PDB-7uie: Crystal structure of HcE-JLE-G6

ID or keywords:

Entry

Database: PDB / ID: 7uie

Title

Crystal structure of HcE-JLE-G6

Components

Botulinum neurotoxin E heavy chain
JLE-G6

Keywords

ANTITOXIN/TOXIN / Single domain antibody / Botulinum neurotoxin / VHH / Receptor / ANTITOXIN / ANTITOXIN-TOXIN complex

Function / homology

Function and homology information

metallopeptidase activity / proteolysis / extracellular region
Similarity search - Function

Biological species

Vicugna pacos (alpaca)

Clostridium botulinum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.23 Å

Authors

Jin, R. / Lam, K.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2023
Title: Structural basis for botulinum neurotoxin E recognition of synaptic vesicle protein 2.
Authors: Liu, Z. / Lee, P.G. / Krez, N. / Lam, K.H. / Liu, H. / Przykopanski, A. / Chen, P. / Yao, G. / Zhang, S. / Tremblay, J.M. / Perry, K. / Shoemaker, C.B. / Rummel, A. / Dong, M. / Jin, R.

History

Deposition	Mar 29, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 5, 2023	Provider: repository / Type: Initial release
Revision 1.1	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 8, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7uie.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb7uie.ent.gz	905.3 KB	Display	PDB format
PDBx/mmJSON format	7uie.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7uie_validation.pdf.gz	501.3 KB	Display	wwPDB validaton report
Full document	7uie_full_validation.pdf.gz	524.7 KB	Display
Data in XML	7uie_validation.xml.gz	85.8 KB	Display
Data in CIF	7uie_validation.cif.gz	114.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ui/7uie ftp://data.pdbj.org/pub/pdb/validation_reports/ui/7uie	HTTPS FTP

-
Related structure data

Related structure data	7uiaC 7uibC 3ffzS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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

B: JLE-G6

A: Botulinum neurotoxin E heavy chain

C: JLE-G6

D: Botulinum neurotoxin E heavy chain

E: JLE-G6

F: Botulinum neurotoxin E heavy chain

I: JLE-G6

G: JLE-G6

H: Botulinum neurotoxin E heavy chain

J: Botulinum neurotoxin E heavy chain

323 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: JLE-G6

A: Botulinum neurotoxin E heavy chain

defined by author
Evidence: gel filtration
64.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: JLE-G6

D: Botulinum neurotoxin E heavy chain

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

3

E: JLE-G6

F: Botulinum neurotoxin E heavy chain

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

4

I: JLE-G6

J: Botulinum neurotoxin E heavy chain

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

5

G: JLE-G6

H: Botulinum neurotoxin E heavy chain

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

Unit cell

Length a, b, c (Å)	88.737, 174.626, 214.439
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Antibody	JLE-G6 Mass: 15386.082 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Protein	Botulinum neurotoxin E heavy chain Mass: 49249.867 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A5H0J8

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.71 Å³/Da / Density % sol: 54.64 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1M HEPES, pH 7.0, 0.2 M NaCl and 18% PEG 3350

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 3.23→174.63 Å / Num. obs: 54051 / % possible obs: 99.6 % / Redundancy: 4.1 % / CC_1/2: 0.987 / R_pim(I) all: 0.1057 / Net I/σ(I): 8.6
Reflection shell	Resolution: 3.23→3.32 Å / Mean I/σ(I) obs: 1.06 / Num. unique obs: 5309 / CC_1/2: 0.328 / R_pim(I) all: 0.8736

-
Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3FFZ

3ffz

Resolution: 3.23→135.41 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.49 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2729	4868	4.85 %
R_work	0.2297	-	-
obs	0.2318	53969	97.25 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.23→135.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21288	0	0	0	21288

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	21768
X-RAY DIFFRACTION	f_angle_d	0.484	29628
X-RAY DIFFRACTION	f_dihedral_angle_d	13.017	7706
X-RAY DIFFRACTION	f_chiral_restr	0.046	3248
X-RAY DIFFRACTION	f_plane_restr	0.003	3837

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 (%)
3.23-3.27	0.3643	134	0.3703	3173	X-RAY DIFFRACTION	95
3.27-3.31	0.4014	156	0.3792	3166	X-RAY DIFFRACTION	97
3.31-3.35	0.3802	156	0.3598	3141	X-RAY DIFFRACTION	97
3.35-3.39	0.3644	158	0.3377	3201	X-RAY DIFFRACTION	96
3.39-3.43	0.3983	168	0.3419	3194	X-RAY DIFFRACTION	97
3.43-3.48	0.3452	172	0.3261	3105	X-RAY DIFFRACTION	97
3.48-3.53	0.362	169	0.3257	3202	X-RAY DIFFRACTION	97
3.53-3.58	0.3334	137	0.326	3193	X-RAY DIFFRACTION	97
3.58-3.64	0.3681	173	0.3116	3202	X-RAY DIFFRACTION	97
3.64-3.7	0.357	158	0.2995	3198	X-RAY DIFFRACTION	97
3.7-3.76	0.3299	155	0.2734	3168	X-RAY DIFFRACTION	97
3.76-3.83	0.2988	163	0.2579	3177	X-RAY DIFFRACTION	97
3.83-3.9	0.2928	165	0.2544	3196	X-RAY DIFFRACTION	98
3.9-3.98	0.3334	160	0.2379	3221	X-RAY DIFFRACTION	97
3.98-4.07	0.2205	157	0.2345	3199	X-RAY DIFFRACTION	98
4.07-4.16	0.2568	183	0.2245	3159	X-RAY DIFFRACTION	97
4.16-4.27	0.2842	178	0.2077	3190	X-RAY DIFFRACTION	98
4.27-4.38	0.2567	170	0.1963	3191	X-RAY DIFFRACTION	98
4.38-4.51	0.2352	130	0.1919	3247	X-RAY DIFFRACTION	98
4.51-4.66	0.2155	173	0.1791	3194	X-RAY DIFFRACTION	97
4.66-4.82	0.2046	161	0.181	3205	X-RAY DIFFRACTION	98
4.82-5.02	0.2411	170	0.1816	3201	X-RAY DIFFRACTION	98
5.02-5.25	0.2719	139	0.1842	3242	X-RAY DIFFRACTION	98
5.25-5.52	0.2089	137	0.2001	3222	X-RAY DIFFRACTION	98
5.52-5.87	0.2665	179	0.1984	3168	X-RAY DIFFRACTION	98
5.87-6.32	0.261	177	0.2137	3232	X-RAY DIFFRACTION	98
6.32-6.96	0.2527	141	0.2125	3197	X-RAY DIFFRACTION	98
6.96-7.97	0.2672	187	0.2168	3166	X-RAY DIFFRACTION	97
7.97-10.04	0.2448	205	0.1983	3122	X-RAY DIFFRACTION	97
10.04-135.41	0.2174	157	0.1877	3120	X-RAY DIFFRACTION	95

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	1.3322	-0.0882	-0.4514	2.1993	-0.4813	0.4127	0.0801	-0.6471	-0.6108	0.0333	-0.121	-0.4083	0.2506	0.4463	0.0202	0.8956	0.3148	-0.0579	0.9666	0.1531	0.6308	64.4304	9.2263	70.7497
2	2.7078	0.4455	-0.3922	2.4175	0.1436	2.805	-0.0711	-0.5745	0.0925	0.683	0.0009	0.0262	-0.1818	0.0346	0.1467	1.0302	0.2798	-0.0761	0.8204	0.0672	0.568	60.5343	18.6266	77.2598
3	2.0493	-0.0472	0.5671	1.171	-0.6302	1.1102	-0.4408	-0.0551	0.2282	0.3717	-0.0042	-0.6011	-0.219	0.6536	0.3618	0.7855	0.2285	-0.1814	0.9666	0.117	0.6815	63.3393	16.0867	69.6379
4	0.2437	0.1248	0.3782	1.5037	-1.1151	1.7717	-0.2155	0.084	0.2024	0.16	0.1616	-0.184	-0.3769	0.4048	0.4358	1.2375	0.5935	-0.3305	1.6411	-0.0284	0.5966	69.7364	9.4039	86.5603
5	1.372	-0.3445	-0.2453	3.1674	-1.0591	5.4248	0.0261	0.1245	0.3331	0.1819	-0.1028	-0.076	0.052	-0.7394	0.0447	0.439	0.082	-0.024	0.4632	-0.0514	0.3282	22.7879	33.3699	27.5685
6	1.5713	0.227	0.843	1.4092	-0.2407	1.933	0.2379	0.3659	-0.189	-0.2611	-0.0916	-0.04	0.4308	0.0719	-0.1216	0.4448	0.02	-0.0141	0.5393	-0.0345	0.4283	32.8626	20.3191	22.2561
7	0.8851	-0.1078	0.2179	1.0452	0.1623	1.8546	-0.223	-0.0114	-0.0534	0.1945	0.3524	-0.0581	0.2048	-0.3163	-0.1181	0.5453	0.0149	-0.0095	0.4962	0.0248	0.3707	36.1364	22.0672	48.3946
8	2.7964	0.7421	-0.974	1.9159	-0.078	5.121	0.1887	-0.2773	0.4344	0.2488	-0.1575	0.4952	-0.3396	-1.1135	0.061	0.6084	-0.0326	0.0048	0.4976	-0.0923	0.5269	27.4124	31.0542	59.274
9	1.4166	-0.0955	-0.1743	1.0276	-0.0135	1.5817	-0.1381	-0.0006	0.0847	0.3492	-0.0081	-0.0383	0.3521	0.2252	0.1345	0.7566	0.068	-0.0865	0.559	0.0138	0.344	41.2055	29.5695	64.1039
10	2.5101	0.1854	1.1102	1.4459	0.5387	2.4553	-0.3393	-0.1269	0.1104	-0.0552	0.266	0.105	0.0152	0.0874	-0.0106	0.6174	-0.0505	-0.0114	0.558	0.0512	0.4171	40.3128	21.209	50.0294
11	1.2579	-0.0607	-0.7575	0.8689	-0.0237	1.3651	0.0543	0.2502	0.1742	-0.4079	0.0009	-0.1398	0.1263	0.4222	-0.0322	0.7274	0.1044	0.0222	0.743	0.1207	0.4316	47.1443	50.5724	-22.067
12	3.1352	0.7852	1.1358	3.4351	1.7633	3.5812	0.0534	-0.0734	-0.3132	-0.0702	-0.0968	-0.1498	0.1114	-0.1177	-0.0175	0.9234	-0.0358	0.0284	0.46	0.0672	0.4287	43.8964	39.1568	-20.5754
13	0.0045	0.1109	0.0271	3.3357	0.6557	0.1371	-0.2115	-0.5803	0.2766	0.4815	-0.0074	-0.1603	-0.1627	0.2242	0.1675	0.794	0.1014	0.0596	1.2289	0.0427	0.5014	49.3478	49.1313	-7.6495
14	2.5178	-0.2107	-0.2193	4.5982	-0.1581	2.5086	0.1967	-0.4206	0.2109	-0.1675	-0.3484	0.0577	0.2952	0.6945	0.0186	0.7089	0.036	-0.0057	0.8594	-0.0225	0.6904	53.1723	48.456	-17.85
15	2.2223	0.3919	-0.1224	0.2968	-0.3388	0.4416	0.1768	-0.147	-0.2172	0.3116	0.2009	-0.0317	0.4106	0.731	-0.3097	0.8588	0.1256	-0.0654	0.8234	0.0076	0.4395	47.7875	42.2844	-23.2774
16	0.7166	0.4457	-0.6884	0.4026	-0.0318	1.6369	-0.0746	-0.0125	-0.4909	-0.1259	-0.2623	-0.0931	0.2624	-0.5767	0.2655	0.9929	0.0774	0.1392	0.5873	-0.1046	0.3957	40.1092	44.0918	-18.7983
17	0.8691	0.2638	0.1921	1.4259	0.6259	4.0733	0.38	-0.2288	0.0094	0.3651	-0.1266	1.378	0.2956	-0.3217	-0.2188	0.5133	-0.1693	0.1158	0.7558	-0.1808	1.0162	5.0383	58.5955	27.2427
18	1.1594	-0.0451	-0.2319	2.181	0.1932	1.4685	0.1257	-0.2783	0.3789	0.1198	-0.34	0.6518	-0.5149	-0.0437	0.1341	0.4541	-0.083	0.0897	0.5077	-0.134	0.7011	16.0684	71.7043	23.4889
19	0.3913	-0.103	0.1653	0.8696	0.6415	2.0975	0.1715	0.098	-0.1729	0.139	-0.1598	0.2051	0.192	-0.0229	-0.0291	0.5123	0.0866	-0.1402	0.7452	-0.063	0.586	18.5064	53.6978	17.5464
20	2.3308	0.2262	-0.3654	1.4947	0.2631	2.2846	0.0693	0.7784	-0.1064	-0.6658	0.09	0.367	-0.2992	-0.5531	-0.1327	0.6237	0.0505	-0.128	0.629	0.0634	0.5139	19.5619	54.6978	-6.7206
21	1.6316	-0.7462	0.5287	3.9332	1.534	3.5243	0.1128	0.517	-0.4951	-0.1576	-0.28	1.1904	0.5585	-0.6852	0.1392	0.5194	-0.0211	-0.1278	0.723	0.0563	0.6778	10.1621	40.6096	0.682
22	1.3692	0.7289	0.26	1.7519	-0.2082	1.457	-0.1117	0.128	-0.114	-0.5073	-0.2166	0.0472	0.2475	-0.1364	0.3246	0.5949	0.007	-0.1235	0.6054	-0.0221	0.382	24.0803	38.5145	-3.7939
23	2.6304	-0.9995	-0.5926	1.8997	0.5133	0.9155	-0.3143	-0.2186	0.318	0.0179	0.2396	-0.1502	-0.1515	-0.0141	0.088	0.569	0.0459	-0.1379	0.6231	0.0274	0.4496	23.5724	53.6847	2.2686
24	1.1732	-0.2789	-0.525	2.0529	0.7836	1.4833	0.0077	-0.0447	-0.2693	-0.751	0.4838	0.1932	-0.1972	0.6862	-0.3181	0.6397	-0.0086	-0.1059	0.6631	-0.2342	0.7568	99.7261	0.8941	8.7197
25	2.745	-1.3969	0.497	3.0572	1.9261	3.4872	0.0887	-0.3835	-0.4649	0.3065	0.1729	0.042	0.569	0.3117	0.0382	0.7733	0.0766	-0.0992	0.7453	-0.2327	0.7512	96.8963	-2.8468	20.3625
26	0.5859	-0.1121	0.1273	1.483	1.0447	0.8301	-0.046	-0.0728	-0.0901	0.6764	0.2489	-0.2485	0.3093	0.4136	-0.1635	0.6665	0.0821	-0.0787	0.7101	-0.1379	0.7135	99.9568	2.2629	15.4692
27	0.3637	-0.5303	-0.5891	2.7964	-0.1508	1.4296	0.149	0.3398	-0.5227	-0.0131	0.1463	0.6826	-0.3009	-0.3273	-0.2213	0.5843	-0.1674	-0.0662	0.7224	0.0446	1.0495	56.8817	47.66	20.0206
28	1.7108	-0.4281	-0.09	1.4104	0.2578	1.7927	0.2841	0.597	0.0057	-1.2231	-0.2353	0.7166	-0.3476	-0.0465	-0.124	0.7275	0.0692	-0.1551	0.6592	0.0282	0.6249	65.0534	50.5197	4.8918
29	0.963	-0.8713	-0.4235	2.669	-0.5935	0.709	0.3047	0.1346	-0.0623	-0.1343	-0.3197	0.5023	-0.0011	0.2549	-0.0149	0.5394	-0.0426	-0.0849	0.6426	-0.0518	0.6691	70.3018	44.3675	12.0243
30	1.539	-0.4078	-0.2196	1.9025	0.2678	1.0135	-0.2386	0.0466	-0.8298	-0.4321	-0.2592	0.8092	0.3762	-0.4834	0.359	0.5474	-0.2102	0.0427	0.7183	-0.1858	0.8911	72.3034	15.2286	11.273
31	1.1586	0.904	0.2261	2.6688	-0.9759	0.7342	0.085	-0.2889	-0.5289	0.7298	-0.387	1.1918	0.0403	-0.3143	-0.0186	0.8068	-0.2844	0.404	0.6699	-0.1503	1.2177	62.8672	16.7937	27.0091
32	1.0087	1.1627	-0.2572	1.3879	-0.0578	1.1054	-0.2409	-0.3098	-0.1748	0.826	0.0572	0.9593	0.2854	0.0654	0.129	0.7011	-0.124	0.2531	0.5572	-0.0239	0.8133	77.025	12.3303	27.3531
33	2.2314	-0.7049	0.5316	1.9459	-0.5004	1.8412	0.0151	-0.1805	0.3486	-0.0065	-0.0875	0.548	-0.4412	-0.005	-0.0987	0.4419	-0.0451	-0.0203	0.5873	-0.1395	0.776	75.9599	23.4532	15.4315
34	0.7993	-0.5138	-0.0297	0.3434	0.0645	0.9242	0.4421	0.1993	0.3435	-0.4203	0.1668	-0.7939	0.2999	0.0318	-0.3651	1.3436	-0.4369	0.2333	2.3546	-1.0096	1.669	35.3161	77.6354	81.6675
35	1.1612	0.1571	0.5501	0.0879	0.2183	0.5629	-0.0017	-0.0722	0.2434	-0.005	0.2079	-0.5838	-0.2716	0.1835	-0.0844	1.8707	-0.6476	0.5305	1.5863	-0.6143	1.2704	26.8657	74.4223	72.0619
36	0.6039	0.4333	0.1777	2.5714	0.8204	0.2719	-0.3199	0.0217	-0.205	-0.3462	0.1954	0.0632	-0.1187	-0.0113	0.0897	0.978	-0.0531	0.2492	1.4715	-0.637	1.9951	36.1782	73.4656	70.9516
37	0.7045	0.6481	0.4278	0.7766	0.3671	0.5901	-0.0913	-0.425	0.2098	0.0943	0.3292	-0.5378	0.395	0.1323	-0.0666	1.8821	-0.7125	0.6304	1.4734	-0.7686	1.3019	24.2925	76.892	72.1713
38	0.2586	0.3811	-0.0822	0.552	-0.1183	0.016	-0.0027	0.2578	0.4799	0.1336	0.0213	-0.2577	-0.2583	0.5379	-0.0907	0.9731	-0.3464	-0.0196	0.9901	0.0891	1.532	81.9419	102.5431	25.5679
39	0.2928	0.1745	-0.2294	2.0996	-0.6028	1.8512	-0.2815	0.8112	0.6181	-0.7539	-0.3016	-0.4427	-0.4571	0.1662	0.2963	1.0914	-0.0824	0.0021	0.976	0.4575	1.4125	76.7759	96.2557	17.3937
40	1.9282	0.8717	-0.4659	1.7433	-0.2835	1.7212	-0.0233	-0.243	0.1245	-0.0773	-0.3748	-0.6514	0.1781	0.3143	0.1044	0.5243	-0.3304	-0.012	1.1568	0.5716	1.4183	85.0323	92.906	24.3716
41	0.4145	0.4189	0.0263	0.8305	0.3421	0.2539	-0.0803	0.3966	0.8327	-0.2958	-0.2825	-0.5716	-0.5322	0.5817	-0.2604	0.8842	-0.3114	0.3099	0.7596	0.6024	1.455	75.8942	97.4706	17.959
42	1.0569	0.1507	0.1449	3.564	-1.092	2.404	0.2592	0.491	0.3451	-0.3151	0.1934	0.0429	0.1081	-0.3913	-0.496	0.449	0.0321	-0.0518	0.5002	0.104	0.6611	38.9947	53.6977	42.9204
43	1.2589	-0.004	-0.0766	1.7437	0.2892	1.0406	0.358	-0.3403	0.6421	0.4838	-0.0116	0.5539	-0.4138	-0.0675	-0.2168	0.5332	0.0501	0.2026	0.4338	-0.0411	0.6977	45.0393	59.9424	53.4428
44	1.4461	0.2397	-0.1553	1.7882	-0.4028	1.5448	0.3801	-0.3195	0.4363	0.283	-0.4141	0.113	-0.0899	0.2119	0.0168	0.5094	-0.0277	0.0824	0.4637	-0.0745	0.5572	51.6156	60.6179	55.8736
45	1.1206	0.6653	-0.6688	1.7418	0.1537	1.1636	0.0265	0.0688	0.5164	-0.3167	0.2208	0.4312	-0.0143	0.362	-0.2002	0.5096	0.0059	0.0316	0.5806	0.1106	0.7466	53.209	70.9182	33.6195
46	1.5862	-0.1652	0.6119	0.8115	0.9954	3.9278	0.0369	-0.1588	0.5366	0.407	0.5924	0.2435	-0.1819	-0.0428	-0.3526	0.7557	0.0069	0.1534	0.3867	0.1211	1.1702	51.1349	85.3744	33.6808
47	0.6581	-0.5742	0.331	2.9628	-1.1056	4.0305	0.3443	0.6095	0.088	-0.6359	-0.0436	0.5223	0.6023	-0.6641	-0.3013	0.6439	0.0058	-0.0789	0.6903	0.1558	0.9585	44.3371	75.4283	19.1816
48	1.4806	-0.3645	0.7008	1.4234	0.0394	2.4819	0.0348	0.571	0.0755	-0.5339	0.1314	0.1257	-0.1758	0.1802	-0.1061	0.6701	-0.035	0.0169	0.7651	0.1939	0.8259	57.5775	79.3252	16.7616
49	1.5722	0.004	-0.729	1.4425	0.1275	2.3621	-0.392	0.1656	-0.0846	0.2437	-0.1797	0.5002	0.1066	0.2247	0.454	0.5282	0.1154	0.0581	0.5455	0.1818	0.788	57.3472	76.7081	32.4127
50	0.8773	0.7596	0.7415	0.6519	0.7921	3.0348	0.5866	-0.5035	0.598	1.2171	-0.2189	0.951	0.3436	0.8102	-0.0447	1.068	-0.1358	0.5596	0.8404	-0.1052	1.0776	-11.4061	35.3948	43.8658
51	2.5561	-0.565	-0.4573	0.1146	0.1015	0.0814	0.9397	-0.9814	0.3006	1.0136	-0.316	-0.0399	1.2304	0.293	0.2996	2.338	-0.3959	0.3095	0.9455	0.0679	0.6693	-2.5731	29.6815	57.5285
52	1.1922	0.4864	0.9562	0.6091	0.973	1.6987	0.9329	-0.8838	0.1119	1.8343	-0.6081	0.2943	0.4334	-0.0373	-0.1086	1.7836	-0.4589	0.5049	1.0572	-0.2873	0.6909	1.009	45.7316	55.9678
53	1.1943	-1.0389	-0.8641	1.8835	-0.0284	1.232	0.118	0.3147	0.1371	-0.0777	0.0479	0.8806	-0.2114	-0.3626	0.494	0.9294	-0.3805	0.7655	1.1882	-0.5771	1.8034	-6.5475	69.8561	53.6602
54	0.5382	-0.187	-0.0421	0.8843	0.2393	1.3683	0.1494	-0.2355	0.3066	0.6629	-0.2731	0.4375	0.2604	0.0501	-1.3619	1.3735	-0.4516	1.1449	1.1024	-0.677	1.2277	6.9352	68.6965	57.1496

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 3 through 39 )
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 40 through 51 )
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 52 through 122 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 123 through 130 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 847 through 886 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 887 through 1050 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 1051 through 1131 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 1132 through 1164 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 1165 through 1226 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 1227 through 1252 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 3 through 39 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 40 through 51 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 52 through 60 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 61 through 84 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 85 through 100 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 101 through 129 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 848 through 886 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 887 through 1050 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 1051 through 1085 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 1086 through 1131 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 1132 through 1164 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 1165 through 1226 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 1227 through 1252 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 1 through 39 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 40 through 51 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 52 through 129 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 848 through 886 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 887 through 976 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 977 through 1085 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 1086 through 1131 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 1132 through 1164 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 1165 through 1226 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 1227 through 1252 )
34	X-RAY DIFFRACTION	34	chain 'I' and (resid 3 through 24 )
35	X-RAY DIFFRACTION	35	chain 'I' and (resid 25 through 51 )
36	X-RAY DIFFRACTION	36	chain 'I' and (resid 52 through 91 )
37	X-RAY DIFFRACTION	37	chain 'I' and (resid 92 through 129 )
38	X-RAY DIFFRACTION	38	chain 'G' and (resid 4 through 31 )
39	X-RAY DIFFRACTION	39	chain 'G' and (resid 32 through 51 )
40	X-RAY DIFFRACTION	40	chain 'G' and (resid 52 through 84 )
41	X-RAY DIFFRACTION	41	chain 'G' and (resid 85 through 129 )
42	X-RAY DIFFRACTION	42	chain 'H' and (resid 849 through 886 )
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 887 through 936 )
44	X-RAY DIFFRACTION	44	chain 'H' and (resid 937 through 1050 )
45	X-RAY DIFFRACTION	45	chain 'H' and (resid 1051 through 1105 )
46	X-RAY DIFFRACTION	46	chain 'H' and (resid 1106 through 1131 )
47	X-RAY DIFFRACTION	47	chain 'H' and (resid 1132 through 1165 )
48	X-RAY DIFFRACTION	48	chain 'H' and (resid 1166 through 1226 )
49	X-RAY DIFFRACTION	49	chain 'H' and (resid 1227 through 1251 )
50	X-RAY DIFFRACTION	50	chain 'J' and (resid 848 through 914 )
51	X-RAY DIFFRACTION	51	chain 'J' and (resid 915 through 976 )
52	X-RAY DIFFRACTION	52	chain 'J' and (resid 977 through 1131 )
53	X-RAY DIFFRACTION	53	chain 'J' and (resid 1132 through 1164 )
54	X-RAY DIFFRACTION	54	chain 'J' and (resid 1165 through 1251 )

-
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