PDB-5mi0: A thermally stabilised version of Plasmodium falciparum RH5

ID or keywords:

Entry

Database: PDB / ID: 5mi0

Title

A thermally stabilised version of Plasmodium falciparum RH5

Components

(MONOCLONAL ANTIBODY 9AD4) x 2
Reticulocyte binding-like protein 5,Reticulocyte binding protein 5

Keywords

IMMUNE SYSTEM / malaria immunogen design Rosetta PROSS

Function / homology

Function and homology information

rhoptry lumen / rhoptry / symbiont entry into host / host cell membrane / bicellular tight junction / apical part of cell / heparin binding / cytoplasmic vesicle / host extracellular space / host cell surface receptor binding ...
Similarity search - Function

Biological species

Plasmodium falciparum (malaria parasite P. falciparum)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.35 Å

Authors

Campeotto, I. / Goldenzweig, A. / Davey, J. / Barfod, L. / Marshall, J.M. / Silk, S.E. / Wright, K.E. / Draper, S.J. / Higgins, M.K. / Fleishman, S.J.

Funding support

United Kingdom, 1items

Citation

Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: One-step design of a stable variant of the malaria invasion protein RH5 for use as a vaccine immunogen.
Authors: Campeotto, I. / Goldenzweig, A. / Davey, J. / Barfod, L. / Marshall, J.M. / Silk, S.E. / Wright, K.E. / Draper, S.J. / Higgins, M.K. / Fleishman, S.J.

History

Deposition	Nov 27, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 28, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jan 25, 2017	Group: Database references
Revision 1.2	Feb 8, 2017	Group: Database references
Revision 1.3	Jan 17, 2024	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5mi0.cif.gz	315.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5mi0.ent.gz	255.5 KB	Display	PDB format
PDBx/mmJSON format	5mi0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5mi0_validation.pdf.gz	447.8 KB	Display	wwPDB validaton report
Full document	5mi0_full_validation.pdf.gz	452.1 KB	Display
Data in XML	5mi0_validation.xml.gz	28 KB	Display
Data in CIF	5mi0_validation.cif.gz	40.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mi/5mi0 ftp://data.pdbj.org/pub/pdb/validation_reports/mi/5mi0	HTTPS FTP

-
Related structure data

Related structure data	4u0rS S: Starting model for refinement
Similar structure data	4u0r-d 4u6v-2 4en3-d 4u6v-1 6c08-2 3dxa-1 6ol5-d 4jrx-d 4qrr-d 2ypl-d 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)

Deposited unit

A: Reticulocyte binding-like protein 5,Reticulocyte binding protein 5

B: MONOCLONAL ANTIBODY 9AD4

C: MONOCLONAL ANTIBODY 9AD4

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	39.656, 85.547, 132.873
Angle α, β, γ (deg.)	90.00, 90.91, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Reticulocyte binding-like protein 5,Reticulocyte binding protein 5 Mass: 43842.387 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: Rh5 / Production host: Escherichia coli (E. coli) References: UniProt: A0A159SJI5, UniProt: B2L3N7, UniProt: Q8IFM5*PLUS
#2: Antibody	MONOCLONAL ANTIBODY 9AD4 Mass: 27641.205 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Oryctolagus cuniculus (rabbit)
#3: Antibody	MONOCLONAL ANTIBODY 9AD4 Mass: 26259.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Oryctolagus cuniculus (rabbit)
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 261 / 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: 2.31 Å³/Da / Density % sol: 46.65 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 18% glycerol 22% PEG 1500 and additive: 0.02M HEPES sodium pH 6.8 and benzidine nicotinamide, pyromellitic acid and sulfaguanidine, each at 0.25% w/v

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 4, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.35→42.77 Å / Num. obs: 36539 / % possible obs: 98.6 % / Redundancy: 6.5 % / B_iso Wilson estimate: 49.1 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.096 / Net I/σ(I): 13.9
Reflection shell	Resolution: 2.35→2.43 Å / Redundancy: 6.9 % / R_merge(I) obs: 0.554 / Mean I/σ(I) obs: 3.1 / CC_1/2: 0.832 / % possible all: 97.9

-
Processing

Software

Name	Version	Classification
BUSTER	2.10.2	refinement
PHENIX	1.9	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4U0R

4u0r

Resolution: 2.35→32.91 Å / Cor.coef. F_o:F_c: 0.9498 / Cor.coef. F_o:F_c free: 0.9201 / SU R Cruickshank DPI: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.284 / SU R_free Blow DPI: 0.209 / SU R_free Cruickshank DPI: 0.212

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.222	1798	4.93 %	RANDOM
R_work	0.1763	-	-	-
obs	0.1786	36504	98.37 %	-

Displacement parameters

B_iso mean: 50.44 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.707 Å²	0 Å²	-1.8019 Å²
2-	-	-2.1608 Å²	0 Å²
3-	-	-	1.4538 Å²

Refine analyze

Luzzati coordinate error obs: 0.343 Å

Refinement step

Cycle: 1 / Resolution: 2.35→32.91 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5747	0	0	261	6008

Refine LS restraints

Refine-ID	Type	Dev ideal	Number	Restraint function	Weight
X-RAY DIFFRACTION	t_bond_d	0.01	5891	HARMONIC	2
X-RAY DIFFRACTION	t_angle_deg	1.11	7978	HARMONIC	2
X-RAY DIFFRACTION	t_dihedral_angle_d		2023	SINUSOIDAL	2
X-RAY DIFFRACTION	t_incorr_chiral_ct
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_trig_c_planes		140	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes		839	HARMONIC	5
X-RAY DIFFRACTION	t_it		5891	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_omega_torsion	3.29
X-RAY DIFFRACTION	t_other_torsion	18.9
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_chiral_improper_torsion		785	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact		6619	SEMIHARMONIC	4

LS refinement shell

Resolution: 2.35→2.42 Å / Total num. of bins used: 18

	R_factor	Num. reflection	% reflection
R_free	0.3056	141	4.79 %
R_work	0.2156	2805	-
all	0.2196	2946	-
obs	-	-	98.37 %

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	0.1122	2.1365	0.1309	2.6668	1.89	3.2762	-0.0033	-0.0127	0.2016	-0.1287	-0.0622	0.0213	0.3315	0.0581	0.0655	0.286	-0.0061	-0.054	-0.1469	-0.1037	-0.2384	-9.2642	-102.484	477.097
2	4.0389	1.2924	1.7709	0.4309	0.8416	2.7167	0.2618	0.2827	0.0827	0.0466	-0.2159	-0.0547	1.0937	-0.0557	-0.0459	0.2462	-0.0238	0.07	-0.2587	-0.0227	-0.3064	3.7053	-93.6417	493.4601
3	0.2732	5.3114	1.3505	1.3737	-1.6102	1.273	0.0341	0.0528	-0.205	0.091	-0.0261	0.2799	-0.0228	-0.1481	-0.0079	0.5561	-0.2932	0.0578	-0.1926	-0.1936	-0.4623	-15.8248	-110.795	479.6422
4	-0.0257	1.1	0.8092	0.7436	-3.0667	0.0257	0.0074	-0.0119	-0.0206	-0.0731	-0.0267	0.0724	0.0329	0.0054	0.0193	0.4083	-0.0329	-0.0724	-0.1546	-0.256	-0.1781	-21.5123	-111.553	465.337
5	3.0739	2.9409	-1.4358	1.8371	0.1311	0.0743	0.0892	-0.0674	0.0524	-0.0587	0.0171	0.3266	-0.0285	-0.247	-0.1063	0.084	-0.2742	0.1256	-0.1643	-0.3084	-0.2206	-22.7598	-104.507	478.2258
6	2.0316	0.8827	-0.7704	0.0107	0.6586	0.436	0.0144	-0.036	-0.0739	0.0602	0.0956	-0.0092	0.0711	-0.1011	-0.11	0.2691	-0.2867	0.3057	-0.0095	-0.1818	-0.1534	-16.9197	-99.0427	493.6675
7	2.2421	1.8918	1.2208	2.2009	1.2252	3.5986	0.1743	0.1722	0.3914	0.2834	-0.1787	-0.0158	0.7208	0.129	0.0044	0.0437	0.0491	0.0756	-0.2496	0.0099	-0.2292	8.3633	-84.7508	492.5039
8	1.6882	0.0565	0.1927	3.602	-0.144	0.0057	0.0233	-0.1853	0.0139	-0.267	-0.0304	0.0652	-0.1952	0.4977	0.0072	0.3754	-0.1154	-0.1255	-0.1035	0.0316	-0.4363	-4.3168	-90.785	460.0685
9	-0.0536	0.2601	1.6719	0	-0.1876	1.9562	0.0019	-0.0082	0.117	-0.0674	-0.0458	0.0308	-0.0728	-0.0748	0.0439	0.288	0.1589	-0.2499	0.0134	-0.2103	-0.1432	-21.3619	-101.86	453.956
10	0.2532	1.3073	2.5501	1.0961	-1.1649	1.191	-0.003	-0.0465	0.191	0.0899	-0.1687	0.2011	-0.1416	-0.0155	0.1718	0.117	0.1557	-0.2467	-0.107	-0.1994	-0.1346	-15.8158	-95.7869	465.5895
11	1.609	0.8868	1.8962	1.9226	3.2774	4.4983	-0.0662	0.1752	0.4556	-0.4967	-0.0043	0.3399	-0.1014	0.1167	0.0705	0.0498	-0.033	-0.083	-0.1556	0.0624	-0.2052	5.5755	-77.5755	481.5053
12	2.5177	2.9226	4.4834	4.4436	5.4122	6.5024	0.0815	0.2715	-0.062	-0.388	-0.0566	0.0634	0.0419	0.1191	-0.0249	0.1753	-0.0385	-0.0358	-0.0437	0.0005	-0.1371	-4.4141	-94.3625	471.9894
13	6.019	0.2908	-3.5716	2.6436	-1.912	7.1693	-0.0585	0.0867	0.1785	0.1208	0.3561	-0.4443	-0.4023	-0.4308	-0.2976	-0.1413	0.0291	-0.0289	-0.1772	-0.0139	-0.0419	2.7753	-78.9322	524.1342
14	5.7178	1.616	0.8114	5.6974	3.04	0.054	-0.1503	0.071	-0.2804	0.2458	0.2601	-0.0211	-0.0819	-0.165	-0.1098	-0.0918	-0.0657	0.0239	-0.006	0.0466	-0.0992	-4.6731	-90.7171	526.9442
15	0.0553	0.2354	2.6974	3.9901	-0.8581	5.2564	-0.0153	-0.0933	-0.104	-0.57	0.4433	0.2312	0.1328	-0.9872	-0.428	-0.1261	-0.1269	-0.064	0.1193	0.1148	-0.0627	-6.1365	-82.7597	514.8915
16	-0.0682	0.4152	2.1244	0.19	-4.4498	2.8126	-0.0538	-0.028	0.2288	-0.0787	0.1365	-0.1264	-0.4098	-0.232	-0.0827	-0.1269	-0.0392	0.034	-0.1167	-0.016	0.0448	2.7325	-74.4554	518.0717
17	1.1946	-2.4152	-0.6345	4.8084	-1.4842	3.7595	-0.0546	0.0361	0.0935	-0.5519	0.3649	0.0465	0.3112	-0.8664	-0.3103	-0.037	-0.1193	-0.0213	-0.013	0.0075	-0.0477	-0.2935	-87.8525	520.244
18	0.4423	1.2348	-1.5863	0	-0.3186	3.7121	0.1036	0.1016	0.0572	0.0177	0.1577	0.1479	-0.395	-0.2067	-0.2614	-0.1142	0.2066	-0.0028	-0.0843	0.0678	-0.0478	-4.4685	-82.0789	541.6543
19	1.9841	1.1536	-0.9726	2.2163	0.3095	0.0848	-0.0648	-0.1197	0.0177	0.2943	0.094	0.1452	0.0475	0.1136	-0.0292	-0.1609	0.0487	-0.008	-0.0227	0.0085	-0.0714	-3.9135	-96.9932	568.2395
20	2.9198	-4.0409	-0.8378	4.4431	1.1453	-0.0274	0.0095	-0.4037	-0.0456	0.1864	0.1536	0.2111	0.2092	0.3044	-0.1631	-0.1885	0.0221	-0.0635	-0.0007	0.0377	-0.0722	1.9701	-100.943	566.2747
21	2.3082	-0.1407	-0.5076	0.0009	0.3733	5.2109	0.2423	0.2188	0.4066	-0.0665	-0.148	-0.1812	-0.462	-0.0404	-0.0942	-0.1048	0.0359	0.0282	-0.1115	0.0331	0.026	0.6583	-85.0593	553.3903
22	0.3238	1.6649	-2.9245	1.7452	1.2944	1.1406	0.0195	0.0875	-0.284	-0.2687	-0.0785	0.0878	-0.3134	-0.1537	0.059	-0.0238	0.0664	-0.0141	0.0171	0.025	-0.061	-1.15	-92.3642	551.2943
23	3.8834	-2.6455	1.5828	1.8035	-1.4911	4.2453	0.0774	-0.2217	0.3766	0.0435	0.0201	-0.1322	-0.2518	-0.1455	-0.0975	-0.0848	0.004	0.0137	-0.016	0.0059	0.015	2.7127	-89.069	560.2377
24	6.4923	0.8845	0.4234	2.2237	3.0268	0.0118	0.155	-0.2603	0.1315	0.2712	0.0029	-0.2022	-0.0243	-0.079	-0.158	-0.1435	0.0666	0.0187	0.0822	-0.0963	-0.0033	0.0746	-86.6503	566.8697
25	1.4784	0.2673	1.6453	3.9394	-3.5542	4.8136	-0.335	0.0963	-0.3939	-0.7006	0.4068	0.0082	1.0508	-0.6012	-0.0718	0.1579	-0.2444	0.0816	-0.1601	-0.0478	-0.2003	2.8808	-109.281	528.4704
26	2.3369	-1.1747	1.9301	0.8918	0.416	3.2823	-0.0463	0.0519	-0.0845	-0.9885	0.1587	-0.0231	0.7751	-0.4004	-0.1124	0.4794	-0.2691	-0.0478	-0.2435	0.0101	-0.2328	0.4846	-103.248	515.9468
27	0.5547	1.1205	-1.5952	3.922	-1.1173	-0.0508	-0.1064	-0.117	0.3832	0.0497	0.057	-0.2931	-0.046	-0.0007	0.0494	-0.0216	-0.007	0.0227	-0.1821	-0.0683	-0.0687	8.8322	-94.8462	529.363
28	1.53	-3.0555	-1.345	2.4796	-4.2326	2.5632	-0.0966	0.2579	-0.0734	-0.8178	-0.0303	-0.4133	0.8346	0.2097	0.127	0.3618	-0.1112	0.1962	-0.2852	-0.0238	-0.0728	11.0554	-103.946	518.365
29	5.5826	-0.8713	1.1354	4.13	-4.8769	2.274	-0.1374	0.0383	-0.3297	-0.5393	0.0056	-0.2592	0.6386	0.2299	0.1318	0.2532	-0.0737	0.1814	-0.2247	-0.0497	-0.1078	10.7166	-109.373	526.0225
30	4.7397	-0.5616	1.0631	6.3953	-4.1712	1.7738	-0.3338	0.0822	-0.1342	-0.6685	0.3719	-0.0451	0.7004	-0.1871	-0.0381	-0.0762	-0.1351	0.0559	-0.2842	-0.0524	-0.2351	3.4841	-100.749	524.7565
31	0.3136	-0.8667	-0.5789	3.1335	-2.2596	0.3412	-0.379	0.2328	-0.3684	-0.4568	0.4881	-0.0104	0.4411	-0.1491	-0.1091	0.0523	-0.2232	-0.0355	0.0545	-0.0229	-0.1241	0.4123	-101.556	527.6271
32	5.0116	-2.5463	-2.9937	2.2872	1.6153	1.9637	0.0856	-0.2508	-0.0793	-0.1484	0.0152	0.0355	0.1197	-0.0544	-0.1007	-0.2154	0.0152	-0.0103	-0.0677	-0.0098	-0.1047	-5.1982	-99.107	559.58
33	-0.0163	1.4411	0.701	2.4099	1.525	2.1875	-0.0688	0.1083	-0.2656	0.039	-0.189	0.4692	0.075	-0.5795	0.2578	-0.2163	-0.0135	-0.029	0.0713	-0.0641	0.012	-10.566	-107.501	553.16
34	9.3502	-3.7092	-5.2694	2.3826	2.2808	2.8394	0.1025	0.4771	-0.2799	-0.1546	-0.1915	0.1448	-0.0171	-0.4508	0.0891	-0.1901	0.0118	-0.0304	0.0304	-0.0498	-0.056	-9.2519	-100.658	555.1861
35	0.5456	0.6449	-0.0079	0.6374	0.2946	2.4605	-0.0327	0.2206	-0.2288	0.0418	-0.1476	-0.2555	0.0458	-0.0917	0.1802	0.0549	-0.0368	0.1416	0.0269	-0.023	0.1892	-5.3566	-115.214	555.864
36	0.0026	1.7434	0.1151	0.0937	-1.729	2.899	-0.0647	-0.1547	-0.053	0.1666	0.076	-0.0679	0.0128	-0.1239	-0.0113	-0.1123	0.0667	0.0199	-0.0036	0.0581	0.0004	-13.7181	-101.925	570.7871

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	{ A\|160 - A\|174 }
2	X-RAY DIFFRACTION	2	{ A\|175 - A\|223 }
3	X-RAY DIFFRACTION	3	{ A\|224 - A\|235 }
4	X-RAY DIFFRACTION	4	{ A\|236 - A\|302 }
5	X-RAY DIFFRACTION	5	{ A\|303 - A\|318 }
6	X-RAY DIFFRACTION	6	{ A\|319 - A\|324 }
7	X-RAY DIFFRACTION	7	{ A\|325 - A\|373 }
8	X-RAY DIFFRACTION	8	{ A\|374 - A\|390 }
9	X-RAY DIFFRACTION	9	{ A\|391 - A\|409 }
10	X-RAY DIFFRACTION	10	{ A\|410 - A\|423 }
11	X-RAY DIFFRACTION	11	{ A\|424 - A\|453 }
12	X-RAY DIFFRACTION	12	{ A\|454 - A\|501 }
13	X-RAY DIFFRACTION	13	{ B\|2 - B\|36 }
14	X-RAY DIFFRACTION	14	{ B\|37 - B\|49 }
15	X-RAY DIFFRACTION	15	{ B\|50 - B\|70 }
16	X-RAY DIFFRACTION	16	{ B\|71 - B\|82 }
17	X-RAY DIFFRACTION	17	{ B\|83 - B\|110 }
18	X-RAY DIFFRACTION	18	{ B\|111 - B\|131 }
19	X-RAY DIFFRACTION	19	{ B\|132 - B\|138 }
20	X-RAY DIFFRACTION	20	{ B\|139 - B\|150 }
21	X-RAY DIFFRACTION	21	{ B\|151 - B\|167 }
22	X-RAY DIFFRACTION	22	{ B\|168 - B\|182 }
23	X-RAY DIFFRACTION	23	{ B\|183 - B\|213 }
24	X-RAY DIFFRACTION	24	{ B\|214 - B\|222 }
25	X-RAY DIFFRACTION	25	{ C\|1 - C\|20 }
26	X-RAY DIFFRACTION	26	{ C\|21 - C\|42 }
27	X-RAY DIFFRACTION	27	{ C\|43 - C\|51 }
28	X-RAY DIFFRACTION	28	{ C\|52 - C\|73 }
29	X-RAY DIFFRACTION	29	{ C\|74 - C\|84 }
30	X-RAY DIFFRACTION	30	{ C\|85 - C\|97 }
31	X-RAY DIFFRACTION	31	{ C\|98 - C\|111 }
32	X-RAY DIFFRACTION	32	{ C\|112 - C\|142 }
33	X-RAY DIFFRACTION	33	{ C\|143 - C\|159 }
34	X-RAY DIFFRACTION	34	{ C\|160 - C\|202 }
35	X-RAY DIFFRACTION	35	{ C\|203 - C\|211 }
36	X-RAY DIFFRACTION	36	{ C\|212 - C\|217 }

-
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://pdbjlvh1.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