PDB-3dwf: Crystal Structure of the Guinea Pig 11beta-Hydroxysteroid Dehydro...

ID or keywords:

Entry

Database: PDB / ID: 3dwf

Title

Crystal Structure of the Guinea Pig 11beta-Hydroxysteroid Dehydrogenase Type 1 Mutant F278E

Components

11-beta-hydroxysteroid dehydrogenase 1

Keywords

OXIDOREDUCTASE /

Rossmann Fold / short chain dehydrogenase reductase / SDR /

Endoplasmic reticulum /

Glycoprotein /

Lipid metabolism /

Membrane /

NADP / Signal-anchor /

Steroid metabolism /

Transmembrane

Function / homology

Function and homology information

11beta-hydroxysteroid dehydrogenase / 11-beta-hydroxysteroid dehydrogenase (NADP+) activity / cortisol dehydrogenase activity /

7beta-hydroxysteroid dehydrogenase (NADP+) / 7-beta-hydroxysteroid dehydrogenase (NADP+) activity / steroid metabolic process / lung development /

NADP binding / endoplasmic reticulum membrane / protein homodimerization activity
Similarity search - Function

Biological species

Cavia porcellus (domestic guinea pig)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.2 Å

Authors

Lawson, A.J. / Ride, J.P. / White, S.A. / Walker, E.A.

Citation

Journal: Protein Sci. / Year: 2009
Title: Mutations of key hydrophobic surface residues of 11 beta-hydroxysteroid dehydrogenase type 1 increase solubility and monodispersity in a bacterial expression system
Authors: Lawson, A.J. / Walker, E.A. / White, S.A. / Dafforn, T.R. / Stewart, P.M. / Ride, J.P.

History

Deposition	Jul 22, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 11, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Non-polymer description / Version format compliance
Revision 1.2	Oct 20, 2021	Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Feb 21, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3dwf.cif.gz	446.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3dwf.ent.gz	370.5 KB	Display	PDB format
PDBx/mmJSON format	3dwf.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/dw/3dwf ftp://data.pdbj.org/pub/pdb/validation_reports/dw/3dwf	HTTPS FTP

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Related structure data

Similar structure data	5ecr-1 5ecp-2 5eco-1 4hlu-d 5eco-2 5dyy-d 6jhx-d 5dyt-d 2x2n-2 3mml-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) 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	#188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (3) #216 - Dec 2017 Biodegradable Plastic similarity (3) #77 - May 2006 Glucose Oxidase similarity (2) #90 - Jun 2007 Fatty Acid Synthase similarity (2)

Deposited unit

A: 11-beta-hydroxysteroid dehydrogenase 1

B: 11-beta-hydroxysteroid dehydrogenase 1

C: 11-beta-hydroxysteroid dehydrogenase 1

D: 11-beta-hydroxysteroid dehydrogenase 1

hetero molecules

126 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

A: 11-beta-hydroxysteroid dehydrogenase 1

B: 11-beta-hydroxysteroid dehydrogenase 1

hetero molecules

defined by software
62.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: 11-beta-hydroxysteroid dehydrogenase 1

D: 11-beta-hydroxysteroid dehydrogenase 1

hetero molecules

defined by software
63 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	78.080, 85.920, 176.280
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	11-beta-hydroxysteroid dehydrogenase 1 / Corticosteroid 11-beta-dehydrogenase isozyme 1 / 11-DH / 11-beta-HSD1 Mass: 30361.188 Da / Num. of mol.: 4 / Mutation: F278E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cavia porcellus (domestic guinea pig) / Gene: HSD11B1 / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q6QLL4, 11beta-hydroxysteroid dehydrogenase
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 452 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.43 Å³/Da / Density % sol: 49.47 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 8 Details: 0.1M Tris-HCl, 1.75M ammonium sulphate and 5% glycerol, pH 8, Vapor diffusion, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
Detector	Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 2007
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.933 Å / Relative weight: 1
Reflection	Resolution: 2.2→34.68 Å / Num. obs: 60967 / B_iso Wilson estimate: 34.468 Å²

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Processing

Software

Name	Version	Classification	NB
PHENIX		refinement
PDB_EXTRACT	3.005	data extraction

Refinement

Resolution: 2.2→34.68 Å / FOM work R set: 0.834 / Stereochemistry target values: ml

	R_factor	Num. reflection	% reflection
R_free	0.255	3085	5.07 %
R_work	0.2	-	-
obs	-	60836	99.77 %

Solvent computation

B_sol: 63.469 Å² / k_sol: 0.375 e/Å³

Displacement parameters

B_iso max: 180.64 Å² / B_iso mean: 43.75 Å² / B_iso min: 10.48 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.133 Å²	0 Å²	0 Å²
2-	-	0.029 Å²	0 Å²
3-	-	-	0.104 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→34.68 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8436	0	265	452	9153

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	0.923	1
X-RAY DIFFRACTION	f_bond_d	0.005	1
X-RAY DIFFRACTION	f_chiral_restr	0.067	1
X-RAY DIFFRACTION	f_dihedral_angle_d	16.81	1
X-RAY DIFFRACTION	f_plane_restr	0.003	1
X-RAY DIFFRACTION	f_nbd_refined	4.12	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
2.2-2.206	0.334	458	X-RAY DIFFRACTION	116	88
2.206-2.213	0.309	444	X-RAY DIFFRACTION	116	91
2.213-2.219	0.305	494	X-RAY DIFFRACTION	116	89
2.219-2.226	0.309	463	X-RAY DIFFRACTION	116	93
2.226-2.233	0.3	485	X-RAY DIFFRACTION	116	92
2.233-2.239	0.298	483	X-RAY DIFFRACTION	116	94
2.239-2.246	0.295	485	X-RAY DIFFRACTION	116	93
2.246-2.253	0.283	474	X-RAY DIFFRACTION	116	95
2.253-2.26	0.282	511	X-RAY DIFFRACTION	116	96
2.26-2.267	0.279	483	X-RAY DIFFRACTION	116	94
2.267-2.274	0.28	498	X-RAY DIFFRACTION	116	96
2.274-2.282	0.259	495	X-RAY DIFFRACTION	116	96
2.282-2.289	0.266	482	X-RAY DIFFRACTION	116	95
2.289-2.296	0.264	508	X-RAY DIFFRACTION	116	94
2.296-2.304	0.271	463	X-RAY DIFFRACTION	116	95
2.304-2.312	0.269	518	X-RAY DIFFRACTION	116	95
2.312-2.319	0.249	504	X-RAY DIFFRACTION	116	95
2.319-2.327	0.265	490	X-RAY DIFFRACTION	116	96
2.327-2.335	0.249	467	X-RAY DIFFRACTION	116	95
2.335-2.343	0.254	513	X-RAY DIFFRACTION	116	97
2.343-2.351	0.245	501	X-RAY DIFFRACTION	116	97
2.351-2.36	0.256	493	X-RAY DIFFRACTION	116	95
2.36-2.368	0.233	526	X-RAY DIFFRACTION	116	96
2.368-2.377	0.243	480	X-RAY DIFFRACTION	116	96
2.377-2.385	0.259	486	X-RAY DIFFRACTION	116	95
2.385-2.394	0.257	473	X-RAY DIFFRACTION	116	93
2.394-2.403	0.25	487	X-RAY DIFFRACTION	116	94
2.403-2.412	0.239	500	X-RAY DIFFRACTION	116	95
2.412-2.421	0.23	495	X-RAY DIFFRACTION	116	94
2.421-2.431	0.261	483	X-RAY DIFFRACTION	116	95
2.431-2.44	0.252	518	X-RAY DIFFRACTION	116	94
2.44-2.45	0.238	483	X-RAY DIFFRACTION	116	96
2.45-2.46	0.239	488	X-RAY DIFFRACTION	116	94
2.46-2.47	0.217	497	X-RAY DIFFRACTION	116	97
2.47-2.48	0.238	498	X-RAY DIFFRACTION	116	95
2.48-2.49	0.226	472	X-RAY DIFFRACTION	116	94
2.49-2.5	0.225	479	X-RAY DIFFRACTION	116	94
2.5-2.511	0.221	537	X-RAY DIFFRACTION	116	95
2.511-2.522	0.226	490	X-RAY DIFFRACTION	116	94
2.522-2.533	0.222	489	X-RAY DIFFRACTION	116	94
2.533-2.544	0.197	472	X-RAY DIFFRACTION	116	94
2.544-2.556	0.207	484	X-RAY DIFFRACTION	116	96
2.556-2.567	0.203	498	X-RAY DIFFRACTION	116	94
2.567-2.579	0.214	508	X-RAY DIFFRACTION	116	94
2.579-2.591	0.19	492	X-RAY DIFFRACTION	116	96
2.591-2.603	0.192	511	X-RAY DIFFRACTION	116	94
2.603-2.616	0.19	496	X-RAY DIFFRACTION	116	96
2.616-2.629	0.195	467	X-RAY DIFFRACTION	116	95
2.629-2.642	0.186	507	X-RAY DIFFRACTION	116	95
2.642-2.655	0.19	485	X-RAY DIFFRACTION	116	96
2.655-2.668	0.198	500	X-RAY DIFFRACTION	116	95
2.668-2.682	0.201	515	X-RAY DIFFRACTION	116	95
2.682-2.696	0.179	490	X-RAY DIFFRACTION	116	93
2.696-2.711	0.196	488	X-RAY DIFFRACTION	116	95
2.711-2.726	0.186	484	X-RAY DIFFRACTION	116	96
2.726-2.74	0.182	491	X-RAY DIFFRACTION	116	94
2.74-2.756	0.178	503	X-RAY DIFFRACTION	116	95
2.756-2.772	0.182	505	X-RAY DIFFRACTION	116	94
2.772-2.788	0.202	470	X-RAY DIFFRACTION	116	94
2.788-2.804	0.19	497	X-RAY DIFFRACTION	116	93
2.804-2.821	0.193	489	X-RAY DIFFRACTION	116	96
2.821-2.838	0.182	515	X-RAY DIFFRACTION	116	96
2.838-2.856	0.179	484	X-RAY DIFFRACTION	116	95
2.856-2.874	0.197	510	X-RAY DIFFRACTION	116	96
2.874-2.893	0.193	499	X-RAY DIFFRACTION	116	94
2.893-2.912	0.198	481	X-RAY DIFFRACTION	116	96
2.912-2.932	0.187	489	X-RAY DIFFRACTION	116	93
2.932-2.952	0.19	503	X-RAY DIFFRACTION	116	97
2.952-2.973	0.205	516	X-RAY DIFFRACTION	116	94
2.973-2.994	0.214	478	X-RAY DIFFRACTION	116	94
2.994-3.016	0.211	500	X-RAY DIFFRACTION	116	97
3.016-3.039	0.193	502	X-RAY DIFFRACTION	116	95
3.039-3.062	0.196	510	X-RAY DIFFRACTION	116	95
3.062-3.086	0.201	479	X-RAY DIFFRACTION	116	96
3.086-3.111	0.204	507	X-RAY DIFFRACTION	116	96
3.111-3.137	0.205	499	X-RAY DIFFRACTION	116	95
3.137-3.163	0.212	487	X-RAY DIFFRACTION	116	95
3.163-3.191	0.201	509	X-RAY DIFFRACTION	116	95
3.191-3.219	0.192	499	X-RAY DIFFRACTION	116	94
3.219-3.249	0.209	496	X-RAY DIFFRACTION	116	94
3.249-3.28	0.196	498	X-RAY DIFFRACTION	116	95
3.28-3.311	0.179	510	X-RAY DIFFRACTION	116	95
3.311-3.344	0.193	474	X-RAY DIFFRACTION	116	96
3.344-3.379	0.194	506	X-RAY DIFFRACTION	116	95
3.379-3.415	0.206	535	X-RAY DIFFRACTION	116	95
3.415-3.452	0.201	475	X-RAY DIFFRACTION	116	96
3.452-3.491	0.195	506	X-RAY DIFFRACTION	116	96
3.491-3.533	0.187	494	X-RAY DIFFRACTION	116	95
3.533-3.576	0.181	512	X-RAY DIFFRACTION	116	94
3.576-3.621	0.171	486	X-RAY DIFFRACTION	116	95
3.621-3.668	0.171	474	X-RAY DIFFRACTION	116	93
3.668-3.718	0.181	539	X-RAY DIFFRACTION	116	96
3.718-3.772	0.174	491	X-RAY DIFFRACTION	116	94
3.772-3.828	0.168	496	X-RAY DIFFRACTION	116	96
3.828-3.888	0.164	511	X-RAY DIFFRACTION	116	96
3.888-3.951	0.172	505	X-RAY DIFFRACTION	116	95
3.951-4.019	0.181	499	X-RAY DIFFRACTION	116	93
4.019-4.092	0.169	520	X-RAY DIFFRACTION	116	95
4.092-4.171	0.167	490	X-RAY DIFFRACTION	116	95
4.171-4.256	0.169	497	X-RAY DIFFRACTION	116	95
4.256-4.348	0.162	525	X-RAY DIFFRACTION	116	97
4.348-4.449	0.161	494	X-RAY DIFFRACTION	116	94
4.449-4.56	0.161	515	X-RAY DIFFRACTION	116	95
4.56-4.683	0.153	514	X-RAY DIFFRACTION	116	96
4.683-4.821	0.159	518	X-RAY DIFFRACTION	116	94
4.821-4.976	0.164	492	X-RAY DIFFRACTION	116	95
4.976-5.153	0.169	518	X-RAY DIFFRACTION	116	95
5.153-5.359	0.188	512	X-RAY DIFFRACTION	116	95
5.359-5.602	0.203	516	X-RAY DIFFRACTION	116	95
5.602-5.896	0.199	510	X-RAY DIFFRACTION	116	95
5.896-6.263	0.199	522	X-RAY DIFFRACTION	116	96
6.263-6.743	0.201	519	X-RAY DIFFRACTION	116	94
6.743-7.416	0.191	531	X-RAY DIFFRACTION	116	96
7.416-8.475	0.185	530	X-RAY DIFFRACTION	116	94
8.475-10.627	0.178	535	X-RAY DIFFRACTION	116	94
10.627-34.684	0.242	574	X-RAY DIFFRACTION	116	95

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	-0.0556	-0.0957	-0.1411	2.0446	0.1873	0.8369	-0.0809	-0.0778	0.0322	0.0893	0.2635	-0.5315	-0.0464	0.2516	-0.0632	0.1169	0.0456	-0.0361	0.2182	0.0237	0.3256	67.4447	85.1233	21.0616
2	0.6364	0.4808	0.5721	-0.107	0.3524	1.1017	-0.0488	-0.1507	-0.0859	0.002	-0.0443	-0.0529	0.0247	-0.0138	0.0954	0.1093	0.0348	0.0016	0.1152	0.0259	0.1759	50.6397	82.505	18.7922
3	0.4583	0.3365	0.4271	0.5895	0.8725	2.1296	0.2052	0.3405	0.3687	0.18	-0.4026	0.1572	1.4614	0.3927	0.0936	1.056	0.398	0.2526	0.3253	0.0802	0.5587	48.6447	64.5438	0.4905
4	1.6859	0.397	-0.224	0.4777	-0.125	1.6425	0.0016	-0.226	-0.6552	0.1436	-0.0157	-0.0685	0.7474	-0.0303	0.1698	0.4006	-0.0681	0.0081	0.0975	0.1056	0.2263	55.8942	78.709	64.8901
5	0.8331	-0.4628	0.2891	1.3357	-0.4728	1.3898	-0.0409	-0.0586	-0.0743	0.1537	0.0186	0.0559	0.1228	-0.2976	0.0305	0.1714	-0.0254	0.0168	0.1922	0.0053	0.1564	53.0248	96.1353	60.5608
6	0.0997	-0.0262	-0.0337	0.045	0.0369	0.3018	0.1382	-0.203	-0.0342	-0.0259	0.1056	-0.1122	-0.4118	0.1853	-0.1312	1.045	-0.6094	0.2643	0.7344	-0.4505	0.5486	40.5167	87.0668	40.1554
7	0.5302	0.35	0.4495	-0.0336	0.3906	0.8751	-0.4695	0.1045	0.1691	-0.3083	-0.1392	0.1833	-0.6328	-0.155	0.4495	0.6261	0.0294	-0.0021	0.3665	-0.1035	0.4411	64.2663	132.2743	44.7693
8	0.8216	0.2831	0.2271	0.7409	0.1143	1.1128	-0.0236	0.0759	0.0338	-0.0787	0.0256	-0.1272	-0.18	-0.0074	-0.0041	0.1441	-0.0206	0.0363	0.1398	-0.0148	0.121	60.9729	112.1075	43.3789
9	0.6931	0.3005	2.2118	2.4875	-0.1706	3.2425	-0.1222	-0.255	-0.3702	0.68	0.3002	-0.9908	-0.067	0.2308	-0.1854	0.3091	-0.0387	-0.2388	0.3202	-0.0101	0.4869	76.7272	108.4259	67.2876
10	-0.425	-0.4208	0.5124	0.0057	0.7489	1.8691	-0.232	0.1112	0.2147	0.1427	-0.3794	0.2637	-0.0979	-0.6132	0.4958	0.3298	0.1669	-0.0271	0.9747	-0.0669	0.5021	13.1043	89.5246	1.9175
11	1.0973	-0.2125	0.5014	1.5235	-0.0924	1.7191	-0.0355	-0.0063	0.0326	-0.1377	-0.0297	0.0513	-0.0145	-0.1953	0.0545	0.0899	0.0417	-0.0079	0.1264	-0.0119	0.0682	33.3974	87.2905	0.2448
12	0.264	-0.152	-0.2068	0.0746	-0.0367	0.108	0.0781	0.2915	-0.42	0.2809	-0.0641	-0.059	0.0959	-0.1442	-0.0293	0.6949	0.3222	-0.1859	0.8958	-0.4069	0.7897	36.602	103.8344	23.9081

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 25:125)	A	25 - 125
2	X-RAY DIFFRACTION	2	(chain A and resid 126:277)	A	126 - 277
3	X-RAY DIFFRACTION	3	(chain A and resid 278:299)	A	278 - 299
4	X-RAY DIFFRACTION	4	(chain B and resid 24:125)	B	24 - 125
5	X-RAY DIFFRACTION	5	(chain B and resid 126:291)	B	126 - 291
6	X-RAY DIFFRACTION	6	(chain B and resid 292:299)	B	292 - 299
7	X-RAY DIFFRACTION	7	(chain C and resid 25:33)	C	25 - 33
8	X-RAY DIFFRACTION	8	(chain C and resid 34:282)	C	34 - 282
9	X-RAY DIFFRACTION	9	(chain C and resid 283:299)	C	283 - 299
10	X-RAY DIFFRACTION	10	(chain D and resid 25:33)	D	25 - 33
11	X-RAY DIFFRACTION	11	(chain D and resid 34:282)	D	34 - 282
12	X-RAY DIFFRACTION	12	(chain D and resid 283:299)	D	283 - 299

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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

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-Related structure data

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-Experimental details

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-Sample preparation

-Data collection

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+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

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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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This web site

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Options

+
Open data

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Basic information

-
Structure visualization

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Downloads & links

-
Download

-
Validation report

-
Related structure data

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Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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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

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Yorodumi