PDB-4cq4: C-terminal fragment of Af1503-sol: transmembrane receptor Af1503 ...

ID or keywords:

Entry

Database: PDB / ID: 4cq4

Title

C-terminal fragment of Af1503-sol: transmembrane receptor Af1503 from Archaeoglobus fulgidus engineered for solubility

Components

ENGINEERED VERSION OF TRANSMEMBRANE RECEPTOR AF1503

Keywords

STRUCTURAL PROTEIN / HAMP DOMAIN / TWO COMPONENT SIGNAL TRANSDUCTION / TRANSMEMBRANE SIGNALLING

Function / homology

Function and homology information

signal transduction / identical protein binding / membrane / metal ion binding
Similarity search - Function

Biological species

ARCHAEOGLOBUS FULGIDUS (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Hartmann, M.D. / Dunin-Horkawicz, S. / Hulko, M. / Martin, J. / Coles, M. / Lupas, A.N.

Citation

Journal: J.Struct.Biol. / Year: 2014
Title: A Soluble Mutant of the Transmembrane Receptor Af1503 Features Strong Changes in Coiled-Coil Periodicity.
Authors: Hartmann, M.D. / Dunin-Horkawicz, S. / Hulko, M. / Martin, J. / Coles, M. / Lupas, A.N.

History

Deposition	Feb 11, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jun 11, 2014	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4cq4.cif.gz	186 KB	Display	PDBx/mmCIF format
PDB format	pdb4cq4.ent.gz	144.5 KB	Display	PDB format
PDBx/mmJSON format	4cq4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4cq4_validation.pdf.gz	449.3 KB	Display	wwPDB validaton report
Full document	4cq4_full_validation.pdf.gz	451 KB	Display
Data in XML	4cq4_validation.xml.gz	20.4 KB	Display
Data in CIF	4cq4_validation.cif.gz	30.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cq/4cq4 ftp://data.pdbj.org/pub/pdb/validation_reports/cq/4cq4	HTTPS FTP

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Related structure data

Related structure data	3zrxS S: Starting model for refinement
Similar structure data	4gn0-3 4qkv-d 5wjb-1 3wuq-d 6fia-1 5wtl-1 5tfk-d 6bxu-2 5w4t-4 5vvm-2 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	#158 - Feb 2013 Proton-Gated Urea Channel similarity (4) #190 - Oct 2015 Two-component Systems similarity (4)

Deposited unit

A: ENGINEERED VERSION OF TRANSMEMBRANE RECEPTOR AF1503

B: ENGINEERED VERSION OF TRANSMEMBRANE RECEPTOR AF1503

C: ENGINEERED VERSION OF TRANSMEMBRANE RECEPTOR AF1503

D: ENGINEERED VERSION OF TRANSMEMBRANE RECEPTOR AF1503

138 kDa, 4 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)	44.069, 48.037, 95.187
Angle α, β, γ (deg.)	90.00, 98.04, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	ENGINEERED VERSION OF TRANSMEMBRANE RECEPTOR AF1503 Mass: 34496.090 Da / Num. of mol.: 4 Fragment: C-TERMINAL PROTEOLYTIC FRAGMENT WITH UNKNOWN CLEAVAGE SITE Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O28769
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THE STRUCTURE CONTAINS ONLY A C-TERMINAL PROTEOLYTIC FRAGMENT OF THE DEPOSITED SEQUENCE WITH ...THE STRUCTURE CONTAINS ONLY A C-TERMINAL PROTEOLYTIC FRAGMENT OF THE DEPOSITED SEQUENCE WITH UNKNOWN CLEAVAGE SITE

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2 Å³/Da / Density % sol: 40 % / Description: NONE
Crystal grow	Details: 25% (W/V) PEG 3350, 100 MM HEPES, PH 6.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.85
Detector	Type: MARRESEARCH / Detector: CCD / Date: Sep 26, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.85 Å / Relative weight: 1
Reflection	Resolution: 1.7→37.7 Å / Num. obs: 43434 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.79 % / R_merge(I) obs: 0.08 / Net I/σ(I): 11.2
Reflection shell	Resolution: 1.7→1.8 Å / Redundancy: 3.75 % / R_merge(I) obs: 0.68 / Mean I/σ(I) obs: 2.17 / % possible all: 97.1

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Processing

Software

Name	Version	Classification
REFMAC	5.7.0029	refinement
XDS		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZRX

3zrx

Resolution: 1.7→37.67 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.93 / SU B: 5.471 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES U VALUES

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24303	2187	5 %	RANDOM
R_work	0.19286	-	-	-
obs	0.19538	41246	99.15 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 26.255 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.99 Å²	0 Å²	2.45 Å²
2-	-	-0.33 Å²	0 Å²
3-	-	-	-0.97 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→37.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3060	0	0	382	3442

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	3098
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3116
X-RAY DIFFRACTION	r_angle_refined_deg	1.852	1.989	4206
X-RAY DIFFRACTION	r_angle_other_deg	0.947	3	7169
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.22	5	420
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.808	26.26	123
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.983	15	589
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.306	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	543
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	3520
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	581
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.698→1.742 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.325	165	-
R_work	0.286	2839	-
obs	-	-	94.26 %

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	9.962	-4.4618	-4.4347	8.1329	3.6671	5.6138	-0.0865	-0.0257	0.5368	-0.1236	0.2732	-0.0982	-0.5286	-0.0481	-0.1868	0.1138	0.0183	-0.0443	0.0499	0.0106	0.0855	23.7302	29.8081	43.2424
2	8.0992	-3.1278	-10.0503	4.6233	4.3253	14.4022	0.1306	0.2806	0.1514	-0.1386	-0.084	-0.0078	-0.3402	-0.1655	-0.0466	0.038	-0.0064	-0.0476	0.0617	0.0088	0.0852	40.1228	22.0784	25.9714
3	11.3517	-2.1092	-10.5379	1.2899	1.4015	11.7637	-0.1611	-0.0042	0.0103	0.2667	0.0118	0.027	-0.2075	0.0224	0.1493	0.1652	0.0016	-0.0165	0.116	-0.0306	0.0997	55.2961	15.976	6.0515
4	8.0198	-2.7927	-7.2623	2.4942	4.3038	12.4223	0.177	0.0619	0.2399	0.0005	0.0314	-0.0713	-0.2226	0.2621	-0.2084	0.1543	0.0006	0.0007	0.1035	0.0134	0.1426	67.6541	12.4126	-11.3617
5	2.7326	2.3266	-5.8624	2.1934	-4.4592	16.0287	0.1429	-0.2386	-0.0084	0.0791	-0.0734	-0.1459	-0.083	0.6494	-0.0695	0.1967	-0.0033	-0.016	0.2885	-0.0071	0.2243	75.154	10.0739	-7.9721
6	4.5995	1.0396	-6.6651	1.0401	-0.6716	10.5403	-0.1032	-0.1577	-0.2603	-0.0536	-0.0599	-0.2696	0.1508	0.2536	0.1631	0.1439	0.0382	-0.0364	0.2415	0.0099	0.1615	73.0563	3.3897	-8.5345
7	9.0993	0.4742	-5.4233	7.4204	1.9783	14.2384	0.0888	0.2921	0.4807	-0.467	-0.0359	-0.0381	-0.7187	0.1775	-0.0529	0.109	0.0152	-0.0627	0.1458	0.0315	0.1528	82.9848	3.1063	-27.3499
8	4.3293	-3.2541	-0.7139	2.6774	2.5982	20.7199	-0.1611	-0.1691	-0.2678	0.2362	0.1229	0.1563	0.7337	-0.1425	0.0381	0.1152	0.0349	-0.0283	0.046	0.0275	0.151	27.9176	13.7834	48.2872
9	5.5044	-0.0748	-6.1906	1.1459	0.5922	10.8437	-0.2312	-0.2261	-0.329	0.0361	0.0485	-0.0385	0.2399	0.5376	0.1827	0.0373	0.0128	-0.0307	0.0426	-0.0064	0.1049	37.6269	8.8884	27.7688
10	7.6989	-3.1515	-6.5305	1.8248	4.6954	13.2349	-0.3074	0.1932	-0.4079	0.1107	-0.1154	0.2059	0.2818	-0.2379	0.4229	0.1373	0.0012	-0.0433	0.1061	-0.0249	0.1349	52.441	4.1084	6.5948
11	10.3975	-3.9551	-11.1098	2.5601	5.7522	14.103	-0.1269	0.1768	-0.2699	0.1323	-0.1995	0.1688	0.2545	-0.2922	0.3264	0.1416	0.0353	-0.0297	0.1767	-0.0469	0.1408	65.5889	-2.1046	-9.4466
12	9.3007	-7.8851	-4.0706	7.6604	5.0482	6.0052	-0.245	0.3221	-0.4312	0.3524	-0.1757	0.5513	0.1466	-0.5498	0.4207	0.1854	0.0092	-0.0549	0.2698	0.0024	0.2664	59.5151	-0.1558	-16.4038
13	6.0827	-5.1	-6.7916	5.5379	5.7958	9.8926	-0.0118	0.0051	0.0414	0.0944	-0.0162	0.1765	0.0954	-0.067	0.0281	0.1072	0.0181	-0.0658	0.146	-0.0099	0.1052	63.3566	6.154	-16.1777
14	14.9309	-5.2753	-5.5636	7.5244	2.7615	11.0956	-0.193	-0.0697	-0.4568	0.1481	-0.023	0.2652	0.0852	-0.1392	0.216	0.0709	-0.0171	-0.063	0.0768	-0.0202	0.1115	75.6009	-4.3741	-31.212
15	9.354	5.2784	-9.5827	5.2466	-3.1978	12.8713	0.0198	0.5802	0.2898	-0.629	0.1095	0.3155	-0.2324	-0.923	-0.1293	0.3391	0.0536	-0.0376	0.2201	-0.0109	0.1061	50.742	12.4597	-1.2642
16	5.6075	-2.9473	-7.7286	1.952	3.7951	13.7065	0.278	0.4576	0.2223	-0.2345	-0.113	-0.1319	-0.443	-0.3199	-0.165	0.0531	-0.0082	-0.0255	0.1437	-0.0003	0.0951	37.1069	13.8965	18.0144
17	10.3626	-0.727	-12.1968	1.4535	0.9909	14.3731	-0.1304	0.1321	-0.0774	-0.2071	0.032	-0.0833	0.133	-0.1465	0.0984	0.0711	0.0127	-0.0327	0.0351	-0.0213	0.0722	23.0537	18.7236	38.9942
18	11.2675	-4.3578	-12.4841	4.4901	3.0587	14.953	0.0118	0.3216	-0.1122	-0.1508	-0.0577	0.1805	0.0925	-0.4074	0.0459	0.0412	-0.0192	-0.0397	0.0432	-0.0157	0.0782	8.8175	22.8912	54.0087
19	9.2909	-6.1284	-4.5503	5.5556	2.7446	3.6861	-0.1838	0.0406	-0.6904	0.4003	-0.0184	0.4269	0.2705	-0.1017	0.2022	0.1273	-0.031	-0.065	0.0674	-0.0228	0.1924	8.8201	15.2743	58.6993
20	11.8525	-4.687	-8.4102	2.7547	2.6857	8.4907	-0.274	-0.1785	-0.4976	0.1375	0.0297	0.1982	0.3704	0.0484	0.2443	0.0507	-0.0054	-0.0398	0.0103	0.0098	0.0947	13.6717	17.9352	63.2361
21	14.4604	-7.5521	-10.6632	6.6359	7.5379	9.4314	-0.4762	0.2752	-1.0064	0.0988	-0.1844	0.5	0.2413	-0.4718	0.6606	0.1426	0.0207	0.0259	0.3795	0.1372	0.1952	-1.7176	23.2248	75.9938
22	10.1641	-1.4343	-2.9914	9.2249	1.6414	8.3364	-0.0513	0.0623	-0.6375	-0.0888	0.2562	-0.4155	0.3402	0.5574	-0.2049	0.0764	0.0277	-0.0438	0.2174	-0.0166	0.1114	60.8473	5.941	8.296
23	9.2973	-3.4019	-9.918	1.3506	4.3241	15.2081	-0.0805	0.0236	0.0189	0.0407	0.0297	-0.0056	0.1274	0.2731	0.0508	0.0238	-0.0046	-0.0424	0.0635	0.0083	0.0847	47.7603	14.4901	25.8445
24	7.9325	-3.3058	-10.0078	2.6066	3.841	12.7166	0.0564	-0.1148	-0.0143	-0.0518	-0.0998	-0.1454	-0.0642	0.1958	0.0433	0.0347	0.0274	-0.047	0.1069	-0.023	0.0935	33.0658	20.5386	45.9631
25	9.482	-4.0394	-11.8612	2.2053	3.4385	20.7631	-0.0223	-0.4374	0.0498	0.0835	0.0226	-0.0866	-0.0721	0.8699	-0.0002	0.0929	-0.0602	-0.0855	0.1587	0.044	0.0798	21.5217	24.2684	63.5256
26	1.3404	0.1575	-1.3915	1.8572	-3.0728	7.7447	0.2085	-0.3154	0.1867	0.0591	0.0688	-0.1425	-0.5763	0.2451	-0.2772	0.1234	-0.0573	0.0513	0.0967	-0.0775	0.1448	18.6581	32.5239	62.6571
27	5.4367	-0.7981	-9.2815	1.3846	1.1924	18.8054	-0.0213	-0.0956	0.0433	-0.038	0.0227	0.1059	-0.2638	0.0498	-0.0013	0.0465	0.0126	-0.0374	0.0061	-0.0051	0.0563	12.7791	30.0619	59.2901
28	9.673	-0.98	-11.4793	3.4142	2.3109	18.255	0.0598	-0.882	0.0942	0.4169	-0.0068	-0.2594	-0.3517	0.6393	-0.053	0.1131	0.0507	-0.0542	0.2192	0.0259	0.1032	3.1784	31.9719	77.9094

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 246
2	X-RAY DIFFRACTION	2	A	247 - 266
3	X-RAY DIFFRACTION	3	A	267 - 280
4	X-RAY DIFFRACTION	4	A	281 - 297
5	X-RAY DIFFRACTION	5	A	298 - 309
6	X-RAY DIFFRACTION	6	A	310 - 326
7	X-RAY DIFFRACTION	7	A	327 - 999
8	X-RAY DIFFRACTION	8	B	1 - 246
9	X-RAY DIFFRACTION	9	B	247 - 266
10	X-RAY DIFFRACTION	10	B	267 - 280
11	X-RAY DIFFRACTION	11	B	281 - 297
12	X-RAY DIFFRACTION	12	B	298 - 309
13	X-RAY DIFFRACTION	13	B	310 - 326
14	X-RAY DIFFRACTION	14	B	327 - 999
15	X-RAY DIFFRACTION	15	C	1 - 246
16	X-RAY DIFFRACTION	16	C	247 - 266
17	X-RAY DIFFRACTION	17	C	267 - 280
18	X-RAY DIFFRACTION	18	C	281 - 297
19	X-RAY DIFFRACTION	19	C	298 - 309
20	X-RAY DIFFRACTION	20	C	310 - 326
21	X-RAY DIFFRACTION	21	C	327 - 999
22	X-RAY DIFFRACTION	22	D	1 - 246
23	X-RAY DIFFRACTION	23	D	247 - 266
24	X-RAY DIFFRACTION	24	D	267 - 280
25	X-RAY DIFFRACTION	25	D	281 - 297
26	X-RAY DIFFRACTION	26	D	298 - 309
27	X-RAY DIFFRACTION	27	D	310 - 326
28	X-RAY DIFFRACTION	28	D	327 - 999

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Movie

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Structure viewers

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Viewer log

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This page

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Open data

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Basic information

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Structure visualization

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi