PDB-4zk7: Crystal structure of rescued two-component self-assembling tetrah...

ID or keywords:

Entry

Database: PDB / ID: 4zk7

Title

Crystal structure of rescued two-component self-assembling tetrahedral cage T33-31

Components

Chorismate mutase
Divalent-cation tolerance protein CutA

Keywords

PROTEIN BINDING /

Tetrahedral / computational design / Rosetta /

self-assembly /

symmetric /

nanomaterial /

solubility

Function / homology

Function and homology information

chorismate metabolic process /

chorismate mutase /

chorismate mutase activity / response to metal ion / aromatic amino acid family biosynthetic process / amino acid biosynthetic process /

cytoplasm
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 3.4 Å

Authors

Liu, Y. / Cascio, D. / Sawaya, M.R. / Bale, J. / Collazo, M.J. / Park, R. / King, N. / Baker, D. / Yeates, T.

Citation

Journal: Protein Sci. / Year: 2015
Title: Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression.
Authors: Bale, J.B. / Park, R.U. / Liu, Y. / Gonen, S. / Gonen, T. / Cascio, D. / King, N.P. / Yeates, T.O. / Baker, D.

History

Deposition	Apr 30, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 29, 2015	Provider: repository / Type: Initial release
Revision 1.1	Oct 7, 2015	Group: Database references
Revision 1.2	Nov 1, 2017	Group: Author supporting evidence / Database references / Derived calculations Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Mar 6, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4zk7.cif.gz	1016.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4zk7.ent.gz	859.1 KB	Display	PDB format
PDBx/mmJSON format	4zk7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zk/4zk7 ftp://data.pdbj.org/pub/pdb/validation_reports/zk/4zk7	HTTPS FTP

-
Related structure data

Similar structure data	5wdk-d 3k35-d 3134 2rd5-1 1z02-3 6lyg-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	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (5)

Deposited unit

A: Chorismate mutase

B: Chorismate mutase

C: Chorismate mutase

D: Chorismate mutase

E: Chorismate mutase

F: Chorismate mutase

G: Chorismate mutase

H: Chorismate mutase

I: Chorismate mutase

J: Chorismate mutase

K: Chorismate mutase

L: Chorismate mutase

M: Divalent-cation tolerance protein CutA

N: Divalent-cation tolerance protein CutA

O: Divalent-cation tolerance protein CutA

P: Divalent-cation tolerance protein CutA

Q: Divalent-cation tolerance protein CutA

R: Divalent-cation tolerance protein CutA

S: Divalent-cation tolerance protein CutA

T: Divalent-cation tolerance protein CutA

U: Divalent-cation tolerance protein CutA

V: Divalent-cation tolerance protein CutA

W: Divalent-cation tolerance protein CutA

X: Divalent-cation tolerance protein CutA

324 kDa, 24 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, scanning transmission electron microscopy

Unit cell

Length a, b, c (Å)	121.100, 128.400, 204.700
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Details

Tetrahedral cage from two protein components by gel filtration, SEC, EM

#1: Protein	Chorismate mutase / Mass: 14495.646 Da / Num. of mol.: 12 / Fragment: Chorismate mutase / Mutation: E17A, H20L, Q21A, R24I, Q64L, R109N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0868 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJY4
#2: Protein	Divalent-cation tolerance protein CutA Mass: 12544.401 Da / Num. of mol.: 12 / Fragment: Divalent cation tolerance protein Mutation: E12A, E13L, R16V, T17K, K20H, W43E, Q44E, E46S, E49S, Q51H, H62D, A73E, T78E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria) Strain: HB8 / ATCC 27634 / DSM 579 / Gene: cutA, TTHA1356 / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIA8

#1: Protein

Chorismate mutase /

Mass: 14495.646 Da / Num. of mol.: 12 / Fragment: Chorismate mutase / Mutation: E17A, H20L, Q21A, R24I, Q64L, R109N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA0868 / Plasmid: pET29b / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5SJY4

#2: Protein

Divalent-cation tolerance protein CutA

Mass: 12544.401 Da / Num. of mol.: 12 / Fragment: Divalent cation tolerance protein
Mutation: E12A, E13L, R16V, T17K, K20H, W43E, Q44E, E46S, E49S, Q51H, H62D, A73E, T78E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: cutA, TTHA1356 / Plasmid: pET29b / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7SIA8

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.84 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM HEPES pH 7.5, 9% (w/v) PEG 8000, 11.7% (v/v) ethylene glycol

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.942 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2014

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.942 Å / Relative weight: 1

Reflection

Resolution: 3.25→88.1 Å / Num. obs: 49099 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 4 % / B_iso Wilson estimate: 90.95 Å² / R_merge F obs: 0.984 / R_merge(I) obs: 0.205 / R_rim(I) all: 0.233 / Χ²: 0.917 / Net I/σ(I): 5.54 / Num. measured all: 198097

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
3.25-3.33	0.733	0.606	1.2	5018	3721	2485	0.777	66.8
3.33-3.43	0.687	0.748	1.43	10329	3630	3364	0.899	92.7
3.43-3.53	0.779	0.625	1.76	11685	3519	3508	0.742	99.7
3.53-3.63	0.893	0.522	2.65	15234	3426	3417	0.586	99.7
3.63-3.75	0.913	0.442	3.08	14702	3342	3325	0.496	99.5
3.75-3.88	0.932	0.383	3.56	14011	3236	3218	0.431	99.4
3.88-4.03	0.948	0.307	4.31	13053	3121	3091	0.347	99
4.03-4.2	0.955	0.263	4.92	11781	2990	2938	0.3	98.3
4.2-4.38	0.976	0.216	6.35	12801	2875	2865	0.241	99.7
4.38-4.6	0.977	0.201	6.97	12202	2764	2748	0.226	99.4
4.6-4.84	0.979	0.177	7.67	11497	2644	2632	0.199	99.5
4.84-5.14	0.978	0.175	7.53	10656	2491	2479	0.197	99.5
5.14-5.49	0.968	0.194	6.45	9202	2346	2325	0.221	99.1
5.49-5.93	0.968	0.207	6.34	9684	2198	2181	0.233	99.2
5.93-6.5	0.972	0.192	6.87	8958	2025	2011	0.215	99.3
6.5-7.27	0.981	0.147	8.5	7973	1859	1849	0.165	99.5
7.27-8.39	0.989	0.099	11.16	6374	1642	1624	0.113	98.9
8.39-10.28	0.993	0.081	14.7	6062	1401	1384	0.091	98.8
10.28-14.53	0.994	0.069	16.13	4524	1117	1078	0.078	96.5
14.53-88.1	0.996	0.061	15.9	2351	657	577	0.069	87.8

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.5.6	phasing
BUSTER	2.10.0	refinement
PDB_EXTRACT	3.15	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.4→88.1 Å / Cor.coef. F_o:F_c: 0.889 / Cor.coef. F_o:F_c free: 0.8487 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R_free Blow DPI: 0.539

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2388	2219	5.02 %	RANDOM
R_work	0.1895	-	-	-
obs	0.192	44218	99.09 %	-

Displacement parameters

B_iso max: 204.2 Å² / B_iso mean: 72.64 Å² / B_iso min: 11.57 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-37.3769 Å²	0 Å²	0 Å²
2-	-	16.0693 Å²	0 Å²
3-	-	-	21.3076 Å²

Refine analyze

Luzzati coordinate error obs: 0.644 Å

Refinement step

Cycle: final / Resolution: 3.4→88.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20510	0	0	0	20510
Num. residues	-	-	-	-	2646

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	7454	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes	456	HARMONIC	2
X-RAY DIFFRACTION	t_gen_planes	3022	HARMONIC	5
X-RAY DIFFRACTION	t_it	21042	HARMONIC	20
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_chiral_improper_torsion	2850	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	25019	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	21042	HARMONIC	2	0.01
X-RAY DIFFRACTION	t_angle_deg	28742	HARMONIC	2	1.2
X-RAY DIFFRACTION	t_omega_torsion				2.68
X-RAY DIFFRACTION	t_other_torsion				18.96

LS refinement shell

Resolution: 3.4→3.49 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3446	158	4.89 %
R_work	0.2416	3076	-
all	0.2466	3234	-
obs	-	-	99.09 %

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	0.421	0.5109	-0.31	3.0067	1.5965	2.3992	0.0303	0.133	0.0291	-0.2639	0.0203	-0.2859	-0.1946	0.1421	-0.0506	0.06	-0.0016	0.0148	-0.0652	0.0004	-0.1293	63.1426	10.3522	29.6006
2	1.9	-0.3919	-0.8385	1.8227	-0.0592	0.9564	-0.0177	-0.0058	-0.0082	0.1215	0.0834	-0.1237	0.2282	0.1798	-0.0658	0.112	0.0205	-0.0422	-0.0874	0.0496	-0.1219	56.7086	-2.2066	45.8041
3	2.3327	0.2761	-0.7407	3.6014	0.2989	2.1372	-0.124	-0.0211	-0.2259	0.0871	0.0367	0.5439	0.0705	-0.3896	0.0874	-0.1543	-0.0023	0.0342	-0.066	0.0084	-0.0215	-1.0639	4.2406	42.4488
4	3.8666	-0.5295	0.4405	2.0555	0.0348	1.4966	0.0995	-0.1263	0.1975	0.0584	-0.0472	-0.0197	-0.0264	-0.0989	-0.0523	0.0758	0.0552	-0.0096	-0.1021	-0.0333	-0.1283	53.4758	19.0765	47.0088
5	2.5118	-1.3685	0.2362	1.8604	-0.5304	0.8175	-0.1518	0.0162	0.2214	0.1122	0.022	0.2078	-0.1821	-0.2	0.1297	-0.066	0.0029	0.0571	-0.0579	-0.0965	-0.0186	8.0784	23.4565	45.9822
6	0.7305	0.6978	-0.0039	2.4646	0.0094	1.7392	-0.1147	-0.1671	0.0362	0.3477	0.041	0.1197	0.144	-0.1203	0.0737	0.0077	0.0639	0.0578	-0.0073	0.0165	-0.1245	13.9461	6.4552	57.836
7	2.816	0.4594	0.2937	0.7336	0.5186	0.9994	0.0793	-0.0303	-0.2944	-0.0792	-0.146	0.1655	0.152	-0.1333	0.0667	0.1683	-0.0012	0.0031	-0.0902	0.0216	-0.1434	23.7443	-28.7178	30.3781
8	0.7089	-0.3798	0.0938	5.1902	-0.0662	1.7648	-0.0513	0.2074	-0.1483	-0.096	0.1211	-0.0215	0.237	0.2776	-0.0698	0.0484	0.0049	-0.0134	-0.0139	-0.0385	-0.1479	39.1031	-25.4304	15.4724
9	1.5801	-0.1918	-0.5411	1.2087	0.2664	1.9868	0.0441	0.0284	-0.0465	-0.0776	-0.0283	0.268	0.2203	-0.0303	-0.0158	0.0703	-0.0519	-0.0828	-0.134	-0.0359	-0.0566	18.3532	-22.0516	10.5692
10	0.8391	0.3216	0.3293	1.8086	-0.101	1.7836	-0.0072	0.1759	0.056	-0.3251	0.0042	-0.026	0.0761	0.2724	0.003	0.1964	0.0021	0.0051	-0.0567	-0.0096	-0.1756	33.481	15.1965	-3.6266
11	1.9687	-0.5737	0.1446	2.6108	-0.1725	2.6492	0.0712	0.074	0.2028	-0.2882	0.0917	0.1465	-0.1182	0.2088	-0.1629	0.1097	-0.0261	-0.0962	-0.1218	-0.0593	-0.1337	33.1506	32.4983	9.3209
12	2.3809	0.4469	-0.6786	1.8892	-0.7005	4.2385	-0.0722	0.0921	0.0993	-0.2028	0.0817	0.2347	0.0714	-0.2757	-0.0094	0.016	0.0399	-0.073	-0.0822	-0.0615	-0.1144	14.6512	22.6677	3.9383
13	2.9743	-0.9611	1.064	4.5663	0.8058	1.7263	-0.0118	0.348	0.0536	-0.3953	0.0811	0.2258	-0.1197	0.0281	-0.0693	0.0251	-0.0598	-0.152	-0.1145	-0.027	-0.1254	-4.5833	2.9067	0.061
14	3.321	-0.8038	-0.2557	0	-0.5167	3.5973	0.0113	-0.3642	-0.1924	0.0369	0.0491	0.5376	-0.2647	-0.3418	-0.0604	-0.2057	0.0515	-0.0827	-0.1258	-0.0274	0.0822	-13.485	5.144	17.485
15	2.1898	0.0186	0.249	2.7152	0.5272	0	0.0055	0.0661	-0.2762	-0.204	0.0454	0.3882	0.5032	-0.2039	-0.0509	-0.119	-0.051	-0.1433	-0.1478	-0.0622	0.1129	-7.8391	-12.6989	11.5466
16	0.659	-0.3113	0.2555	3.1069	0.3463	0.8668	-0.0747	0.024	-0.3448	0.2071	0.0735	0.0988	-0.1121	-0.147	0.0012	0.0651	0.0218	0.0214	-0.0464	0.0983	-0.122	36.4085	-29.3291	55.1454
17	0.8753	0.1748	0.338	0	-0.0019	0.2676	-0.0322	-0.316	0.0772	0.3888	-0.0083	0.1982	-0.0297	-0.2749	0.0404	0.2084	0.0017	0.0946	-0.0443	0.0722	-0.1193	22.3514	-18.7846	66.1838
18	2.073	0.0833	-0.5526	2.0837	-0.2464	1.4736	0.0235	-0.2184	0.1816	0.2692	-0.0177	-0.4396	-0.0044	0.1643	-0.0058	0.2019	0.0123	-0.0514	-0.0451	0.0072	-0.2477	41.8289	-13.6476	65.7645
19	1.1933	-0.0827	0.6123	1.0016	0.5346	4.4102	-0.0054	0.4471	0.0953	-0.5394	-0.043	-0.2089	-0.27	0.0876	0.0484	0.1148	-0.0473	0.0871	-0.0209	-0.0326	-0.1833	59.494	5.5725	-5.2164
20	0.0004	-0.2345	-0.2133	3.3309	-0.3047	1.4998	-0.0554	0.2834	-0.4066	-0.5406	0.1004	-0.0368	0.2847	-0.0258	-0.045	0.2367	-0.0207	0.0188	-0.0609	-0.101	-0.2216	54.5623	-13.359	-4.27
21	2.1622	0.2227	1.4915	2.4811	0.6156	1.3619	0.0553	-0.056	-0.0783	-0.0095	0.0506	-0.5429	0.1459	0.4581	-0.1059	0.052	0.0911	0.0706	-0.0761	-0.0682	-0.1193	68.1333	-6.1193	7.9142
22	2.4529	1.8871	-0.2326	0.3403	0.6668	2.6913	0.0363	-0.3886	0.193	0.3888	-0.0344	0.3211	-0.2256	-0.3095	-0.0019	0.062	0.0164	0.014	-0.1173	-0.0942	-0.107	27.1274	43.18	49.7406
23	2.4474	-0.4755	-0.161	2.7371	-0.8197	3.5825	-0.0982	0.3607	0.2727	-0.0877	0.0454	0.3666	-0.3425	-0.2004	0.0528	0.0951	0.0739	-0.0849	-0.2107	-0.0427	-0.0926	27.7609	48.9966	31.0341
24	1.045	0.6452	1.194	2.4675	-0.4311	4.0355	-0.0067	-0.03	0.0856	-0.0139	-0.3373	-0.3461	-0.1602	0.4592	0.344	-0.0523	-0.0326	-0.0405	-0.0757	0.0065	-0.0353	44.3511	44.7957	40.6323

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ A\|* }	A	1 - 117
2	X-RAY DIFFRACTION	2	{ B\|* }	B	1 - 117
3	X-RAY DIFFRACTION	3	{ C\|* }	C	1 - 117
4	X-RAY DIFFRACTION	4	{ D\|* }	D	1 - 117
5	X-RAY DIFFRACTION	5	{ E\|* }	E	1 - 117
6	X-RAY DIFFRACTION	6	{ F\|* }	F	1 - 117
7	X-RAY DIFFRACTION	7	{ G\|* }	G	1 - 117
8	X-RAY DIFFRACTION	8	{ H\|* }	H	1 - 117
9	X-RAY DIFFRACTION	9	{ I\|* }	I	1 - 117
10	X-RAY DIFFRACTION	10	{ J\|* }	J	1 - 117
11	X-RAY DIFFRACTION	11	{ K\|* }	K	1 - 117
12	X-RAY DIFFRACTION	12	{ L\|* }	L	1 - 117
13	X-RAY DIFFRACTION	13	{ M\|* }	M	1 - 103
14	X-RAY DIFFRACTION	14	{ N\|* }	N	1 - 103
15	X-RAY DIFFRACTION	15	{ O\|* }	O	1 - 103
16	X-RAY DIFFRACTION	16	{ P\|* }	P	1 - 103
17	X-RAY DIFFRACTION	17	{ Q\|* }	Q	1 - 109
18	X-RAY DIFFRACTION	18	{ R\|* }	R	1 - 103
19	X-RAY DIFFRACTION	19	{ S\|* }	S	1 - 103
20	X-RAY DIFFRACTION	20	{ T\|* }	T	1 - 103
21	X-RAY DIFFRACTION	21	{ U\|* }	U	1 - 103
22	X-RAY DIFFRACTION	22	{ V\|* }	V	1 - 103
23	X-RAY DIFFRACTION	23	{ W\|* }	W	1 - 103
24	X-RAY DIFFRACTION	24	{ X\|* }	X	1 - 103

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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