0.3133	-0.0139	0.4899	-8.6282	-10.9963	10.1485
19	0.2344	-0.236	-0.0289	0.2674	0.1289	0.6923	-0.0729	0.0777	-0.2183	-0.1575	-0.1968	0.3795	0.3477	-0.5301	-0.0002	0.5239	-0.0186	-0.0116	0.4141	-0.0713	0.5597	-10.566	-14.1842	3.77
20	1.3977	0.5221	-0.5852	0.3537	0.4601	1.8153	-0.1413	0.1092	0.0405	-0.3256	-0.0282	-0.1613	0.2355	-0.0116	0.0025	0.665	-0.0389	0.0559	0.3478	-0.0721	0.5497	-5.3	-14.3134	2.4825
21	0.4765	-0.0505	0.3326	0.8219	-0.2889	0.59	-0.1611	0.2123	-0.0721	-0.1912	-0.1357	0.5471	0.8254	-0.8186	0.0153	0.8091	-0.1487	-0.0164	0.5341	-0.0529	0.6234	-14.7767	-19.8164	-0.1115
22	0.9512	0.4889	0.3851	0.367	-0.0939	1.3001	0.0427	0.0948	-0.1401	0.0096	-0.1133	-0.0526	0.0863	-0.2463	-0.0042	0.3679	-0.0394	0.0497	0.407	0.0334	0.4065	-19.5272	27.5262	-19.1073
23	1.924	-0.4359	0.6209	1.8298	-0.6499	1.6893	0.0403	0.1157	-0.0064	-0.1238	0.0475	0.1366	0.1051	0.0694	0.0003	0.2725	-0.0325	0.0229	0.3157	0.0066	0.3568	-9.912	29.4703	-18.9211
24	0.2476	-0.0867	0.0817	0.2319	-0.2894	0.5247	0.1475	0.4768	-0.0267	-0.352	-0.3869	-0.1468	-0.2138	0.1773	-0.0055	0.4737	0.0628	-0.0867	0.4048	0.0018	0.4662	-25.614	37.007	-33.5493
25	0.3676	0.1452	-0.1805	0.4724	0.0168	0.4375	0.3093	0.5954	-0.0251	-0.5726	0.2465	-0.1523	0.0431	0.066	0.0033	0.9499	0.0824	-0.0619	0.8293	-0.1278	0.4686	-20.8347	29.296	-62.6531
26	0.8246	-0.1359	-0.1477	0.7842	-0.2056	0.4547	0.139	0.2804	-0.1118	-0.1005	-0.2384	0.461	0.6552	-0.0851	0.0215	0.6053	0.0472	-0.1124	0.6062	-0.0276	0.5368	-27.9879	30.3706	-49.4075
27	1.1374	-0.9566	-0.3549	1.0181	-0.2982	0.9779	-0.1756	0.3028	0.0236	-0.561	0.1005	0.1509	-0.2218	-0.1608	-0.0037	0.5652	-0.0057	-0.0453	0.5499	-0.0098	0.574	-25.4217	29.0017	-46.9062
28	0.3053	0.2642	-0.3934	0.5129	0.136	0.6541	0.2747	0.3618	-0.3455	-0.4395	-0.1111	0.7071	0.6899	-0.116	0.0129	0.9447	0.0792	-0.3213	0.6417	-0.1579	0.5256	-24.8186	24.1544	-58.1298
29	0.5022	-0.008	-0.7115	0.6534	0.7949	1.7403	0.8987	0.971	-0.1053	-0.9291	-0.2839	0.6769	0.3451	-0.2216	0.407	1.144	0.2335	-0.5069	1.0986	-0.1301	0.628	-33.4273	28.1721	-58.274
30	0.5173	0.7083	0.4588	1.0086	0.4581	0.2954	0.4666	0.453	0.2959	-0.988	-0.6972	1.7516	0.9467	-0.6262	0.1713	1.0428	0.3678	-0.4525	1.18	0.1182	0.3089	-34.2022	34.5577	-55.5654
31	1.0187	-0.6804	0.1839	1.8217	0.3783	4.277	0.2371	0.2736	-0.0691	-0.2664	-0.0583	-0.3985	0.2495	0.7467	-0.0141	0.39	0.0868	0.0168	0.5192	-0.0412	0.49	3.8708	18.9481	-25.9773
32	0.765	0.4828	0.2394	1.027	-0.0268	2.0145	0.0847	0.3698	0.0169	-0.4945	-0.1167	0.0839	-0.2028	0.1986	-0.0268	0.6529	0.1284	0.0221	0.5193	-0.0176	0.4273	-9.0773	27.8204	-46.8883
33	0.7022	-0.4688	-0.138	1.0106	-0.0462	1.3534	0.2175	0.264	-0.0146	-0.5448	-0.0763	-0.1114	-0.0114	0.2247	-0.0007	0.7082	0.0522	0.0676	0.6149	0.0187	0.5001	-10.9962	32.2922	-54.6625
34	1.0711	-0.4466	0.0799	0.5178	-0.0306	1.0923	-0.1429	-0.2711	-0.0418	0.2793	0.281	0.5801	-0.29	-0.4599	-0.0039	0.474	0.0688	0.0715	0.6326	0.0918	0.573	-2.9554	-17.9916	-62.7805
35	0.2814	-0.4823	0.6521	2.525	-0.3923	1.3482	-0.0057	0.0102	0.0073	-0.0067	0.1808	0.3344	-0.0481	-0.2771	-0.0044	0.3486	-0.0003	0.0386	0.4787	0.0492	0.4046	4.7085	-20.8532	-64.7102
36	0.9997	-0.4052	1.0078	1.3052	-0.7926	1.007	0.2642	0.081	0.1004	-0.449	-0.016	0.169	0.0914	-0.8355	0.0353	0.709	-0.0774	-0.0577	0.7751	0.1574	0.5188	-7.1518	-16.1215	-98.3457
37	0.9712	-0.3279	-0.7885	1.3577	-0.2277	1.7693	-0.1257	-0.076	0.0181	-0.3481	0.0698	0.4786	0.1372	-0.7307	0.0095	0.6831	-0.0147	-0.1348	0.7324	0.1445	0.6372	-10.4863	-14.5636	-97.6615
38	0.9037	0.1934	0.5256	2.732	-0.0807	4.1232	0.016	0.0535	-0.2272	-0.4912	0.1948	0.0026	0.6088	0.2041	-0.0098	0.5738	-0.0344	-0.0411	0.4309	0.0295	0.4341	8.5303	-39.5631	-69.7794
39	1.4499	0.6377	0.8498	1.5194	0.0935	2.6443	0.1713	0.3537	0.0023	-0.3505	0.1181	-0.0582	0.561	0.1898	-0.0018	0.7922	-0.0102	-0.0467	0.6066	0.0744	0.5824	4.3504	-22.8108	-98.9862
40	1.5062	0.8542	-0.0982	1.6526	0.2179	1.0067	-0.0221	-0.0055	-0.0157	0.011	-0.006	0.0243	0.0801	-0.0079	-0.0051	0.2743	0.031	-0.0185	0.3089	0.0122	0.3474	-20.8529	-56.0933	-21.6221
41	0.0612	-0.0591	0.0801	0.0593	-0.0117	0.09	0.2143	0.217	-0.0849	0.1309	-0.2661	0.066	0.4778	-0.2359	0.0055	0.3443	-0.0563	-0.0537	0.5434	-0.0288	0.398	-35.4094	-63.7068	-35.4844
42	2.3052	1.1287	0.0951	3.8589	-0.4943	1.5502	-0.0492	0.3504	-0.2453	-0.2455	0.1045	-0.3455	-0.0667	-0.1059	0.0096	0.452	-0.0055	-0.0825	0.613	-0.0529	0.5954	-33.2734	-57.2316	-55.4647
43	1.0616	0.1588	-0.0758	0.4431	0.5825	0.6515	-0.0674	0.7476	-0.1821	-0.3358	0.3913	-0.0785	0.842	-0.486	-0.0043	0.6577	-0.1024	-0.045	0.8818	-0.091	0.5614	-38.1925	-64.3358	-60.3566
44	1.5565	0.0588	1.174	1.8401	-0.4842	0.9208	-0.1177	0.0446	0.521	0.4286	0.2009	0.2054	-0.4424	-0.3357	-0.0138	0.4997	0.0363	0.0047	0.3782	0.09	0.6764	-16.1048	-32.7129	-29.8531
45	1.6947	-0.2745	1.0631	0.5426	-0.5553	1.9763	-0.031	0.1537	0.2993	0.0567	0.0414	0.0017	-0.1725	0.0102	0.0022	0.353	-0.0331	-0.0063	0.2946	0.0065	0.4417	-13.0153	-40.4575	-28.557
46	0.5575	-0.6831	-0.1888	1.0405	-0.3904	1.7012	-0.2226	0.5848	-0.3611	-0.3698	0.1192	0.1914	0.2027	-0.3258	0.0007	0.4992	-0.043	-0.0634	0.6471	-0.0059	0.6127	-41.8207	-50.1125	-55.8986
47	1.2591	0.7059	0.2385	0.7843	-0.1779	0.957	0.0327	0.3012	0.2816	0.0828	0.0154	-0.015	-0.2043	0.0516	0.0011	0.3794	0.0179	-0.0599	0.5599	0.0675	0.5371	-36.1602	-42.7252	-50.7523
48	0.4632	-0.3199	0.2037	1.2568	0.2365	0.668	0.1443	-0.0685	0.195	-0.1617	-0.1759	-0.2358	-0.6461	0.2015	-0.006	0.6507	-0.1167	0.0125	0.4879	-0.0897	0.4647	-52.8245	5.9804	-74.9612
49	0.5752	-0.0436	0.3997	0.2042	0.4755	2.2787	0.0265	-0.0643	0.0235	0.0468	0.0685	-0.0796	-0.0784	0.2185	0.005	0.5411	-0.0707	0.0205	0.4058	-0.0063	0.3853	-50.4495	-3.1285	-70.7137
50	0.4332	-0.0221	0.1354	0.2209	0.5033	0.9483	0.2652	0.0269	0.2327	-0.0995	-0.182	-0.0193	-0.3287	0.496	0.0229	0.6307	-0.1687	0.0162	0.7122	-0.0727	0.4636	-47.1699	1.5534	-44.571
51	1.3373	0.1537	0.0552	1.9958	-0.2112	1.9776	0.0838	-0.2451	0.0898	0.035	-0.0346	-0.0015	0.0464	0.1932	-0.0074	0.6719	-0.1317	0.0435	0.6196	-0.0933	0.4515	-44.5144	1.2809	-40.8342
52	0.5976	-0.6871	-0.1964	0.6472	0.0211	1.474	0.1362	-0.0364	-0.4411	-0.0785	-0.0015	0.2999	0.8175	0.8652	-0.0093	0.8159	0.1667	-0.0784	0.8109	-0.0609	0.7653	-33.636	-18.5221	-76.4483
53	0.6047	-0.2863	0.3578	0.2679	-0.3816	0.3593	-0.0333	-0.1163	0.0242	0.1402	0.2323	-0.4107	0.5118	0.6981	-0.0284	0.4773	-0.033	0.0301	0.6702	-0.1153	0.4264	-36.3685	-7.5096	-78.7354
54	1.2779	-0.6774	0.3448	0.3987	-0.5869	1.6164	0.1484	0.4574	-0.2217	-0.0302	0.2897	-0.3896	0.3005	1.3179	-0.0063	0.5927	0.0193	0.021	1.0941	-0.1454	0.6105	-28.0314	-11.5237	-81.2804
55	0.842	0.1754	-1.0871	1.0045	-0.4677	1.077	0.1541	-0.0212	-0.2672	-0.2881	0.0793	0.0598	0.6556	-0.137	-0.0138	0.564	-0.0731	0.0181	0.5358	-0.0471	0.3986	-46.8942	-10.6474	-87.7587
56	0.0754	0.0443	0.2881	0.3971	-0.0505	0.5429	-0.0184	-0.0168	-0.1697	0.0108	-0.025	-0.3199	0.519	1.0961	-0.0004	0.5886	0.0029	-0.0952	0.8613	-0.0534	0.5684	-30.8264	-11.9994	-56.3813
57	0.792	0.1707	0.9141	0.8233	-0.1059	1.0168	0.6295	-0.6914	0.8887	0.5488	0.3616	0.5955	0.7487	0.0123	-0.0269	0.9296	-0.2141	-0.0765	0.921	0.0442	0.7204	-46.0266	-11.4881	-40.0949
58	1.8692	-1.0418	-0.5802	0.4959	0.1908	1.6782	0.0966	-0.2062	-0.4445	0.1979	0.0261	-0.0751	0.5203	0.5558	0.0156	0.8181	-0.0271	-0.042	0.6449	-0.0001	0.5211	-41.405	-15.7134	-47.8259
59	0.1393	-0.1612	0.0585	0.5281	-0.0126	0.2114	0.0346	-0.4905	1.3017	0.3262	0.1969	0.0821	-0.5999	0.1237	-0.0055	0.5549	-0.0744	-0.0343	0.4886	-0.0549	0.4046	-13.9217	38.9208	34.6882
60	0.4184	-0.4307	-0.1067	0.3207	0.1979	0.6071	-0.3177	-0.6833	0.0872	0.0522	-0.0795	0.2251	0.2643	0.6542	0.0033	0.405	0.0354	-0.0262	0.5008	-0.0563	0.4423	-8.9535	29.9413	34.0581
61	0.7234	0.2525	-0.0218	0.2516	0.1173	0.3847	0.0375	-0.6533	-0.1343	0.8634	-0.1511	0.3901	-0.0034	-0.1177	0.0024	0.6168	-0.089	0.1229	0.5627	-0.0175	0.4471	-1.3456	-3.0287	52.8817
62	0.2303	0.3802	-0.0785	0.5164	-0.0456	0.4912	0.168	0.6452	0.2251	-0.3304	-0.2063	-0.3438	-0.57	0.1782	0.0069	0.5851	-0.1437	0.1014	0.5539	-0.0095	0.3985	7.861	1.4462	51.0953
63	0.314	-0.146	-0.0625	0.0554	0.0121	0.1772	0.3933	0.0102	-0.0878	0.689	-0.4024	-0.7043	0.5346	0.3702	0.0026	0.4037	0.0852	-0.0504	0.4676	-0.0017	0.5526	6.9024	17.6287	-6.189
64	0.5075	0.225	0.0407	0.1228	-0.0617	0.0944	0.1203	-0.1736	-0.0669	0.2578	0.0206	0.2593	0.2861	-0.3221	-0.0081	0.4051	0.0471	-0.0558	0.4319	0.044	0.4953	-2.6357	17.0696	-1.9015
65	0.563	-0.3819	-0.2336	0.2429	0.0118	0.6818	0.2085	0.176	-0.1569	-0.0078	-0.6144	-0.7394	1.1013	0.7087	0.004	0.5929	-0.008	-0.0132	0.5608	0.0393	0.4593	13.7092	-41.6861	-48.4242
66	1.5381	0.1224	0.4444	0.1565	0.0328	1.1054	0.201	-0.3389	0.0366	-0.4809	-0.5866	0.9508	0.457	-0.942	0.0098	0.5458	-0.0354	-0.0205	0.6867	0.034	0.4438	5.0097	-37.9958	-44.5754
67	0.1479	-0.0725	0.0401	0.402	-0.2276	0.1553	-0.5162	-0.1241	1.0819	-0.1535	0.0468	0.0787	-0.2823	0.7106	0.0007	0.4119	-0.0733	-0.022	0.4595	-0.0783	0.4828	-2.9996	-43.1834	-8.4849
68	0.4926	0.0325	0.2124	1.0954	-0.1938	0.8902	-0.7064	0.3302	-0.4744	-0.0554	0.0791	-0.5493	0.4991	0.5496	0.0084	0.423	-0.0177	-0.0248	0.4664	-0.0537	0.4826	-2.2836	-53.4364	-8.3313
69	0.3454	-0.4329	-0.0092	0.6475	0.0526	0.7493	-0.1149	0.1758	-0.4117	-0.5078	-0.089	-0.2948	0.7313	0.5083	0.0012	0.7064	-0.0448	0.0541	0.7529	-0.0872	0.4621	-40.7664	-7.7963	-100.3177
70	0.0588	0.1347	0.0893	1.0235	0.2362	0.7538	0.1233	-0.1647	1.0206	0.1275	-0.3225	-0.1647	-0.8214	0.4157	0.0002	0.7234	-0.0605	0.0377	0.5954	-0.0136	0.4159	-44.5951	1.8513	-99.7836

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'D' and (resid 1 through 115 )	D	1 - 115
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 116 through 152 )	D	116 - 152
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 153 through 214 )	D	153 - 214
4	X-RAY DIFFRACTION	4	chain 'E' and (resid 220 through 355 )	E	220 - 355
5	X-RAY DIFFRACTION	5	chain 'E' and (resid 356 through 370 )	E	356 - 370
6	X-RAY DIFFRACTION	6	chain 'E' and (resid 371 through 449 )	E	371 - 449
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1 through 25 )	A	1 - 25
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 26 through 115 )	A	26 - 115
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 116 through 130 )	A	116 - 130
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 131 through 152 )	A	131 - 152
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 153 through 174 )	A	153 - 174
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 175 through 189 )	A	175 - 189
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 190 through 200 )	A	190 - 200
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 201 through 214 )	A	201 - 214
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 220 through 236 )	B	220 - 236
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 237 through 319 )	B	237 - 319
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 320 through 333 )	B	320 - 333
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 334 through 370 )	B	334 - 370
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 371 through 393 )	B	371 - 393
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 394 through 424 )	B	394 - 424
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 425 through 451 )	B	425 - 451
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 1 through 25 )	C	1 - 25
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 26 through 103 )	C	26 - 103
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 104 through 115 )	C	104 - 115
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 116 through 130 )	C	116 - 130
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 131 through 152 )	C	131 - 152
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 153 through 174 )	C	153 - 174
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 175 through 189 )	C	175 - 189
29	X-RAY DIFFRACTION	29	chain 'C' and (resid 190 through 200 )	C	190 - 200
30	X-RAY DIFFRACTION	30	chain 'C' and (resid 201 through 214 )	C	201 - 214
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 220 through 333 )	F	220 - 333
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 334 through 370 )	F	334 - 370
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 371 through 450 )	F	371 - 450
34	X-RAY DIFFRACTION	34	chain 'G' and (resid 1 through 25 )	G	1 - 25
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 26 through 115 )	G	26 - 115
36	X-RAY DIFFRACTION	36	chain 'G' and (resid 116 through 152 )	G	116 - 152
37	X-RAY DIFFRACTION	37	chain 'G' and (resid 153 through 214 )	G	153 - 214
38	X-RAY DIFFRACTION	38	chain 'H' and (resid 220 through 355 )	H	220 - 355
39	X-RAY DIFFRACTION	39	chain 'H' and (resid 356 through 450 )	H	356 - 450
40	X-RAY DIFFRACTION	40	chain 'I' and (resid 1 through 103 )	I	1 - 103
41	X-RAY DIFFRACTION	41	chain 'I' and (resid 104 through 115 )	I	104 - 115
42	X-RAY DIFFRACTION	42	chain 'I' and (resid 116 through 189 )	I	116 - 189
43	X-RAY DIFFRACTION	43	chain 'I' and (resid 190 through 214 )	I	190 - 214
44	X-RAY DIFFRACTION	44	chain 'J' and (resid 220 through 250 )	J	220 - 250
45	X-RAY DIFFRACTION	45	chain 'J' and (resid 251 through 360 )	J	251 - 360
46	X-RAY DIFFRACTION	46	chain 'J' and (resid 361 through 381 )	J	361 - 381
47	X-RAY DIFFRACTION	47	chain 'J' and (resid 382 through 449 )	J	382 - 449
48	X-RAY DIFFRACTION	48	chain 'K' and (resid 1 through 25 )	K	1 - 25
49	X-RAY DIFFRACTION	49	chain 'K' and (resid 26 through 130 )	K	26 - 130
50	X-RAY DIFFRACTION	50	chain 'K' and (resid 131 through 152 )	K	131 - 152
51	X-RAY DIFFRACTION	51	chain 'K' and (resid 153 through 214 )	K	153 - 214
52	X-RAY DIFFRACTION	52	chain 'L' and (resid 220 through 250 )	L	220 - 250
53	X-RAY DIFFRACTION	53	chain 'L' and (resid 251 through 271 )	L	251 - 271
54	X-RAY DIFFRACTION	54	chain 'L' and (resid 272 through 310 )	L	272 - 310
55	X-RAY DIFFRACTION	55	chain 'L' and (resid 311 through 339 )	L	311 - 339
56	X-RAY DIFFRACTION	56	chain 'L' and (resid 340 through 360 )	L	340 - 360
57	X-RAY DIFFRACTION	57	chain 'L' and (resid 361 through 381 )	L	361 - 381
58	X-RAY DIFFRACTION	58	chain 'L' and (resid 382 through 451 )	L	382 - 451
59	X-RAY DIFFRACTION	59	chain 'M' and (resid 1 through 11 )	M	1 - 11
60	X-RAY DIFFRACTION	60	chain 'M' and (resid 12 through 23 )	M	12 - 23
61	X-RAY DIFFRACTION	61	chain 'N' and (resid 1 through 11 )	N	1 - 11
62	X-RAY DIFFRACTION	62	chain 'N' and (resid 12 through 23 )	N	12 - 23
63	X-RAY DIFFRACTION	63	chain 'O' and (resid 1 through 11 )	O	1 - 11
64	X-RAY DIFFRACTION	64	chain 'O' and (resid 12 through 23 )	O	12 - 23
65	X-RAY DIFFRACTION	65	chain 'P' and (resid 1 through 11 )	P	1 - 11
66	X-RAY DIFFRACTION	66	chain 'P' and (resid 12 through 23 )	P	12 - 23
67	X-RAY DIFFRACTION	67	chain 'Q' and (resid 1 through 11 )	Q	1 - 11
68	X-RAY DIFFRACTION	68	chain 'Q' and (resid 12 through 23 )	Q	12 - 23
69	X-RAY DIFFRACTION	69	chain 'R' and (resid 1 through 11 )	R	1 - 11
70	X-RAY DIFFRACTION	70	chain 'R' and (resid 12 through 23 )	R	12 - 23

-
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