PDB-4wgl: Crystal structure of a GroEL D83A/R197A double mutant

ID or keywords:

Entry

Database: PDB / ID: 4wgl

Title

Crystal structure of a GroEL D83A/R197A double mutant

Components

60 kDa chaperonin

Keywords

CHAPERONE / chaperonin / protein folding

Function / homology

Function and homology information

GroEL-GroES complex / chaperonin ATPase / virion assembly / ATP-dependent protein folding chaperone / response to radiation / protein refolding / response to heat / protein folding / magnesium ion binding / ATP hydrolysis activity ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.13 Å

Authors

Yang, D. / Fei, X. / LaRonde, N.A. / Beckett, D. / Lund, P.A. / Lorimer, G.H.

Citation

Journal: To Be Published
Title: Crystal structure of a GroEL D83A/R197A double mutant
Authors: Yang, D. / Fei, X. / LaRonde, N.A. / Beckett, D. / Lund, P.A. / Lorimer, G.H.

History

Deposition	Sep 19, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 30, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4wgl.cif.gz	2.5 MB	Display	PDBx/mmCIF format
PDB format	pdb4wgl.ent.gz	2.2 MB	Display	PDB format
PDBx/mmJSON format	4wgl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

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

-
Related structure data

Related structure data	1xckS S: Starting model for refinement
Similar structure data	6kfv-d 2nwc-d 4wsc-d 4hel-d 2ynj-d 5w0s-d 1xck-d 5opw-d 2yey-d 1ss8-1 4v43-2 5cdi-d 1oel-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	#32 - Aug 2002 Chaperones similarity (11)

Deposited unit

A: 60 kDa chaperonin

B: 60 kDa chaperonin

C: 60 kDa chaperonin

D: 60 kDa chaperonin

E: 60 kDa chaperonin

F: 60 kDa chaperonin

G: 60 kDa chaperonin

H: 60 kDa chaperonin

I: 60 kDa chaperonin

J: 60 kDa chaperonin

K: 60 kDa chaperonin

L: 60 kDa chaperonin

M: 60 kDa chaperonin

N: 60 kDa chaperonin

802 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	135.619, 259.710, 280.848
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	60 kDa chaperonin / GroEL protein / Protein Cpn60 Mass: 57261.578 Da / Num. of mol.: 14 / Mutation: D83A, R197A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: groL, groEL, mopA, b4143, JW4103 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A6F5

#1: Protein

60 kDa chaperonin / GroEL protein / Protein Cpn60

Mass: 57261.578 Da / Num. of mol.: 14 / Mutation: D83A, R197A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Strain: K12 / Gene: groL, groEL, mopA, b4143, JW4103 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P0A6F5

-
Experiment

Experiment	Method: X-RAY DIFFRACTION

-
Sample preparation

Crystal	Density Matthews: 3.08 Å³/Da / Density % sol: 60.13 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 25% PEG 3000, 0.1M acetic acid

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 3.13→190.68 Å / Num. obs: 174190 / % possible obs: 99.8 % / Redundancy: 5.3 % / R_merge(I) obs: 0.138 / R_sym value: 0.153 / Net I/σ(I): 10.2
Reflection shell	Resolution: 3.13→3.31 Å / Redundancy: 5.6 % / R_merge(I) obs: 0.688 / Mean I/σ(I) obs: 3 / % possible all: 99.9

-
Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
iMOSFLM		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1xck

1xck

Resolution: 3.13→123.524 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.11 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2327	2003	1.15 %
R_work	0.1655	-	-
obs	0.1663	174035	99.61 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.13→123.524 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	53844	0	0	0	53844

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	54236
X-RAY DIFFRACTION	f_angle_d	1.221	73248
X-RAY DIFFRACTION	f_dihedral_angle_d	16.168	20398
X-RAY DIFFRACTION	f_chiral_restr	0.048	8932
X-RAY DIFFRACTION	f_plane_restr	0.005	9590

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.13-3.2083	0.3307	135	0.2518	12181	X-RAY DIFFRACTION	100
3.2083-3.295	0.2959	151	0.2168	12192	X-RAY DIFFRACTION	100
3.295-3.392	0.2758	128	0.205	12221	X-RAY DIFFRACTION	100
3.392-3.5015	0.2782	152	0.1948	12186	X-RAY DIFFRACTION	100
3.5015-3.6266	0.2637	144	0.1919	12191	X-RAY DIFFRACTION	100
3.6266-3.7719	0.2553	144	0.1816	12199	X-RAY DIFFRACTION	100
3.7719-3.9435	0.2392	130	0.1667	12276	X-RAY DIFFRACTION	100
3.9435-4.1515	0.2167	156	0.1505	12232	X-RAY DIFFRACTION	100
4.1515-4.4116	0.2174	139	0.1393	12258	X-RAY DIFFRACTION	100
4.4116-4.7522	0.2205	137	0.1374	12253	X-RAY DIFFRACTION	100
4.7522-5.2304	0.1959	150	0.1376	12326	X-RAY DIFFRACTION	100
5.2304-5.9873	0.2347	147	0.1667	12384	X-RAY DIFFRACTION	100
5.9873-7.5432	0.2345	139	0.1742	12427	X-RAY DIFFRACTION	99
7.5432-123.6201	0.1985	151	0.1514	12706	X-RAY DIFFRACTION	99

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	0.1137	0.1496	-0.0139	0.2285	0.0249	0.1121	-0.0438	0.1177	0.1399	-0.0581	0.0815	0.2784	0.0382	-0.0223	0.0442	0.157	0.0367	0.0017	0.1498	-0.0641	-0.0884	28.9363	-0.308	19.2409
2	0.0936	-0.0082	0.0132	0.0649	-0.0015	0.044	0.0934	-0.0569	0.0814	-0.2772	0.0791	0.1743	0.2217	-0.1203	0.0014	0.5631	-0.0487	-0.1025	0.4928	0.0495	0.3277	25.2247	3.4384	-13.0104
3	0.0875	0.0213	-0.1171	0.1391	-0.0784	0.1845	-0.0692	-0.0498	0.0925	-0.0398	0.006	-0.0831	0.0213	0.069	-0.0801	0.1618	-0.0025	-0.0263	0.181	-0.0067	0.1281	37.9309	0.651	18.5196
4	0.1131	-0.0215	0.0185	0.1457	-0.0958	0.1202	0.0284	0.1194	0.0543	-0.0936	-0.0646	0.026	-0.0184	0.0229	-0.0501	0.1527	0.0151	0.0026	0.1244	-0.033	0.1381	14.2595	-30.6865	24.6269
5	0.2282	-0.0598	-0.2034	0.0671	0.0296	0.252	-0.4453	0.2016	0.3229	-0.1219	0.0624	-0.0165	-0.0819	0.2723	-0.3001	0.3929	-0.2334	-0.2177	0.2893	0.0649	0.0667	19.2554	-39.699	-5.7967
6	0.1185	0.0458	0.0232	0.032	-0.0398	0.1183	0.0192	0.0345	0.0054	0.013	-0.0125	0.0629	0.1099	0.0928	-0.044	0.2467	0.0321	-0.0386	0.221	-0.0149	0.1531	20.755	-41.4159	28.6754
7	0.1251	-0.0466	-0.1103	0.1211	-0.0132	0.1285	0.0882	0.1183	0.0545	-0.0742	-0.0447	0.0012	0.0537	0.0881	0.1365	0.2102	0.006	-0.0825	0.2048	-0.0459	0.1423	-21.3539	-49.1204	20.197
8	0.0494	0.0083	-0.0273	0.0274	-0.0011	0.0108	-0.1253	0.3588	0.3437	-0.0412	-0.07	-0.0916	0.0345	-0.2287	-0.0001	0.6339	0.025	-0.1497	0.9321	0.094	0.8607	-16.519	-46.9343	-11.4013
9	0.1163	0.0372	-0.0264	0.0697	0.0249	0.0932	-0.0345	0.0615	-0.173	0.0586	-0.1161	-0.06	0.0566	-0.0575	-0.3551	0.1331	0.0136	-0.1103	0.1743	-0.0942	0.0369	-22.6703	-57.9352	20.0577
10	0.0467	0.0417	-0.0678	0.0887	-0.0598	0.1448	0.0481	0.0098	0.0331	-0.0458	0.1196	0.0241	0.0474	0.0359	0.1165	0.0628	0.0069	-0.0467	0.0921	-0.0091	0.1081	-45.0716	-19.6001	24.9485
11	0.0674	-0.0482	-0.0109	0.0631	-0.0021	0.0188	0.0249	0.0221	-0.0193	-0.0708	-0.0024	-0.0116	0.0833	0.0337	-0.0102	0.1409	0.0223	-0.0268	0.2059	-0.0164	0.0911	-50.019	-35.3761	26.384
12	0.0283	-0.0387	0.0385	0.0354	-0.0415	0.0627	0.2088	0.0426	-0.0312	-0.1956	-0.191	0.0323	0.134	-0.0839	-0.001	0.6399	0.2073	-0.0651	0.7081	0.0736	0.4027	-56.9537	-25.5892	-1.9589
13	-0.0019	0.0013	0.007	0.0004	-0.0007	0.0085	0.0729	-0.0282	0.0289	-0.0091	0.0621	-0.0427	0.0518	0.0374	0.0001	1.1357	0.1493	0.016	1.0209	0.0487	0.9653	-39.3168	-24.4651	-2.9503
14	0.0506	0.0103	0.0097	0.0205	0.0022	0.044	0.1956	0.0475	0.0234	-0.1997	-0.0412	0.074	-0.0449	0.0094	0.0023	0.7981	0.3232	-0.0995	0.9665	0.0019	0.3974	-54.4524	-35.6457	-12.2129
15	0.0628	-0.0316	0.0313	0.0572	-0.0028	0.1827	-0.0135	0.0121	-0.1161	-0.0247	-0.0612	0.1179	0.1452	-0.1401	-0.1293	0.0744	0.0149	-0.0946	0.1803	-0.0363	0.1702	-61.3693	-31.1185	25.8348
16	0.0659	0.0117	0.0083	0.0244	0.007	0.0187	0.0375	0.0447	0.0949	0.0079	-0.0479	-0.0603	0.0133	0.1018	0.0355	0.1463	0.0176	-0.0282	0.202	-0.0034	0.2229	-49.5466	7.4248	25.1164
17	0.0673	0.0819	0.0514	0.322	0.0451	0.0655	-0.0699	0.0984	-0.0962	0.0276	0.0186	-0.37	-0.0833	0.0335	0.1241	0.2521	-0.0251	0.0782	0.4203	0.0796	0.4095	-59.3585	9.0304	-3.1174
18	0.1273	0.0334	0.1657	0.113	0.043	0.1523	-0.1082	-0.0056	0.1379	0.0274	0.1343	-0.0685	0.0045	-0.1231	0.014	0.1859	0.01	0.0098	0.2938	0.0416	0.2611	-65.7121	14.3997	20.7711
19	0.0378	-0.0074	0.0309	0.0803	0.0558	0.1443	0.069	0.1149	-0.0664	-0.0398	-0.0401	-0.0085	-0.0455	-0.1252	0.0081	0.2161	-0.0061	-0.031	0.2404	-0.0039	0.2849	-31.0061	32.1516	25.5641
20	0.0572	-0.0536	-0.0325	0.0329	0.0416	0.0331	-0.0632	-0.0019	0.0828	-0.0284	0.1866	0.113	-0.0497	0.0222	0	0.6393	-0.0756	0.0328	0.7166	0.1423	0.5649	-31.4709	39.6531	-6.6938
21	0.0722	-0.0108	0.0463	0.0341	0.0217	0.1715	-0.0153	0.029	0.1354	0.0271	-0.0636	0.017	-0.1232	-0.2189	-0.1112	0.1281	0.0379	-0.0106	0.0867	0.0473	0.2271	-31.1705	46.4077	25.7713
22	0.0885	-0.0029	0.0662	0.0779	0.0018	0.086	-0.0027	-0.039	-0.069	-0.0812	0.0254	0.0204	-0.0465	-0.0484	0.0688	0.1547	-0.0037	-0.0317	0.1584	-0.0259	0.1696	3.3751	30.5081	24.8402
23	0.0155	-0.0172	0.0062	0.0088	-0.0188	0.0297	0.1999	0.1734	-0.1033	0.0161	-0.0965	0.2419	0.0226	0.0529	-0.0001	0.5653	0.1809	-0.0257	0.7548	-0.0196	0.6171	8.8621	36.2276	-8.1936
24	0.1369	-0.0412	0.1117	0.0686	-0.0342	0.1213	-0.0454	-0.0228	0.134	-0.0946	-0.0129	-0.0969	-0.136	0.0025	-0.0319	0.2054	-0.0255	-0.0069	0.2053	-0.0304	0.2566	14.4018	39.5628	24.5952
25	0.0619	-0.0101	-0.0385	0.0638	0.038	0.0778	0.0336	-0.0407	0.0672	0.0313	-0.0001	-0.0552	0.0229	-0.0334	0.0513	0.1166	0.0176	-0.0385	0.1216	0.0077	0.1418	-33.5942	-39.6319	62.1276
26	0.0659	0.0099	-0.0734	0.0819	0.0273	0.0327	0.0641	-0.0634	0.0024	0.0781	-0.0099	0.025	0.0854	0.0604	0	0.406	-0.0112	-0.0695	0.4234	0.1013	0.3064	-33.4793	-47.2092	94.8162
27	0.1343	-0.0314	-0.0735	0.1079	0.0109	0.1115	0.0708	0.0119	-0.0599	-0.0135	-0.1082	0.0192	0.0456	-0.0407	-0.0992	0.1429	-0.0275	-0.0476	0.1268	0.0498	0.1974	-34.8663	-53.8226	62.0166
28	0.0707	-0.0248	-0.0169	0.0361	0.0233	0.1074	0.0377	-0.0151	0.079	0.0374	-0.0163	-0.0721	0.0177	-0.0172	0.0212	0.1142	0.0072	-0.0259	0.1323	0.0134	0.1677	0.7004	-40.3749	61.7727
29	0.0721	0.0743	-0.014	0.1228	-0.015	0.0957	0.1217	0.027	0.4106	-0.0034	-0.0299	0.6382	-0.1601	0.2231	0.1483	0.2395	-0.192	0.0329	-0.0646	-0.1383	0.7507	6.5828	-41.7433	95.4703
30	0.055	0.0656	0.0139	0.116	-0.1384	0.0618	0.1943	0.3121	-0.2073	-0.0618	-0.1713	0.0921	0.0449	0.0518	-0.021	0.0241	-0.1424	-0.0138	-0.2402	0.0641	0.1073	10.0618	-52.0934	71.3219
31	0.0534	-0.0171	0.0286	0.185	-0.0147	0.1257	-0.0674	0.0088	-0.0258	0.0272	0.0928	0.1161	-0.0352	0.0336	0.1727	0.1628	-0.0088	0.0006	0.1413	-0.0328	0.095	29.2466	-12.1497	65.9761
32	0.0429	-0.0293	0.0083	0.0754	0.0336	0.0556	0.0304	-0.074	-0.0523	-0.0536	-0.0288	0.1677	-0.0886	-0.0447	0.0888	0.5015	-0.2223	0.1088	0.2409	-0.1803	0.1574	25.457	-13.8791	98.7956
33	0.2283	0.0403	0.0502	0.2656	-0.0687	0.0948	0.0089	0.1106	0.0878	0.1635	-0.0008	0.0353	-0.0359	0.0597	0.0768	0.1036	-0.0235	-0.0075	0.0254	0.0098	0.0377	38.9001	-14.9913	69.999
34	0.0334	0.0026	-0.0308	0.0364	-0.0282	0.0159	0.0523	-0.0477	0.0482	-0.0143	-0.0447	0.1094	-0.0177	0.0009	-0.0162	0.193	-0.0045	-0.0168	0.1087	-0.0023	0.1873	12.7646	18.9669	61.9512
35	0.2044	-0.0659	0.0718	0.1549	0.113	0.2211	-0.2369	-0.1021	-0.293	0.1691	0.2776	0.1385	0.0161	0.3243	0.0644	0.4721	0.3164	0.0465	0.102	-0.0459	0.2079	23.9692	25.0254	92.1432
36	0.0875	-0.0897	0.072	0.0777	0.0285	0.0574	-0.0497	0.002	0.1011	0.0693	0.0095	-0.0455	0.0373	0.0976	-0.0857	0.1359	-0.0166	-0.0174	0.0743	-0.0481	0.1006	25.7548	31.412	66.1049
37	0.1732	-0.0113	0.0794	0.0726	-0.0499	0.0777	0.101	0.0205	-0.144	0.0535	-0.1071	0.0034	-0.0363	0.0225	-0.0083	0.1722	-0.0343	-0.0038	0.1134	-0.0183	0.1717	-17.0459	40.0989	67.1877
38	0.1197	-0.0002	-0.0393	0.0973	0.005	0.0612	-0.0442	-0.1511	-0.3034	-0.0121	0.1476	-0.1996	0.2022	-0.1911	0.0703	0.4873	-0.1509	-0.0391	0.4012	0.0508	0.4741	-12.0362	35.7104	97.3439
39	0.1097	0.0931	0.0535	0.1179	0.0688	0.0588	0.0488	-0.1513	-0.0723	-0.0796	-0.1157	-0.0525	0.0328	-0.0098	-0.1186	-0.0029	-0.1715	-0.0776	-0.1889	-0.1351	0.087	-17.8424	48.7485	67.3532
40	0.0682	0.0127	0.0331	0.0672	0.013	0.0673	-0.0212	-0.0249	-0.0385	0.0495	0.0156	-0.0791	-0.0805	0.003	-0.0096	0.2429	-0.0249	-0.0109	0.228	-0.0297	0.301	-45.0322	21.25	62.4754
41	0.0663	0.001	-0.0459	0.119	0.0095	0.0125	0.225	-0.2355	-0.1691	0.1438	-0.3073	-0.077	0.1151	-0.0384	-0.0039	0.5448	-0.1474	0.0197	0.6212	0.1683	0.4619	-51.6744	24.5546	95.8397
42	0.0813	0.0056	-0.0129	0.069	0.046	0.1271	-0.053	0.0254	0.1344	0.1325	-0.0209	0.1371	-0.0781	-0.0539	-0.0274	0.2115	0.0182	0.0439	0.2172	-0.0012	0.3516	-58.5004	25.8451	62.7148
43	0.1348	0.0021	0.0215	0.0853	0.0496	0.1415	-0.0482	-0.1358	0.0531	-0.0304	0.0212	-0.052	-0.0778	-0.0059	0.0091	0.0952	-0.0073	-0.0184	0.0877	0.0015	0.1009	-53.8787	-11.9575	62.6271
44	0.1165	-0.0721	-0.0758	0.0458	0.0593	0.0389	0.1937	0.0483	0.0465	0.1474	0.088	-0.3038	0.0649	-0.0853	0.0039	0.5325	0.0078	-0.0685	0.3104	0.0139	0.4091	-58.7537	-15.4249	95.5527
45	0.1273	-0.004	-0.0451	0.1518	0.0272	0.14	-0.0566	-0.025	-0.0265	-0.0566	-0.0126	-0.0825	0.0094	-0.0277	-0.1924	0.1281	-0.0019	-0.0102	0.182	0.0127	0.1603	-65.7958	-19.5585	62.9244

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 179 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 180 through 355 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 356 through 525 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 134 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 135 through 433 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 434 through 525 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 2 through 179 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 180 through 358 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 359 through 525 )
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 2 through 64 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 65 through 134 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 135 through 255 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 256 through 281 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 282 through 385 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 386 through 525 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 2 through 109 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 110 through 358 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 359 through 525 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 2 through 134 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 135 through 385 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 386 through 525 )
22	X-RAY DIFFRACTION	22	chain 'G' and (resid 2 through 134 )
23	X-RAY DIFFRACTION	23	chain 'G' and (resid 135 through 385 )
24	X-RAY DIFFRACTION	24	chain 'G' and (resid 386 through 525 )
25	X-RAY DIFFRACTION	25	chain 'H' and (resid 2 through 134 )
26	X-RAY DIFFRACTION	26	chain 'H' and (resid 135 through 385 )
27	X-RAY DIFFRACTION	27	chain 'H' and (resid 386 through 525 )
28	X-RAY DIFFRACTION	28	chain 'I' and (resid 2 through 134 )
29	X-RAY DIFFRACTION	29	chain 'I' and (resid 135 through 338 )
30	X-RAY DIFFRACTION	30	chain 'I' and (resid 339 through 525 )
31	X-RAY DIFFRACTION	31	chain 'J' and (resid 2 through 179 )
32	X-RAY DIFFRACTION	32	chain 'J' and (resid 180 through 338 )
33	X-RAY DIFFRACTION	33	chain 'J' and (resid 339 through 525 )
34	X-RAY DIFFRACTION	34	chain 'K' and (resid 2 through 109 )
35	X-RAY DIFFRACTION	35	chain 'K' and (resid 110 through 358 )
36	X-RAY DIFFRACTION	36	chain 'K' and (resid 359 through 525 )
37	X-RAY DIFFRACTION	37	chain 'L' and (resid 2 through 179 )
38	X-RAY DIFFRACTION	38	chain 'L' and (resid 180 through 358 )
39	X-RAY DIFFRACTION	39	chain 'L' and (resid 359 through 525 )
40	X-RAY DIFFRACTION	40	chain 'M' and (resid 2 through 134 )
41	X-RAY DIFFRACTION	41	chain 'M' and (resid 135 through 385 )
42	X-RAY DIFFRACTION	42	chain 'M' and (resid 386 through 525 )
43	X-RAY DIFFRACTION	43	chain 'N' and (resid 2 through 134 )
44	X-RAY DIFFRACTION	44	chain 'N' and (resid 135 through 385 )
45	X-RAY DIFFRACTION	45	chain 'N' and (resid 386 through 525 )

-
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