PDB-4ma8: Crystal structure of mouse prion protein complexed with Chlorpromazine

ID or keywords:

Entry

Database: PDB / ID: 4ma8

Title

Crystal structure of mouse prion protein complexed with Chlorpromazine

Components

Major prion protein
POM1 heavy chain
POM1 light chain

Keywords

IMMUNE SYSTEM / Immunoglobulin fold / Fab / Antibody / Mouse prion protein

Function / homology

Function and homology information

Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / glycosaminoglycan binding / type 5 metabotropic glutamate receptor binding / ATP-dependent protein binding ...Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / negative regulation of amyloid precursor protein catabolic process / regulation of glutamate receptor signaling pathway / lamin binding / aspartic-type endopeptidase inhibitor activity / regulation of calcium ion import across plasma membrane / positive regulation of glutamate receptor signaling pathway / glycosaminoglycan binding / type 5 metabotropic glutamate receptor binding / ATP-dependent protein binding / negative regulation of interleukin-17 production / cupric ion binding / regulation of potassium ion transmembrane transport / negative regulation of dendritic spine maintenance / nucleobase-containing compound metabolic process / negative regulation of calcineurin-NFAT signaling cascade / negative regulation of interleukin-2 production / negative regulation of T cell receptor signaling pathway / negative regulation of activated T cell proliferation / negative regulation of amyloid-beta formation / response to amyloid-beta / cuprous ion binding / negative regulation of type II interferon production / negative regulation of long-term synaptic potentiation / intracellular copper ion homeostasis / positive regulation of protein targeting to membrane / response to cadmium ion / side of membrane / inclusion body / neuron projection maintenance / positive regulation of calcium-mediated signaling / cellular response to copper ion / molecular function activator activity / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / protein destabilization / protein homooligomerization / cellular response to xenobiotic stimulus / cellular response to amyloid-beta / terminal bouton / positive regulation of neuron apoptotic process / signaling receptor activity / regulation of protein localization / protein-folding chaperone binding / amyloid-beta binding / response to oxidative stress / protease binding / nuclear membrane / microtubule binding / molecular adaptor activity / transmembrane transporter binding / learning or memory / postsynaptic density / intracellular signal transduction / membrane raft / copper ion binding / dendrite / negative regulation of apoptotic process / protein-containing complex binding / cell surface / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / Golgi apparatus / metal ion binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Baral, P.K. / Swayampakula, M. / James, M.N.G.

Citation

Journal: Structure / Year: 2014
Title: Structural basis of prion inhibition by phenothiazine compounds.
Authors: Baral, P.K. / Swayampakula, M. / Rout, M.K. / Kav, N.N. / Spyracopoulos, L. / Aguzzi, A. / James, M.N.

History

Deposition	Aug 15, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 22, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 26, 2014	Group: Database references
Revision 1.2	Oct 12, 2022	Group: Database references / Derived calculations / Structure summary Category: chem_comp / database_2 / struct_site Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Sep 20, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4	Nov 20, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4ma8.cif.gz	239.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4ma8.ent.gz	192.7 KB	Display	PDB format
PDBx/mmJSON format	4ma8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4ma8_validation.pdf.gz	748.1 KB	Display	wwPDB validaton report
Full document	4ma8_full_validation.pdf.gz	756.8 KB	Display
Data in XML	4ma8_validation.xml.gz	27.1 KB	Display
Data in CIF	4ma8_validation.cif.gz	39.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ma/4ma8 ftp://data.pdbj.org/pub/pdb/validation_reports/ma/4ma8	HTTPS FTP

-
Related structure data

Related structure data	4ma7C 4h88S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4h88-d 4yxh-d 4yxk-d 4yx2-d 2iff-d 1fbi-2 1yjd-d 6d2p-d 3rkd-2 3uc0-2 6ktr-1 1fbi-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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) #101 - May 2008 Prions similarity (9) #189 - Sep 2015 Amyloids similarity (9)

Deposited unit

C: Major prion protein

H: POM1 heavy chain

L: POM1 light chain

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	83.262, 106.883, 75.594
Angle α, β, γ (deg.)	90.00, 95.32, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-454- HOH
2	1	C-488- HOH

#1: Protein	Major prion protein / PrP / PrP27-30 / PrP33-35C Mass: 13360.877 Da / Num. of mol.: 1 / Fragment: UNP residues 116-229 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Prnp, Prn-p, Prp / Production host: Escherichia coli (E. coli) / References: UniProt: P04925
#2: Antibody	POM1 heavy chain Mass: 23397.078 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Details: hybridoma / Source: (gene. exp.) Mus musculus (house mouse) / Cell: hybridoma
#3: Antibody	POM1 light chain Mass: 23509.701 Da / Num. of mol.: 1 / Fragment: Fab Source method: isolated from a genetically manipulated source Details: hybridoma / Source: (gene. exp.) Mus musculus (house mouse) / Cell: hybridoma
#4: Chemical	ChemComp-Z80 / 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine / Chlorpromazine Mass: 318.864 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₇H₁₉ClN₂S
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.78 Å³/Da / Density % sol: 55.73 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG3350, 0.1 M Bis-Tris, pH 6.5, 0.2 M lithium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.007 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2012
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.007 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 32491 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / R_merge(I) obs: 0.08 / Net I/σ(I): 14
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 2.2 % / R_merge(I) obs: 0.57 / Mean I/σ(I) obs: 1.5 / % possible all: 86.4

-
Processing

Software

Name	Version	Classification
MOLREP		phasing
REFMAC	5.7.0032	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H88

4h88

Resolution: 2.2→34.99 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.93 / SU B: 12.02 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23585	1634	5 %	RANDOM
R_work	0.19458	-	-	-
obs	0.19664	30848	97.22 %	-

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: 60.404 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.22 Å²	0 Å²	-0.46 Å²
2-	-	1.8 Å²	0 Å²
3-	-	-	-1.5 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→34.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4184	0	21	444	4649

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.02	4314
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3866
X-RAY DIFFRACTION	r_angle_refined_deg	1.322	1.944	5871
X-RAY DIFFRACTION	r_angle_other_deg	0.834	3.004	8933
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.036	5	536
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.923	24.439	187
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.753	15	687
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.948	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.098	0.2	639
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	4922
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	996
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	1.327	3.101	2153
X-RAY DIFFRACTION	r_mcbond_other	1.326	3.1	2152
X-RAY DIFFRACTION	r_mcangle_it	2.097	4.645	2686
X-RAY DIFFRACTION	r_mcangle_other	3.297	7.424	2687
X-RAY DIFFRACTION	r_scbond_it	1.538	3.203	2161
X-RAY DIFFRACTION	r_scbond_other	2.302	5.062	2162
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.666	7.523	3186
X-RAY DIFFRACTION	r_long_range_B_refined	7.674	52.352	11915
X-RAY DIFFRACTION	r_long_range_B_other	7.418	52.194	11704
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.201→2.258 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.32	113	-
R_work	0.308	1980	-
obs	-	-	84.29 %

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	14.4699	8.3772	-19.5919	10.6032	-4.9879	33.5663	-1.0539	0.5984	0.2801	-0.5627	0.8721	0.7189	1.4189	-0.2805	0.1819	0.3351	0.2312	-0.151	0.4589	-0.0192	0.3855	-17.6193	31.4799	-37.9103
2	11.3585	-8.6356	-2.5054	15.4461	4.2216	1.6215	-0.0482	-0.3259	0.2312	0.3416	0.0147	0.516	-0.3782	-0.0261	0.0335	0.5813	0.1679	0.0229	0.399	-0.0138	0.2608	-8.5287	24.1459	-38.1532
3	3.3907	-1.3752	1.743	7.7174	-0.1867	6.7949	0.0926	0.403	-0.2716	-0.4071	-0.2023	-0.0361	0.1966	0.0021	0.1097	0.1243	0.0504	0.0243	0.245	-0.0065	0.156	-0.8394	5.1985	-32.237
4	0.3799	-1.9277	-0.3786	10.9565	1.4127	2.0336	0.022	0.0211	-0.1053	-0.4781	0.149	1.1073	-0.6594	-0.6057	-0.171	0.4571	0.1794	-0.0953	0.5055	-0.0155	0.4177	-10.9079	21.5142	-34.8929
5	12.2865	-8.5938	1.6059	22.1221	-3.0668	3.7916	0.1566	-0.4584	0.5099	0.798	-0.0295	-0.2429	-0.1646	-0.0455	-0.1271	0.2459	0.1026	0.0459	0.2385	-0.1033	0.2334	-8.8451	30.1632	-23.6379
6	9.3643	13.2389	6.6696	19.6871	5.5255	23.4231	0.1826	-0.5757	0.801	0.5574	-0.588	1.3671	-0.7671	-1.0385	0.4054	0.2021	0.2223	0.0735	0.3593	-0.0947	0.4521	-15.2077	20.0786	-30.3027
7	20.7942	12.8025	2.4062	10.3865	-6.1696	23.6585	-0.5007	0.8606	0.6601	-0.5249	0.576	0.4784	0.5433	0.0382	-0.0754	0.1392	0.1393	-0.1864	0.3707	-0.0893	0.4373	-20.7876	11.8544	-37.5225
8	21.2039	6.6088	3.9321	4.8005	1.6389	2.7294	0.1103	-0.2731	0.0045	0.5608	-0.2318	0.4555	0.2032	-0.3632	0.1215	0.2009	0.0453	0.0529	0.2485	-0.0252	0.1819	-10.2858	9.1892	-28.1293
9	7.4977	2.5961	-3.1025	21.2999	-7.3264	3.248	0.2329	-0.1493	0.2843	-0.15	-0.3152	-0.3874	-0.1319	0.1821	0.0822	0.3938	0.0419	-0.0274	0.2548	-0.0439	0.2601	-3.3164	24.9837	-31.1194
10	9.0947	-7.4571	-8.9408	6.3007	5.4016	31.5585	-0.1649	0.0021	0.0843	0.1475	-0.0485	0.0625	0.4894	0.9853	0.2134	0.5603	-0.0207	-0.0663	0.5476	0.0094	1.0895	-0.2072	39.2344	-32.6258
11	11.5765	-9.5057	-21.0093	10.8782	15.6764	38.939	0.1914	-0.6553	0.5461	-0.1858	0.4454	-1.081	-0.2742	1.2701	-0.6369	0.0487	-0.0261	0.0217	0.262	0.0461	0.1704	23.1336	10.4223	-20.1955
12	4.1039	-1.5582	-3.9849	2.3	1.7431	4.1888	0.4162	-0.457	0.4175	-0.1092	-0.0094	-0.218	-0.8088	0.6184	-0.4067	0.5353	-0.2746	-0.0306	0.287	-0.0208	0.0822	13.9531	14.7717	-3.591
13	1.2478	0.1499	0.2704	1.4977	-0.2091	2.0862	-0.0882	-0.0929	0.0548	0.1006	0.0883	-0.0512	-0.1842	-0.0028	-0.0001	0.0733	0.0048	0.004	0.1566	0.0098	0.0696	9.0209	7.7213	-16.3663
14	10.0914	5.9473	-5.876	6.0087	-4.1241	8.0496	-0.1482	0.0307	0.1168	0.0502	0.1444	-0.0462	-0.352	-0.1495	0.0038	0.0726	-0.0043	-0.0197	0.0877	-0.0123	0.0336	6.0605	13.7269	-12.0982
15	1.2806	-0.0528	-0.0439	1.3787	0.0609	3.4577	-0.0136	-0.007	-0.0226	0.1058	-0.0361	-0.0643	0.061	0.2445	0.0497	0.0506	-0.005	-0.0163	0.1335	0.0034	0.0464	12.5299	6.191	-10.9807
16	6.9713	-7.2909	0.9012	12.7904	-1.7786	2.8141	-0.2367	-0.4392	-0.3149	0.6701	0.0972	-0.0853	0.2586	0.4519	0.1395	0.2225	0.1373	-0.1178	0.4419	-0.0092	0.1462	31.1447	-4.3418	18.5832
17	2.9825	-3.3523	2.3425	8.2741	-1.9945	1.9337	0.1098	0.5498	0.1793	-0.1196	-0.2752	-0.1246	0.0682	0.503	0.1654	0.1218	0.0367	-0.0776	0.3887	0.0263	0.1361	30.7474	1.905	11.0978
18	0.7101	-1.5259	1.4168	6.8789	-0.3462	5.3306	-0.0991	0.1627	0.1079	0.6503	-0.1369	-0.1361	0.2917	0.2038	0.2361	0.2448	0.0591	-0.094	0.3043	0.0317	0.1695	30.0277	-5.198	13.0452
19	17.3458	-18.5654	11.0473	22.1951	-10.1298	8.4621	-0.4045	-0.0446	0.8496	0.5827	0.0689	-1.1047	-0.079	0.2116	0.3356	0.1106	-0.0078	-0.0443	0.347	-0.0304	0.3391	35.6403	5.0711	14.4421
20	4.9681	6.0585	-8.6037	15.0197	-4.6192	24.4545	-0.1552	-0.7884	-0.3185	1.1851	-0.6107	-0.6838	0.5008	0.1063	0.7659	0.4422	0.3406	-0.2173	0.7962	0.0288	0.3485	38.6263	-4.983	25.809
21	2.062	-0.0317	2.0412	3.9836	-2.186	3.4434	0.2405	-0.2094	-0.4638	0.0266	0.1778	0.4209	0.4586	-0.1495	-0.4183	0.3288	0.1034	0.1533	0.179	0.1815	0.4416	13.4871	-16.9057	-13.1562
22	26.849	-18.4985	0.1725	13.0237	1.1064	6.6463	-0.3271	0.1338	-0.0248	0.3383	-0.0497	0.0122	0.9193	0.076	0.3768	0.3179	0.0356	0.0089	0.1646	-0.0505	0.2657	11.7779	-18.0972	-16.963
23	1.2951	-0.5107	-0.3166	2.185	0.1633	2.3428	-0.0584	0.204	-0.2333	-0.1186	0.051	-0.1726	0.2412	0.2891	0.0073	0.1225	0.0544	0.0199	0.1658	-0.001	0.171	15.8619	-7.703	-21.0169
24	23.1648	-8.2445	-1.5397	9.657	10.5836	15.0847	0.5067	0.0024	-0.0479	0.4775	-0.2202	-0.1503	0.9569	-0.2958	-0.2865	0.2657	-0.0566	-0.0049	0.0428	-0.0995	0.3791	3.8984	-16.0028	-24.8976
25	0.6027	-0.1232	0.1673	0.2472	0.3685	1.6792	-0.0552	0.0002	-0.2233	0.1818	0.1093	-0.0494	0.3087	0.2933	-0.0541	0.2123	0.0859	-0.0194	0.1637	0.0439	0.2396	19.2133	-11.3011	-3.9693
26	0.8125	2.5133	2.3064	11.6862	9.4559	13.8002	0.1106	-0.382	-0.2391	0.1478	-0.6862	0.6659	0.2184	-0.6458	0.5756	0.3017	0.1614	-0.1038	0.4048	0.2664	0.6068	22.8718	-14.4403	11.8893
27	0.6038	-1.6239	0.0245	6.9878	-1.1268	0.4384	0.3436	0.718	-0.5223	0.2378	-0.7602	0.6297	-0.3171	-0.4599	0.4166	0.7768	0.5673	-0.0743	1.7977	-0.8941	1.1583	13.7978	-15.8793	22.7429
28	8.9571	-5.187	-10.3265	7.8273	9.387	21.4089	0.0166	-0.364	-0.2516	0.2631	-0.0611	0.3347	0.3604	0.5967	0.0445	0.1158	0.0538	-0.029	0.1242	0.0363	0.1947	22.7884	-11.0713	8.632
29	4.8677	1.479	1.2618	9.823	7.5277	6.0472	-0.2389	-0.927	-0.8227	1.6321	-0.2575	1.2696	1.3982	-0.0805	0.4963	0.8939	0.1528	0.1331	0.4607	0.2022	0.7824	19.4778	-16.2696	23.0405
30	0.8975	-5.6827	-3.668	38.3128	24.9083	16.2123	0.2691	0.1214	-0.0259	-0.5462	-0.3432	0.1784	-0.2781	-0.1608	0.074	0.731	0.0827	0.0337	0.5129	0.0161	0.4651	25.4826	-14.8387	32.8628

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	C	120 - 127
2	X-RAY DIFFRACTION	2	C	128 - 136
3	X-RAY DIFFRACTION	3	C	137 - 154
4	X-RAY DIFFRACTION	4	C	155 - 166
5	X-RAY DIFFRACTION	5	C	167 - 178
6	X-RAY DIFFRACTION	6	C	179 - 187
7	X-RAY DIFFRACTION	7	C	188 - 196
8	X-RAY DIFFRACTION	8	C	197 - 208
9	X-RAY DIFFRACTION	9	C	209 - 221
10	X-RAY DIFFRACTION	10	C	222 - 226
11	X-RAY DIFFRACTION	11	H	1 - 5
12	X-RAY DIFFRACTION	12	H	6 - 23
13	X-RAY DIFFRACTION	13	H	24 - 61
14	X-RAY DIFFRACTION	14	H	62 - 83
15	X-RAY DIFFRACTION	15	H	84 - 119
16	X-RAY DIFFRACTION	16	H	120 - 145
17	X-RAY DIFFRACTION	17	H	146 - 165
18	X-RAY DIFFRACTION	18	H	166 - 195
19	X-RAY DIFFRACTION	19	H	196 - 213
20	X-RAY DIFFRACTION	20	H	214 - 218
21	X-RAY DIFFRACTION	21	L	1 - 18
22	X-RAY DIFFRACTION	22	L	19 - 24
23	X-RAY DIFFRACTION	23	L	25 - 65
24	X-RAY DIFFRACTION	24	L	66 - 70
25	X-RAY DIFFRACTION	25	L	71 - 127
26	X-RAY DIFFRACTION	26	L	128 - 145
27	X-RAY DIFFRACTION	27	L	146 - 156
28	X-RAY DIFFRACTION	28	L	157 - 180
29	X-RAY DIFFRACTION	29	L	181 - 208
30	X-RAY DIFFRACTION	30	L	209 - 213

-
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