PDB-5s4m: Tubulin-Z2142244288-complex

ID or keywords:

Entry

Database: PDB / ID: 5s4m

Title

Tubulin-Z2142244288-complex

Components

Stathmin-4
Tubulin alpha-1B chain
Tubulin beta-2B chain
Tubulin-Tyrosine Ligase

Keywords

CELL CYCLE / TUBULIN FOLD / CYTOSKELETON / MICROTUBULE

Function / homology

Function and homology information

tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...
Similarity search - Function

Biological species

Rattus norvegicus (Norway rat)

Gallus gallus (chicken)

Bos taurus (cattle)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

FOURIER SYNTHESIS / Resolution: 2.15 Å

Authors

Muehlethaler, T. / Gioia, D. / Prota, A.E. / Sharpe, M.E. / Cavalli, A. / Steinmetz, M.O.

Funding support

European Union,

Italy,

Switzerland, 4items

Organization	Grant number	Country
iNEXT/Horizon 2020	PID2692	European Union
NEON/Regione Lombardia	ID239047	Italy
Swiss National Science Foundation	31003A_166608	Switzerland
Swiss National Science Foundation	31030A_192566	Switzerland

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Comprehensive Analysis of Binding Sites in Tubulin.
Authors: Muhlethaler, T. / Gioia, D. / Prota, A.E. / Sharpe, M.E. / Cavalli, A. / Steinmetz, M.O.

History

Deposition	Nov 8, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 30, 2021	Provider: repository / Type: Initial release
Revision 1.1	Mar 6, 2024	Group: Advisory / Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5s4m.cif.gz	916.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5s4m.ent.gz	752.1 KB	Display	PDB format
PDBx/mmJSON format	5s4m.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5s4m_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	5s4m_full_validation.pdf.gz	2.6 MB	Display
Data in XML	5s4m_validation.xml.gz	84.4 KB	Display
Data in CIF	5s4m_validation.cif.gz	113 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s4/5s4m ftp://data.pdbj.org/pub/pdb/validation_reports/s4/5s4m	HTTPS FTP

-
Group deposition

ID	G_1002173 (59 entries) 5s4l 5s4m 5s4n 5s4o 5s4p 5s4q 5s4r 5s4s 5s4t 5s4u
Title	XChem fragment screening on T2R-TTL
Type	undefined
Description	Crystal structures of Tubulin-XChem-fragment complexes

-
Related structure data

Related structure data	5lxtS S: Starting model for refinement
Similar structure data	6lsm-d 6qtn-d 5z4p-d 5ylj-d 6brf-d 6y6d-d 6kpp-d 5yl2-d 4yj2-d 5s56-d 5s5a-d 5m8g-d 6gj4-d 5mf4-d 5s52-d 5s4w-d 5h74-d 6agk-d 5xaf-d 5lxs-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	#175 - Jul 2014 Microtubules similarity (28) #176 - Aug 2014 Dynein similarity (19) #241 - Jan 2020 Twenty Years of Molecules similarity (19) #118 - Oct 2009 Sodium-Potassium Pump similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1)

Deposited unit

A: Tubulin alpha-1B chain

B: Tubulin beta-2B chain

C: Tubulin alpha-1B chain

D: Tubulin beta-2B chain

E: Stathmin-4

F: Tubulin-Tyrosine Ligase

hetero molecules

265 kDa, 6 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)	104.670, 157.870, 179.170
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

-
Protein , 4 types, 6 molecules ACBDEF

#1: Protein	Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: P81947
#2: Protein	Tubulin beta-2B chain Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: Q6B856
#3: Protein	Stathmin-4 / Stathmin-like protein B3 / RB3 Mass: 16844.162 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043
#4: Protein	Tubulin-Tyrosine Ligase Mass: 44378.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43

-
Non-polymers , 8 types, 433 molecules

#5: Chemical	ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₄P₃ / Comment: GTP, energy-carrying molecule*YM
#6: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical	ChemComp-WV4 / N-ethyl-2-fluoro-4-(methylsulfonyl)aniline Mass: 217.260 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₉H₁₂FNO₂S / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical	ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₁P₂ / Comment: GDP, energy-carrying molecule*YM
#10: Chemical	ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₃NO₄S / Comment: pH buffer*YM
#11: Chemical	ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₂P₃ / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#12: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.8 Å³/Da / Density % sol: 56.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2% PEG 4K, 4% glycerol, 30 mM MgCl2, 30 mM CaCl2, 0.1 M MES/Imidazole, 5 mM L-tyrosine

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

Diamond

/ Beamline: I04-1 / Wavelength: 0.91587 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.91587 Å / Relative weight: 1

Reflection

Resolution: 2.15→63.02 Å / Num. obs: 159163 / % possible obs: 98.6 % / Redundancy: 6.759 % / B_iso Wilson estimate: 60.125 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.104 / R_rim(I) all: 0.113 / Χ²: 1.021 / Net I/σ(I): 9.48 / Num. measured all: 1075851 / Scaling rejects: 154

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.15-2.21	6.305	2.842	0.58	74403	11851	11800	0.238	3.099	99.6
2.21-2.27	6.342	2.261	0.74	60615	11523	9557	0.322	2.46	82.9
2.27-2.33	7.091	1.688	1.11	79385	11220	11195	0.473	1.821	99.8
2.33-2.4	7.063	1.329	1.42	76564	10858	10840	0.619	1.434	99.8
2.4-2.48	6.974	0.983	1.93	73683	10578	10566	0.727	1.062	99.9
2.48-2.57	6.855	0.791	2.39	70064	10236	10221	0.803	0.856	99.9
2.57-2.67	6.524	0.608	3.03	64493	9903	9885	0.857	0.661	99.8
2.67-2.78	6.614	0.472	3.86	62752	9500	9488	0.901	0.513	99.9
2.78-2.9	7.082	0.346	5.39	64554	9123	9115	0.953	0.373	99.9
2.9-3.04	7.01	0.248	7.18	61307	8754	8746	0.973	0.268	99.9
3.04-3.21	6.948	0.178	9.77	57850	8334	8326	0.986	0.192	99.9
3.21-3.4	6.739	0.128	12.72	53059	7885	7874	0.991	0.139	99.9
3.4-3.63	6.444	0.092	16.33	47843	7430	7424	0.994	0.1	99.9
3.63-3.93	7.007	0.072	21.28	48500	6929	6922	0.997	0.078	99.9
3.93-4.3	6.947	0.06	25.1	44455	6401	6399	0.998	0.065	100
4.3-4.81	6.739	0.05	28.78	39174	5820	5813	0.998	0.054	99.9
4.81-5.55	6.25	0.051	27.75	32236	5162	5158	0.998	0.055	99.9
5.55-6.8	6.945	0.053	28.57	30426	4383	4381	0.998	0.057	100
6.8-9.62	6.389	0.042	33.97	22113	3464	3461	0.998	0.046	99.9
9.62-63.02	6.212	0.037	39.87	12375	2000	1992	0.998	0.04	99.6

-
Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
XSCALE		data scaling
PDB_EXTRACT	3.27	data extraction
XDS		data reduction
PHENIX	1.18.2_3874	phasing

Refinement

Method to determine structure:

FOURIER SYNTHESIS
Starting model: 5lxt

5lxt

Resolution: 2.15→63.02 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2435	7882	4.95 %
R_work	0.2061	151259	-
obs	0.2079	159141	98.63 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 195.26 Å² / B_iso mean: 71.4894 Å² / B_iso min: 36.73 Å²

Refinement step

Cycle: final / Resolution: 2.15→63.02 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17468	0	250	415	18133
B_iso mean	-	-	66	60.16	-
Num. residues	-	-	-	-	2209

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.15-2.17	0.4173	260	0.386	5063	5323	99
2.17-2.2	0.3471	305	0.3606	4978	5283	100
2.2-2.23	0.3976	285	0.3488	5052	5337	100
2.23-2.25	0.3576	172	0.343	3200	3372	63
2.25-2.28	0.3773	280	0.3343	5027	5307	100
2.28-2.32	0.3861	269	0.3188	5021	5290	100
2.32-2.35	0.3534	258	0.3075	5062	5320	100
2.35-2.38	0.3398	232	0.3028	5112	5344	100
2.38-2.42	0.3563	250	0.2908	5064	5314	100
2.42-2.46	0.3005	302	0.2779	5042	5344	100
2.46-2.5	0.3137	283	0.2676	5030	5313	100
2.5-2.55	0.3239	260	0.2723	5076	5336	100
2.55-2.6	0.3077	285	0.2684	5049	5334	100
2.6-2.65	0.3218	249	0.2709	5060	5309	100
2.65-2.71	0.3087	271	0.2649	5084	5355	100
2.71-2.77	0.2972	261	0.2578	5093	5354	100
2.77-2.84	0.2923	271	0.2473	5080	5351	100
2.84-2.92	0.2817	213	0.2454	5141	5354	100
2.92-3	0.2914	253	0.2421	5085	5338	100
3-3.1	0.2767	276	0.2406	5111	5387	100
3.1-3.21	0.2964	264	0.2363	5084	5348	100
3.21-3.34	0.2691	268	0.2271	5105	5373	100
3.34-3.49	0.2648	293	0.2135	5126	5419	100
3.49-3.68	0.2369	274	0.2034	5094	5368	100
3.68-3.91	0.2341	249	0.1883	5152	5401	100
3.91-4.21	0.1992	240	0.1705	5187	5427	100
4.21-4.63	0.1836	269	0.1513	5158	5427	100
4.63-5.3	0.1818	284	0.1593	5196	5480	100
5.3-6.68	0.251	268	0.1908	5246	5514	100
6.68-63.02	0.1675	238	0.1573	5481	5719	100

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	1.9015	-0.9239	-0.2074	4.0079	0.7257	2.9649	0.0253	0.1153	0.2909	-0.3316	0.1814	-0.2866	-0.7088	0.268	-0.2148	0.5812	-0.1331	0.1141	0.4828	-0.1037	0.4603	32.137	89.6303	50.4046
2	2.5821	-0.8245	-2.0474	4.3973	-0.5479	2.4419	0.0325	-0.1832	-0.3015	0.3504	-0.0183	-0.0869	0.1989	0.1499	-0.0038	0.4929	0.0341	-0.026	0.4826	-0.1249	0.429	30.1442	74.25	58.7368
3	1.9229	-0.2893	0.3903	3.9394	0.4567	4.9949	0.0909	0.0483	0.0414	0.3747	-0.014	0.3718	-0.2648	-0.2003	-0.0595	0.4362	0.0329	0.0827	0.3459	-0.09	0.478	17.2643	84.6172	66.5433
4	1.2474	-0.271	0.1563	6.2092	1.518	3.0506	0.0375	-0.186	0.2863	0.904	-0.0024	0.1744	-0.1845	-0.1203	-0.042	0.5801	-0.0196	0.1293	0.5315	-0.1035	0.5219	19.25	83.3645	73.0149
5	2.0254	0.931	1.0039	5.881	4.8909	7.1169	-0.1613	-0.2308	-0.0724	0.7589	0.2691	-0.2311	0.7524	0.7557	-0.0639	0.4946	0.1332	-0.0513	0.4899	-0.0709	0.5768	32.6411	62.2998	61.3772
6	5.9097	-1.5796	-1.0029	7.8896	0.5144	4.871	0.1996	0.118	0.7407	-0.4521	-0.1216	0.3057	-0.9385	-0.1147	-0.0273	0.515	0.0323	0.0012	0.371	-0.0004	0.4599	15.8796	69.9696	18.943
7	1.972	0.0888	-0.1555	1.8046	1.0477	3.2991	0.0403	0.0215	0.117	-0.1236	-0.016	0.0309	-0.3154	0.0636	-0.0123	0.3916	0.0099	0.0131	0.4395	-0.0911	0.4499	20.1681	56.1452	25.1886
8	4.7741	-2.5716	1.6992	3.7941	-0.9995	3.8148	-0.1784	-0.2212	-0.0614	0.2913	0.0385	0.49	-0.1516	-0.9555	0.1271	0.4643	0.0286	0.0656	0.6292	-0.1753	0.5404	5.7904	60.1418	42.2513
9	1.1294	-1.5419	-0.2877	4.3888	2.5422	4.4292	-0.0572	-0.2189	-0.1703	0.6938	0.1386	0.0314	0.8245	0.304	-0.1029	0.3726	-0.0392	-0.0016	0.4446	-0.049	0.4409	21.0139	41.2838	31.1893
10	1.5078	-0.5249	-0.0393	3.0543	0.2178	2.0787	-0.0619	0.1385	0.1218	-0.2256	0.1364	-0.025	-0.2063	0.0815	-0.0667	0.3996	-0.0688	0.034	0.4751	-0.052	0.4216	20.0891	32.9648	-12.1148
11	1.285	-0.8692	-0.013	1.8344	0.8951	1.5937	-0.0274	-0.0218	0.0262	0.1248	-0.0335	0.1275	0.0395	-0.202	0.0619	0.3532	-0.0574	0.0486	0.4081	-0.0314	0.4161	7.7878	25.974	3.0972
12	5.2508	-1.968	0.4148	8.7277	0.8056	1.732	-0.0552	0.731	0.2553	-0.8132	0.1268	0.1695	-0.0937	-0.088	-0.0738	0.5454	-0.1058	0.0515	0.7619	0.0145	0.356	17.2242	9.5202	-44.0956
13	2.4444	0.2651	-0.3913	1.6685	0.011	2.4656	-0.0452	0.481	-0.2076	-0.217	0.1377	-0.2316	0.2901	0.105	-0.0811	0.5382	-0.0236	0.0653	0.6376	-0.1901	0.4751	22.7722	-2.41	-34.2373
14	0.9825	-0.4947	-1.3092	5.9359	2.8012	2.5577	0.0368	0.6702	-0.7321	-0.3903	-0.3831	0.9477	0.2437	-0.6849	0.2619	0.6248	-0.1499	0.0076	0.8874	-0.2051	0.6609	0.6286	-5.942	-25.8695
15	2.3978	-0.6737	0.0559	1.5626	-0.228	2.892	-0.1947	0.1339	-0.239	0.12	0.2031	0.1683	0.2045	-0.3852	0.001	0.5673	-0.1293	0.0313	0.5005	-0.1127	0.5318	8.6513	-1.7712	-20.8906
16	4.7333	0.7699	-2.1374	1.285	-1.816	2.8043	-0.4392	0.0103	-0.9653	0.2566	-0.1012	0.0285	0.8054	0.4028	0.3566	0.8083	0.102	0.0205	0.6195	-0.2028	0.824	30.3386	-17.2796	-24.4722
17	3.1325	-2.0449	0.3601	4.6247	1.5176	1.2905	0.0668	-0.2318	0.2874	0.7493	0.2815	-0.4532	-0.0266	0.1783	-0.3368	1.0877	-0.1446	-0.0303	0.872	-0.1938	0.7715	27.9975	93.0058	81.4141
18	0.0669	-0.2058	-0.4271	5.7372	6.1529	6.9391	-0.1321	0.0007	-0.0654	0.6969	0.7348	-0.5258	0.8443	1.1205	-0.6831	0.5223	0.1139	0.0012	0.9106	-0.2221	0.804	42.9872	28.0597	3.943
19	3.6901	1.7203	-0.7738	7.3527	1.5373	3.0843	-0.3573	0.661	-0.5081	-0.2552	0.0911	-0.304	1.3409	-0.3694	0.2045	1.0054	-0.17	0.1357	0.6644	-0.1521	0.5654	6.6365	54.7349	69.5106
20	5.2265	0.9651	3.4149	3.5597	-2.2624	7.0789	0.0817	-0.5128	0.2314	0.5007	-0.5649	-0.8297	-0.3169	1.7946	0.4226	0.7785	0.003	-0.0972	1.1368	0.0452	0.7102	16.7631	64.2237	102.3934
21	4.4989	-0.1872	2.5551	3.9629	-0.6742	4.4694	-0.0603	-0.4147	-0.4448	0.7596	-0.1265	-0.9088	1.1146	1.6568	0.191	0.9972	0.3328	-0.0139	1.0655	0.1711	0.8966	12.0238	52.1162	105.1662
22	2.2043	0.9819	-1.0761	4.0633	-0.9691	1.9857	-0.427	-0.0103	-0.6248	0.4409	0.1688	-0.3221	1.074	0.0801	0.1772	1.2175	0.0882	0.1812	0.5294	0.0637	0.7695	-1.943	49.8593	99.1875
23	2.8026	-0.0424	-2.1536	0.2116	0.3071	4.8823	-0.3119	0.1154	-0.4353	0.0068	0.2636	0.0156	0.8924	-0.1688	-0.0092	0.7799	-0.0208	0.068	0.3972	0.0073	0.5372	1.2898	58.2011	87.4117
24	6.4436	-4.3255	-3.5146	4.5358	1.6626	2.7896	-0.1503	0.8352	-0.0399	-0.4638	0.3815	0.6579	0.0867	-1.211	-0.1476	0.6136	-0.1841	-0.0056	0.8222	0.037	0.7083	-7.9586	63.0778	79.1824

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 1 through 160 )	A	1 - 160
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 161 through 199 )	A	161 - 199
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 200 through 311 )	A	200 - 311
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 312 through 401 )	A	312 - 401
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 402 through 438 )	A	402 - 438
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1 through 88 )	B	1 - 88
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 89 through 259 )	B	89 - 259
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 260 through 372 )	B	260 - 372
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 373 through 438 )	B	373 - 438
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1 through 197 )	C	1 - 197
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 198 through 440 )	C	198 - 440
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 1 through 88 )	D	1 - 88
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 89 through 273 )	D	89 - 273
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 274 through 311 )	D	274 - 311
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 312 through 399 )	D	312 - 399
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 400 through 441 )	D	400 - 441
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 6 through 46 )	E	6 - 46
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 47 through 143 )	E	47 - 143
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 1 through 66 )	F	1 - 66
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 67 through 140 )	F	67 - 140
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 141 through 207 )	F	141 - 207
22	X-RAY DIFFRACTION	22	chain 'F' and (resid 208 through 297 )	F	208 - 297
23	X-RAY DIFFRACTION	23	chain 'F' and (resid 298 through 354 )	F	298 - 354
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 355 through 382 )	F	355 - 382

-
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

-
Group deposition

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 4 types, 6 molecules ACBDEF

-
Non-polymers , 8 types, 433 molecules

-
Details

-
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

-Group deposition

-Related structure data

-Links

-Assembly

-Components

-Protein , 4 types, 6 molecules ACBDEF

-Non-polymers , 8 types, 433 molecules

-Details

-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

-
Group deposition

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 4 types, 6 molecules ACBDEF

-
Non-polymers , 8 types, 433 molecules

-
Details

-
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