PDB-2x4f: The Crystal Structure of the human myosin light chain kinase LOC3...

ID or keywords:

Entry

Database: PDB / ID: 2x4f

Title

The Crystal Structure of the human myosin light chain kinase LOC340156.

Components

MYOSIN LIGHT CHAIN KINASE FAMILY MEMBER 4

Keywords

TRANSFERASE /

LUNG /

KINASE /

MYOSIN / BREAST CANCER

Function / homology

Function and homology information

myosin light chain kinase activity /

non-specific serine/threonine protein kinase /

Biological species

HOMO SAPIENS (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.67 Å

Authors

Muniz, J.R.C. / Mahajan, P. / Rellos, P. / Fedorov, O. / Shrestha, B. / Wang, J. / Elkins, J.M. / Daga, N. / Cocking, R. / Chaikuad, A. ...

Citation

Journal: To be Published
Title: The Crystal Structure of the Human Myosin Light Chain Kinase Loc340156
Authors: Muniz, J.R.C. / Mahajan, P. / Rellos, P. / Fedorov, O. / Shrestha, B. / Wang, J. / Elkins, J.M. / Daga, N. / Cocking, R. / Chaikuad, A. / Krojer, T. / Ugochukwu, E. / Yue, W. / von Delft, F. ...

History

Deposition	Jan 29, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 9, 2010	Provider: repository / Type: Initial release
Revision 1.1	Dec 5, 2012	Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2	Jan 24, 2018	Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3	May 8, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	2x4f.cif.gz	138.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2x4f.ent.gz	107.9 KB	Display	PDB format
PDBx/mmJSON format	2x4f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x4/2x4f ftp://data.pdbj.org/pub/pdb/validation_reports/x4/2x4f	HTTPS FTP

-
Related structure data

Similar structure data	4ckj-d 1qga-2 3w29-d 3w28-d 2g1t-4 6n8g-2 4ztn-1 2oic-4 1qfz-2 4fvq-d 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#18 - Jun 2001 Myosin similarity (1)

Deposited unit

A: MYOSIN LIGHT CHAIN KINASE FAMILY MEMBER 4

B: MYOSIN LIGHT CHAIN KINASE FAMILY MEMBER 4

hetero molecules

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

1

A: MYOSIN LIGHT CHAIN KINASE FAMILY MEMBER 4

hetero molecules

defined by author&software
43.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: MYOSIN LIGHT CHAIN KINASE FAMILY MEMBER 4

hetero molecules

defined by author&software
42.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	148.880, 70.650, 96.570
Angle α, β, γ (deg.)	90.00, 118.96, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	65 - 176
2	1	1	1	B	65 - 176
1	2	1	4	A	177 - 186
2	2	1	4	B	177 - 186
1	3	1	4	A	187 - 237
2	3	1	4	B	187 - 237
1	4	1	1	A	238 - 355
2	4	1	1	B	238 - 355

NCS oper: (Code: given
Matrix: (-0.5003, 0.2219, -0.8369), (-0.2325, -0.9655, -0.117), (-0.834, 0.136, 0.5347)
Vector: 99.3039, 104.7071, 61.0736)

-
Protein , 1 types, 2 molecules AB

#1: Protein	MYOSIN LIGHT CHAIN KINASE FAMILY MEMBER 4 / SERINE/THREONINE-PROTEIN KINASE SGK085 / SUGEN KINASE 85 Mass: 42496.262 Da / Num. of mol.: 2 / Fragment: LIGHT CHAIN, RESIDUES 40-388 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: Q86YV6, non-specific serine/threonine protein kinase

#1: Protein

MYOSIN LIGHT CHAIN KINASE FAMILY MEMBER 4 / SERINE/THREONINE-PROTEIN KINASE SGK085 / SUGEN KINASE 85

Mass: 42496.262 Da / Num. of mol.: 2 / Fragment: LIGHT CHAIN, RESIDUES 40-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host:

SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q86YV6,

non-specific serine/threonine protein kinase

-
Non-polymers , 5 types, 259 molecules

#2: Chemical	ChemComp-16X / 4-(2-amino-4-methyl-1,3-thiazol-5-yl)-N-(3-dioxaziridin-3-ylphenyl)pyrimidin-2-amine Mass: 328.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₁₂N₆O₂S
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.62 Å³/Da / Density % sol: 53.12 % / Description: NONE
Crystal grow	Details: 2M AMMONIUM_SULFATE, 2.5% W/V PEG 400, PH 8.0 HEPES

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
Detector	Type: ADSC CCD / Detector: CCD / Date: Dec 9, 2009
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.67→65.13 Å / Num. obs: 25080 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / R_merge(I) obs: 0.04 / Net I/σ(I): 8.4
Reflection shell	Resolution: 2.67→2.81 Å / Redundancy: 3.7 % / R_merge(I) obs: 0.65 / Mean I/σ(I) obs: 2 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
REFMAC	5.5.0089	refinement
iMOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.67→84.49 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.904 / SU B: 22.377 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.559 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24105	1278	5.1 %	RANDOM
R_work	0.19012	-	-	-
obs	0.19267	23801	99.78 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 20.744 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.73 Å²	0 Å²	-0.01 Å²
2-	-	1.45 Å²	0 Å²
3-	-	-	-0.73 Å²

Refinement step

Cycle: LAST / Resolution: 2.67→84.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4552	0	79	252	4883

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.022	4742
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.526	1.98	6417
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.295	5	577
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.973	25.278	216
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.065	15	822
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.902	15	18
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	714
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	3556
X-RAY DIFFRACTION	r_gen_planes_other
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	0.749	1.5	2888
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.372	2	4656
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.806	3	1854
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	3.148	4.5	1755
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

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	1719	tight positional	0.21	0.05
2	B	1719	tight positional	0.21	0.05
1	A	504	medium positional	0.25	0.5
2	B	504	medium positional	0.25	0.5
1	A	1719	tight thermal	0.2	0.5
2	B	1719	tight thermal	0.2	0.5
1	A	504	medium thermal	0.2	2
2	B	504	medium thermal	0.2	2

LS refinement shell

Resolution: 2.67→2.739 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.335	112	-
R_work	0.281	1729	-
obs	-	-	99.89 %

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	7.4609	2.1557	0.4941	3.5739	-2.1212	5.6749	0.0775	0.4447	-0.0685	-0.6628	-0.3986	0.1207	0.2084	0.2079	0.3211	0.2841	0.077	0.0116	0.4203	-0.0097	0.165	82.1716	45.1034	17.6701
2	10.3784	0.613	-0.2672	15.9726	1.1801	8.4289	0.0285	-0.474	-1.3511	0.225	-0.3477	-1.1032	0.9165	0.7916	0.3191	0.3312	0.2123	0.1039	0.5578	0.2232	0.3898	94.9772	35.726	23.6185
3	4.7017	-0.5574	0.3495	8.5637	-3.0222	6.8879	0.2582	-0.3238	0.4998	0.1753	-0.5371	-0.8081	-0.1497	1.1063	0.279	0.4452	-0.2359	-0.0354	1.0102	0.087	0.7606	95.9479	47.5182	32.9004
4	7.446	-2.742	-3.4415	5.6932	2.1968	17.6006	0.0769	-0.4862	0.3099	0.2439	-0.3752	-0.7808	-0.1114	1.0685	0.2984	0.068	0.0377	-0.0002	0.3443	0.1755	0.1655	94.9639	44.6565	22.1298
5	9.715	-0.3506	-0.2948	4.4605	-2.0987	5.7207	-0.1944	-1.3253	-1.7008	0.3934	-0.0591	0.2359	0.8192	0.243	0.2535	0.3521	0.0614	0.1304	0.393	0.2349	0.3261	82.124	34.6629	33.3606
6	6.6343	-1.5158	-0.824	2.793	-0.5914	4.8645	0.039	-0.254	-0.3179	0.0408	-0.2011	-0.1962	0.1616	0.6775	0.1621	0.1379	0.0004	0.0555	0.3258	0.0846	0.0843	83.4814	43.8055	25.3754
7	0.6249	1.4552	0.187	5.3631	1.0062	1.7505	0.1039	-0.0559	0.1113	-0.0113	-0.0104	-0.2045	-0.4127	0.5179	-0.0935	0.1804	-0.1217	0.0715	0.375	0.0082	0.186	74.7198	58.9276	31.7003
8	6.259	0.0358	-5.1677	7.1778	-5.0971	10.657	0.6065	-0.6296	0.7238	0.4943	-0.5549	-0.7353	-1.2167	1.7278	-0.0515	0.2447	-0.2444	0.0308	0.4693	-0.1046	0.2648	82.0702	59.0343	30.3925
9	3.0338	-0.1799	-1.5366	0.2836	-0.1207	5.2137	-0.0117	-0.4921	-0.2973	-0.0111	0.0492	-0.0259	0.4249	0.5461	-0.0375	0.0952	0.0209	-0.0199	0.2355	0.04	0.0758	70.5003	43.6642	38.6252
10	2.0645	-0.2659	-0.2137	1.2128	-0.9661	3.1729	0.1768	-0.4143	0.1055	0.2973	-0.1503	-0.0722	-0.4761	0.2396	-0.0264	0.1477	-0.0952	0.0192	0.2471	0.0132	0.0298	68.2375	54.2073	45.5479
11	3.7699	0.5042	-0.9512	8.7881	-3.8857	7.0099	0.1901	-0.5616	0.7717	0.6299	-0.1074	0.1017	-1.2016	0.0129	-0.0827	0.3664	-0.0371	0.0745	0.2129	-0.0936	0.1897	65.2147	66.9489	42.1226
12	3.8238	0.7663	1.8337	3.8558	-1.5276	5.8598	0.0136	0.1752	0.5555	-0.3191	0.1408	0.5232	-0.4719	-0.1043	-0.1544	0.2374	0.0163	0.0703	0.1501	0.0333	0.1855	62.0091	62.569	31.0602
13	5.3574	-0.9913	1.0138	3.9318	-0.9272	5.003	0.0298	0.3206	0.1828	0.0165	-0.116	-0.0141	-0.3228	-0.0372	0.0861	0.1296	-0.0104	0.0715	0.28	0.0201	0.0609	51.4174	52.6845	-4.8185
14	1.5723	0.8427	-0.7733	1.7383	1.2141	2.4599	0.1453	0.5752	0.1094	-0.3428	-0.4249	0.394	-0.712	-1.1704	0.2796	0.4527	0.253	0.0993	0.9072	0.0498	0.4083	39.4348	54.0047	1.2925
15	5.8959	-3.0292	-3.8293	6.1628	3.087	12.1363	-0.0344	0.5482	0.1803	-0.1048	-0.0616	0.0878	-0.0907	-0.2429	0.096	0.0808	0.0075	0.0369	0.2701	0.0415	0.126	48.3046	53.3625	-6.9057
16	14.0728	-14.6006	-3.0891	23.8737	-0.9331	15.1763	-0.2283	-0.5599	0.8494	1.0439	0.235	0.1884	-1.9439	-0.5983	-0.0067	0.5661	0.0027	0.026	0.2132	-0.1278	0.2702	48.962	62.3987	11.0142
17	2.7376	-0.8969	0.0818	2.4232	-1.9581	5.3579	-0.06	0.2267	0.1376	0.0365	-0.0366	-0.0345	-0.2131	-0.1219	0.0966	0.0737	-0.0159	0.0521	0.2092	-0.027	0.0715	51.0682	49.5323	1.6469
18	15.8293	13.5667	0.4778	23.6276	10.6152	10.2857	-0.0786	0.6761	0.6906	-0.7521	-0.0889	0.9721	-0.4197	-0.6105	0.1676	0.1778	-0.0856	-0.0147	0.2317	-0.0968	0.2345	34.6204	32.0806	5.4887
19	7.0172	6.7343	0.8506	8.9526	2.0197	1.2139	0.0002	0.3035	-0.7476	0.229	0.1146	-0.5336	0.2784	0.1978	-0.1148	0.1609	0.0564	0.0049	0.2563	-0.0371	0.1881	52.1098	32.7527	10.8069
20	4.1561	0.6903	1.4741	2.8303	2.3612	9.1999	-0.1396	0.1781	-0.1375	-0.035	-0.0614	0.2279	0.0174	-0.3515	0.2011	0.0145	0.0025	0.0172	0.1085	0.0226	0.055	49.1407	43.9769	12.1466
21	1.5041	0.1635	0.1837	2.0724	1.3909	3.1773	0.0776	-0.1674	0.0308	0.1506	-0.2571	0.2022	0.0206	-0.6082	0.1795	0.0626	-0.025	0.0311	0.2857	-0.0104	0.0334	39.6067	40.1239	23.2278
22	32.793	0.8272	3.3491	34.0121	5.9888	33.4133	-0.0782	-0.161	-0.1181	0.4501	-0.2968	1.6073	0.5244	-1.8229	0.375	0.2775	-0.2479	0.1101	0.3465	-0.019	0.3356	32.8101	23.1433	19.8946
23	5.2152	0.6843	-0.4955	5.2612	1.7708	4.9285	0.0118	-0.3005	-0.5913	0.4746	0.0434	-0.2978	0.6599	0.1201	-0.0552	0.1898	0.0042	-0.0195	0.1936	0.1094	0.1141	49.2561	28.6227	22.6178
24	0.6577	1.6802	0.3125	4.3034	0.795	0.4484	0.1303	0.0111	-0.2419	0.2991	0.0488	-0.5467	0.4349	0.1545	-0.1791	0.7228	-0.0013	-0.2399	0.2291	0.0516	0.5672	52.0031	18.4696	12.4628

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	67 - 81
2	X-RAY DIFFRACTION	2	A	82 - 92
3	X-RAY DIFFRACTION	3	A	93 - 103
4	X-RAY DIFFRACTION	4	A	104 - 117
5	X-RAY DIFFRACTION	5	A	118 - 136
6	X-RAY DIFFRACTION	6	A	137 - 173
7	X-RAY DIFFRACTION	7	A	174 - 213
8	X-RAY DIFFRACTION	8	A	214 - 229
9	X-RAY DIFFRACTION	9	A	230 - 255
10	X-RAY DIFFRACTION	10	A	256 - 304
11	X-RAY DIFFRACTION	11	A	305 - 330
12	X-RAY DIFFRACTION	12	A	331 - 350
13	X-RAY DIFFRACTION	13	B	67 - 99
14	X-RAY DIFFRACTION	14	B	100 - 106
15	X-RAY DIFFRACTION	15	B	107 - 124
16	X-RAY DIFFRACTION	16	B	125 - 135
17	X-RAY DIFFRACTION	17	B	136 - 174
18	X-RAY DIFFRACTION	18	B	175 - 183
19	X-RAY DIFFRACTION	19	B	184 - 207
20	X-RAY DIFFRACTION	20	B	208 - 246
21	X-RAY DIFFRACTION	21	B	247 - 307
22	X-RAY DIFFRACTION	22	B	308 - 313
23	X-RAY DIFFRACTION	23	B	314 - 345
24	X-RAY DIFFRACTION	24	B	346 - 351

-
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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 259 molecules

-
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

-Protein , 1 types, 2 molecules AB

-Non-polymers , 5 types, 259 molecules

-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

-
Protein , 1 types, 2 molecules AB

-
Non-polymers , 5 types, 259 molecules

-
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