PDB-5ocl: Nanobody-anti-VGLUT nanobody complex

ID or keywords:

Entry

Database: PDB / ID: 5ocl

Title

Nanobody-anti-VGLUT nanobody complex

Components

anti-llama nanobody
anti-vglut nanobody

Keywords

IMMUNE SYSTEM / nanobody / vesicular glutamate transporter / inhibitor

Biological species

Vicugna pacos (alpaca)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Dutzler, R. / Schenck, S. / Kunz, L.

Funding support

Switzerland, 1items

Citation

Journal: Biochemistry / Year: 2017
Title: Generation and Characterization of Anti-VGLUT Nanobodies Acting as Inhibitors of Transport.
Authors: Schenck, S. / Kunz, L. / Sahlender, D. / Pardon, E. / Geertsma, E.R. / Savtchouk, I. / Suzuki, T. / Neldner, Y. / Stefanic, S. / Steyaert, J. / Volterra, A. / Dutzler, R.

History

Deposition	Jul 3, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 26, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 2, 2017	Group: Database references / Category: citation Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Aug 9, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ocl.cif.gz	391.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5ocl.ent.gz	325.1 KB	Display	PDB format
PDBx/mmJSON format	5ocl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oc/5ocl ftp://data.pdbj.org/pub/pdb/validation_reports/oc/5ocl	HTTPS FTP

-
Related structure data

Related structure data	4wgv PDB Unreleased entryS S: Starting model for refinement
Similar structure data	4q6s-d 1k6z-d 6fxo-d 4q7l-3 1ppy-d 4uob-d 5ftw-d 3epz-1 5rdi-d 2rha-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) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details)

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: anti-llama nanobody

B: anti-vglut nanobody

C: anti-llama nanobody

D: anti-vglut nanobody

E: anti-vglut nanobody

F: anti-llama nanobody

G: anti-vglut nanobody

H: anti-llama nanobody

107 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: anti-llama nanobody

B: anti-vglut nanobody

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

2

C: anti-llama nanobody

D: anti-vglut nanobody

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

3

E: anti-vglut nanobody

F: anti-llama nanobody

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

4

G: anti-vglut nanobody

H: anti-llama nanobody

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

Unit cell

Length a, b, c (Å)	126.295, 126.295, 240.270
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	90
Space group name H-M	P42₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-209- HOH
2	1	B-242- HOH
3	1	G-276- HOH
4	1	G-299- HOH

#1: Antibody	anti-llama nanobody Mass: 12725.299 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#2: Antibody	anti-vglut nanobody Mass: 13936.374 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 479 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.49 Å³/Da / Density % sol: 72.62 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 3.5 M Sodiumformate

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 24, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. obs: 99098 / % possible obs: 100 % / Redundancy: 26.2 % / CC_1/2: 1 / R_merge(I) obs: 0.166 / Net I/σ(I): 14.7
Reflection shell	Resolution: 2.2→2.3 Å / Redundancy: 26.6 % / R_merge(I) obs: 1.49 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 12196 / CC_1/2: 0.85 / % possible all: 100

-
Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4WGV

4wgv
PDB Unreleased entry

Resolution: 2.2→29.812 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.62

	R_factor	Num. reflection	% reflection
R_free	0.2077	4949	5 %
R_work	0.1879	-	-
obs	0.1889	99028	99.98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.2→29.812 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7373	0	0	479	7852

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7539
X-RAY DIFFRACTION	f_angle_d	0.539	10202
X-RAY DIFFRACTION	f_dihedral_angle_d	15.213	2727
X-RAY DIFFRACTION	f_chiral_restr	0.043	1072
X-RAY DIFFRACTION	f_plane_restr	0.003	1330

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 (%)
2.2-2.225	0.3088	162	0.2748	3080	X-RAY DIFFRACTION	100
2.225-2.2512	0.2797	163	0.2703	3095	X-RAY DIFFRACTION	100
2.2512-2.2786	0.2796	162	0.2512	3080	X-RAY DIFFRACTION	100
2.2786-2.3074	0.2662	163	0.2349	3088	X-RAY DIFFRACTION	100
2.3074-2.3378	0.2252	163	0.2382	3112	X-RAY DIFFRACTION	100
2.3378-2.3698	0.2453	161	0.2443	3066	X-RAY DIFFRACTION	100
2.3698-2.4036	0.3015	163	0.2505	3099	X-RAY DIFFRACTION	100
2.4036-2.4395	0.3081	163	0.2399	3101	X-RAY DIFFRACTION	100
2.4395-2.4776	0.2477	165	0.2438	3120	X-RAY DIFFRACTION	100
2.4776-2.5182	0.2745	162	0.2427	3087	X-RAY DIFFRACTION	100
2.5182-2.5616	0.2357	163	0.2324	3098	X-RAY DIFFRACTION	100
2.5616-2.6082	0.2513	163	0.2324	3083	X-RAY DIFFRACTION	100
2.6082-2.6583	0.2438	163	0.2265	3100	X-RAY DIFFRACTION	100
2.6583-2.7125	0.2232	164	0.2301	3119	X-RAY DIFFRACTION	100
2.7125-2.7715	0.2564	164	0.2295	3109	X-RAY DIFFRACTION	100
2.7715-2.8359	0.2739	163	0.2366	3111	X-RAY DIFFRACTION	100
2.8359-2.9067	0.2875	164	0.2424	3109	X-RAY DIFFRACTION	100
2.9067-2.9853	0.2744	164	0.2394	3122	X-RAY DIFFRACTION	100
2.9853-3.073	0.2092	165	0.2301	3139	X-RAY DIFFRACTION	100
3.073-3.1721	0.2453	165	0.2152	3134	X-RAY DIFFRACTION	100
3.1721-3.2853	0.2313	163	0.2052	3111	X-RAY DIFFRACTION	100
3.2853-3.4167	0.2088	167	0.1882	3161	X-RAY DIFFRACTION	100
3.4167-3.572	0.1971	165	0.1751	3145	X-RAY DIFFRACTION	100
3.572-3.7599	0.1999	166	0.1674	3145	X-RAY DIFFRACTION	100
3.7599-3.995	0.1788	166	0.157	3163	X-RAY DIFFRACTION	100
3.995-4.3026	0.139	167	0.1359	3177	X-RAY DIFFRACTION	100
4.3026-4.7341	0.1385	168	0.1266	3191	X-RAY DIFFRACTION	100
4.7341-5.4155	0.1654	170	0.1403	3224	X-RAY DIFFRACTION	100
5.4155-6.8096	0.2197	172	0.183	3264	X-RAY DIFFRACTION	100
6.8096-29.815	0.1905	180	0.1828	3446	X-RAY DIFFRACTION	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	0.0494	-0.0156	0.008	0.029	-0.0041	0.021	-0.2158	0.4582	0.2541	-0.2737	0.6451	-0.3026	-0.1507	0.1886	0.0039	0.6193	-0.0746	-0.02	0.6166	0.2051	0.9117	-18.8458	11.5695	228.248
2	0.0213	0.027	0.0063	0.0796	0.0785	0.0588	-0.1785	-0.37	0.3579	0.3189	0.4269	-0.5649	-0.497	-0.0693	-0	0.6939	0.0166	-0.2059	0.7215	0.1437	0.9904	-10.7516	-1.1752	245.5773
3	0.213	-0.0449	-0.0255	0.0137	-0.0422	0.0298	-0.1503	-0.1743	0.8155	-0.1692	0.0518	0.2259	-0.1017	0.3027	0.0049	0.589	-0.0702	-0.2604	0.5712	0.1721	0.8711	-19.3805	9.1017	237.676
4	0.0138	-0.0049	0.0042	0.0089	-0.0429	0.0334	0.2153	0.5008	0.3978	0.3109	-0.1062	-0.0381	-0.469	-0.2616	-0	0.572	0.0337	-0.0505	0.5716	0.2689	0.8936	-31.3506	14.2413	229.8
5	0.2804	-0.0357	0.3943	0.0354	-0.1068	0.3175	0.1868	0.4208	-0.0442	0.1963	-0.1352	-0.5274	0.0808	0.0411	0	0.4473	0.0453	-0.0706	0.5308	0.1053	0.7523	-22.7051	-3.6095	232.3533
6	0.1444	0.0946	-0.0503	0.0564	-0.0701	0.0921	-0.1102	-0.093	-0.3304	0.244	0.1116	0.1329	0.0066	-0.2193	0	0.526	0.0222	-0.1195	0.4569	0.1191	0.6645	-31.9137	-0.6328	239.3895
7	0.0489	0.0426	-0.0348	0.0406	0.0059	0.0776	-0.2677	-0.2261	0.3649	0.189	0.3151	-0.1178	-0.0028	-0.2055	-0	0.5332	0.0219	-0.1592	0.4759	0.0908	0.6259	-26.5112	2.4529	242.8193
8	-0.0041	0.0384	0.0531	0.0699	0.0857	0.0498	-0.0153	-0.0718	0.3328	-0.2915	0.0333	-0.1848	0.1033	0.1514	0	0.6093	-0.0314	-0.155	0.5726	0.1197	0.8809	-23.8662	10.4762	239.8605
9	0.0382	-0.0587	0.0111	0.0259	-0.0277	0.0205	0.0939	0.2342	-0.3112	0.1881	-0.1884	0.0458	0.0608	-0.0845	-0	0.5943	0.0269	-0.1269	0.5107	0.0991	0.7147	-16.5858	-7.1331	243.8026
10	0.0417	0.0184	-0.0305	0.0096	-0.0552	0.0636	0.0729	-0.0352	0.2164	-0.1893	-0.1694	-0.0956	-0.1127	0.0541	-0	0.4246	-0.0509	-0.0799	0.5034	0.137	0.7819	-19.0478	0.6258	231.7263
11	0.1307	-0.097	-0.2752	0.2624	0.156	0.2353	0.0156	0.571	0.3806	-0.3013	-0.1009	-0.6472	-0.0545	0.1355	0	0.4931	0.0184	0.0233	0.5787	0.2289	0.6958	-25.5393	6.2796	223.283
12	0.0506	0.0021	-0.0495	0.0184	-0.0677	0.0369	-0.1358	0.2845	0.1361	0.2683	0.279	0.141	0.4568	0.1457	0	0.5936	-0.0062	-0.1451	0.5947	0.1117	0.9174	-9.807	-3.3928	239.5858
13	0.0273	0.0153	0.0256	0.0299	-0.0248	0.0526	0.1915	0.0756	-0.248	-0.2756	-0.3173	0.489	0.3068	0.072	-0	0.5137	0.1044	0.07	0.5398	0.0775	0.4829	-40.9982	-10.1897	217.2629
14	0.2107	0.0868	0.0753	0.0217	0.12	0.1286	-0.0817	-0.0268	-0.3087	0.2688	-0.1956	-0.3237	-0.1841	-0.031	-0	0.4908	0.0432	0.0355	0.4581	0.1406	0.556	-41.6177	-15.6836	234.0372
15	0.6238	-0.5244	0.5148	0.7261	0.1929	0.6539	0.0589	0.0745	0.1384	0.0531	-0.1321	0.0134	0.0093	0.0149	0	0.4313	0.0034	0.0177	0.4674	0.0932	0.4617	-45.494	-2.9885	226.7623
16	0.2675	-0.0163	0.3825	0.3155	-0.3093	0.4404	-0.0328	0.028	-0.2077	0.1241	-0.116	-0.1506	0.0355	0.0005	-0	0.4481	-0.0201	-0.0128	0.511	0.0971	0.4676	-41.167	-5.6681	234.0336
17	0.1819	-0.0028	0.1916	0.1706	-0.1045	0.1286	-0.0734	0.017	-0.0305	0.016	-0.1672	-0.0905	0.0741	-0.1439	-0	0.4662	-0.0013	0.0585	0.4678	0.0797	0.5328	-49.7221	-12.9846	234.2984
18	0.0226	-0.0314	-0.0234	0.0425	-0.0067	-0.0005	0.1129	-0.0823	-0.2938	-0.2924	0.0006	0.0937	0.0196	0.031	-0	0.4508	0.0241	-0.0239	0.4385	0.0494	0.5339	-52.7081	1.108	218.9063
19	0.1362	0.0697	0.0739	0.021	0.0145	0.0482	-0.1271	0.3239	0.0055	0.1227	-0.1168	-0.4819	-0.2465	0.0429	-0	0.4151	0.0202	0.069	0.4846	0.0501	0.5738	-49.4592	-6.0025	218.5792
20	0.0739	-0.0472	0.0359	0.0283	0.0044	0.0654	-0.3103	0.1139	-0.2821	0.2164	-0.1168	-0.0243	0.2221	0.0803	0.0001	0.5321	-0.0424	0.0854	0.4256	0.1436	0.4919	-49.6309	-20.3216	235.6198
21	0.0093	0.0298	-0.0369	0.0493	-0.0783	0.1159	-0.4648	-0.2311	0.0637	0.1417	0.063	0.2647	0.4376	-0.7222	0	0.5661	0.0099	0.0569	0.6236	-0.046	0.683	-57.9601	-16.5534	213.0234
22	1.9828	0.7252	1.048	1.7244	0.9933	1.0043	-0.0462	-0.2353	0.0335	0.0555	-0.4623	0.4118	1.0625	0.1731	-0.7043	0.7862	0.228	0.3045	0.6018	0.3077	0.418	-44.6461	-28.2763	214.5537
23	0.0126	-0.0011	-0.0158	-0.0231	0.0018	0.0279	-0.9943	-0.6294	0.103	-0.1843	-0.3218	0.643	0.387	-0.5004	0	0.6395	-0.1453	0.2269	0.8054	-0.1824	0.9172	-61.5555	-20.2165	201.3627
24	0.2658	-0.1414	0.017	-0.0297	0.072	0.3978	-0.4673	-0.1462	-0.2036	-0.1376	0.0784	-0.2314	0.278	0.1694	-0.0004	0.6541	0.0661	0.1951	0.5097	0.0771	0.5303	-42.7174	-21.4034	202.6466
25	0.073	-0.081	-0.1267	-0.0212	0.0395	0.2151	-0.6693	-0.0133	-0.3282	-0.1081	-0.0724	-0.2852	0.9998	-0.1002	-0.0044	0.8178	-0.0281	0.3712	0.5366	0.0044	0.7876	-52.0364	-29.1828	206.1891
26	0.0217	-0.056	-0.0677	0.0463	0.0594	0.0778	-0.3657	0.3698	-0.4499	-0.0341	0.2442	-0.365	0.0987	0.3167	-0	0.767	0.1998	0.2379	0.7781	0.1015	0.8296	-34.1444	-27.5123	210.3284
27	0.2693	0.0512	-0.3237	-0.0475	0.0153	0.3967	-0.3358	-0.1834	-0.215	-0.0352	0.0492	0.0559	0.1259	-0.0734	0	0.5526	0.0173	0.0714	0.4963	0.0442	0.4403	-51.4764	-13.946	206.9982
28	0.0217	0.0125	0.0188	0.0142	0.0126	0.0213	0.031	-0.3207	0.1351	0.3215	-0.2153	-0.0527	-0.1071	0.5403	0	0.6036	0.2459	0.1153	0.7413	0.1954	0.7285	-36.7928	-24.0973	217.7466
29	0.0586	0.0506	-0.0174	0.0691	-0.0194	-0.0061	0.1471	-0.1523	0.4467	-0.05	-0.0345	0.5967	-0.5452	0.8966	-0.0001	0.6826	-0.008	0.0375	0.632	0.028	0.6043	-44.3694	-3.2496	185.9532
30	0.0224	0.034	0.016	0.0122	0.0448	0.0204	-0.3917	0.2479	-0.1513	0.1607	-0.772	-0.2206	0.3529	0.3853	-0.003	0.6996	0.1847	0.3451	1.0021	0.0425	1.0662	-29.2394	-22.8471	180.9668
31	0.3638	0.5156	-0.4437	0.3782	-0.3728	0.4177	-0.1024	-0.0022	0.3059	-0.0556	0.0944	0.0441	-0.0433	0.1055	0	0.5875	-0.0282	0.0803	0.5962	0.0043	0.4375	-46.4154	-10.9516	187.0313
32	0.1666	-0.0039	0.0866	0.0907	-0.0253	0.0672	0.1036	0.2093	-0.12	-0.1507	-0.2829	0.0831	-0.3421	-0.1143	-0	0.6808	-0.0157	0.0872	0.6116	-0.05	0.4908	-46.4605	-17.5216	175.5385
33	0.0256	0.043	-0.0791	0.0536	-0.0682	0.0489	0.0839	0.1546	0.0611	0.2704	0.262	0.4371	0.0066	-0.5892	0	0.7299	-0.0215	0.1558	0.5631	-0.0392	0.5135	-52.9014	-19.3661	190.1491
34	0.0048	0.0109	-0.0076	0.0291	0.0061	0.0233	-0.2973	0.3413	-0.5522	-0.3346	0.0464	0.1497	0.5362	-0.1956	-0	1.0389	-0.0444	0.1556	0.7239	-0.1682	0.5849	-45.063	-28.3307	178.8272
35	0.2288	0.1602	0.0126	0.0801	-0.1301	0.1921	0.0549	-0.3266	-0.4465	-0.135	-0.3894	-0.4393	-0.1049	0.2247	0	0.6239	-0.0065	0.1142	0.5678	0.0469	0.4988	-43.5852	-17.1699	191.6376
36	0.0421	0.037	0.0228	0.0267	-0.0019	0.0078	0.2946	0.3852	-0.3331	-0.0592	-0.0217	0.023	0.594	0.2521	-0	1.1486	0.2083	0.2503	0.959	-0.0915	0.7405	-35.7029	-25.9358	176.728
37	0.0098	0.0176	0.0015	0.0133	0.0137	-0.0044	-0.6678	-0.4537	-0.3025	-0.0853	-0.0103	0.0258	0.0691	0.2699	-0	0.6633	-0.0236	0.0621	0.6997	0.0037	0.387	-42.3352	-12.9099	179.3291
38	0.097	-0.0511	-0.0679	0.1395	-0.0171	0.0685	-0.7527	0.8444	0.3947	-0.3809	0.2224	0.1147	-0.5183	-0.2649	-0	0.7504	-0.0679	-0.0311	0.8524	0.0027	0.7425	-51.7282	-8.1068	179.22
39	0.1938	0.1151	0.0881	0.0731	0.0082	0.2138	-0.1794	0.3522	-0.0984	-0.13	0.1275	-0.1798	0.2433	0.644	0.2463	0.9564	0.1823	0.3961	1.0099	0.0571	0.5509	-31.407	-19.0903	176.1779
40	0.0176	0.0325	-0.0173	0.0285	-0.0513	0.0233	0.4387	-0.1513	-0.2207	-0.0382	0.0287	0.3836	0.8024	0.0709	0	0.6812	-0.0485	-0.0509	0.4998	0.0137	0.5121	-47.7686	-11.1525	156.6254
41	0.0542	0.4899	-0.2524	1.3215	-0.8763	1.0956	0.0015	-0.1797	-0.2224	0.0847	0.0472	0.0436	0.3374	0.0431	-0	0.5779	0.0426	-0.077	0.4583	0.0032	0.3623	-38.2468	-5.5039	157.1389
42	0.0932	-0.0497	-0.0074	0.0348	0.09	0.1043	-0.0306	-0.2378	-0.0386	-0.0364	0.0112	-0.1206	-0.0858	0.064	0	0.6616	0.0498	-0.1013	0.5695	0.0194	0.3453	-38.6962	0.2533	166.9624
43	0.3577	0.1231	-0.375	0.2947	-0.1369	0.2755	-0.0721	0.1375	0.2419	0.2654	-0.0532	0.0314	-0.571	0.0575	0.0323	0.6771	-0.0749	-0.1758	0.4222	0.006	0.3422	-36.415	6.4861	157.3664
44	0.1824	-0.2237	-0.4453	1.1478	0.2576	1.261	-0.1152	-0.1245	-0.0674	0.1104	-0.0235	-0.101	0.1789	0.1745	-0	0.5792	0.0425	-0.0561	0.5011	0.0693	0.3218	-37.253	-3.6009	159.842
45	-0.0048	-0.1457	0.0444	0.5712	-0.5565	1.2577	-0.0985	0.1505	-0.1148	0.2065	-0.0592	-0.1027	-0.2874	0.0851	-0	0.4209	-0.0374	-0.0295	0.4019	-0.0018	0.4521	-38.8076	8.103	131.3413
46	0.2664	0.0689	0.0794	0.112	-0.1994	0.3434	-0.0413	0.2198	-0.1532	0.2672	-0.1273	-0.09	0.0529	0.0202	0	0.4109	0.0052	-0.021	0.4027	-0.0047	0.3955	-36.2444	-4.9933	135.4279
47	-0.0566	-0.2609	-0.1203	0.1286	0.0098	1.2876	-0.0178	0.0446	0.035	0.3027	-0.1084	-0.2624	-0.1844	0.256	-0	0.4184	-0.0654	-0.1127	0.4376	0.0383	0.4591	-30.5416	5.3692	138.3235
48	0.3295	-0.0958	0.5478	0.4723	-0.0305	0.565	-0.043	0.3435	0.0649	0.1645	-0.1053	-0.2205	-0.1264	-0.0823	0	0.3532	-0.0158	-0.0396	0.3631	0.0018	0.3151	-40.3194	0.1647	132.7829
49	0.1845	0.2353	0.0541	0.4092	-0.0796	0.6257	0.0127	0.0217	-0.0198	-0.0411	-0.0381	-0.0575	0.0398	0.0759	0	0.2836	0.0236	0.0122	0.3063	-0.003	0.3289	-44.5577	-9.0106	115.7862
50	0.5021	0.3798	-0.177	0.5716	0.2228	0.3766	-0.0206	-0.031	0.053	-0.0293	0.0566	-0.0399	0	0.0531	0	0.2462	0.0249	0.0105	0.2592	-0.004	0.2739	-46.1893	-7.8368	111.2653
51	0.7465	-0.2747	0.14	0.5471	0.3242	0.1431	-0.1164	-0.0514	-0.3195	-0.0388	-0.0869	-0.2274	-0.0023	0.0106	-0	0.2849	0.0032	-0.0103	0.3073	-0.0084	0.3427	-45.8049	-2.3237	118.385
52	0.0378	-0.0721	0.0322	0.0712	-0.0685	0.0416	0.0794	-0.2093	-0.2805	-0.102	0.3757	0.1948	0.1107	0.0972	0	0.3703	0.0155	-0.014	0.4077	0.0559	0.3443	-41.4357	-39.8097	114.0866
53	0.4373	-0.2192	-0.08	0.1676	0.0236	0.1233	0.0016	0.4187	-0.5433	-0.2913	-0.2751	0.0965	0.394	-0.0236	0.0114	0.5057	0.0898	0.0676	0.4029	-0.0162	0.3228	-26.5643	-36.6952	96.4908
54	0.0209	0.026	-0.1335	-0.0308	-0.0127	-0.0186	0.2656	0.1018	-0.0895	-0.3788	-0.2603	0.6174	-0.036	-0.1294	0.0007	0.4649	0.014	0.0184	0.4056	-0.1107	0.4065	-40.0427	-37.658	104.6581
55	0.0052	-0.0033	-0.0031	0.0228	0.0039	0.0413	-0.0013	-0.3664	0.5573	-0.4928	0.2727	0.5359	0.0792	-0.4984	-0	0.337	-0.0154	-0.0133	0.4191	0.0217	0.4388	-51.8362	-32.4791	113.2022
56	0.1068	-0.0034	-0.2754	0.8352	0.1636	0.2688	0.0226	-0.0093	0.0888	-0.069	0.0222	-0.035	-0.0171	0.0538	0	0.3163	0.0267	0.0246	0.3734	-0.0249	0.3436	-36.3462	-26.1544	108.8165
57	0.3338	-0.4166	-0.0031	0.3784	-0.1876	0.4543	-0.1037	-0.0658	0.4526	-0.1492	-0.0834	0.216	0.0679	0.078	0	0.3463	0.0117	0.0217	0.3794	-0.0055	0.3831	-37.8963	-25.888	100.5335
58	0.1086	0.1049	0.1274	0.0184	0.0303	0.0499	0.1139	-0.1568	-0.4643	-0.1506	-0.137	0.0415	0.1478	0.0775	-0	0.3901	0.0248	0.0232	0.3939	-0.0392	0.3914	-44.0416	-35.3338	102.6853
59	-0.0299	-0.0467	0.1426	0.1187	0.1733	0.3505	-0.0524	0.0909	0.2303	0.0005	-0.078	-0.0344	-0.0062	0.0906	0	0.3456	0.0567	0.0191	0.3465	0.0172	0.3581	-29.5865	-30.4776	104.2994
60	0.1868	0.057	0.2237	0.2405	-0.1986	0.3766	-0.2178	-0.1738	-0.5421	0.3569	0.0505	0.0169	0.1506	0.127	0	0.3437	0.0518	0.0323	0.3291	0.0094	0.3475	-41.9699	-31.6419	119.6573
61	0.0239	0.028	0.0275	0.2672	0.0024	0.0973	-0.4024	-0.0238	0.3083	0.5538	0.3439	-0.907	0.1341	0.1441	-0.004	0.385	0.0969	0.0114	0.3971	-0.0644	0.4819	-24.5278	-35.8483	102.8327

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 9 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 10 through 19 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 20 through 27 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 28 through 35 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 36 through 53 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 54 through 65 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 66 through 74 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 75 through 84 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 85 through 92 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 93 through 98 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 99 through 110 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 111 through 117 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 0 through 9 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 10 through 28 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 29 through 62 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 63 through 85 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 86 through 100 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 101 through 109 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 110 through 119 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 120 through 126 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 1 through 9 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 10 through 27 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 28 through 35 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 36 through 68 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 69 through 84 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 85 through 92 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 93 through 110 )
28	X-RAY DIFFRACTION	28	chain 'C' and (resid 111 through 117 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 1 through 9 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 10 through 19 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 20 through 41 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 42 through 54 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 55 through 62 )
34	X-RAY DIFFRACTION	34	chain 'D' and (resid 63 through 69 )
35	X-RAY DIFFRACTION	35	chain 'D' and (resid 70 through 85 )
36	X-RAY DIFFRACTION	36	chain 'D' and (resid 86 through 93 )
37	X-RAY DIFFRACTION	37	chain 'D' and (resid 94 through 100 )
38	X-RAY DIFFRACTION	38	chain 'D' and (resid 101 through 119 )
39	X-RAY DIFFRACTION	39	chain 'D' and (resid 120 through 126 )
40	X-RAY DIFFRACTION	40	chain 'E' and (resid 1 through 9 )
41	X-RAY DIFFRACTION	41	chain 'E' and (resid 10 through 41 )
42	X-RAY DIFFRACTION	42	chain 'E' and (resid 42 through 54 )
43	X-RAY DIFFRACTION	43	chain 'E' and (resid 55 through 69 )
44	X-RAY DIFFRACTION	44	chain 'E' and (resid 70 through 126 )
45	X-RAY DIFFRACTION	45	chain 'F' and (resid 0 through 35 )
46	X-RAY DIFFRACTION	46	chain 'F' and (resid 36 through 47 )
47	X-RAY DIFFRACTION	47	chain 'F' and (resid 48 through 92 )
48	X-RAY DIFFRACTION	48	chain 'F' and (resid 93 through 117 )
49	X-RAY DIFFRACTION	49	chain 'G' and (resid 0 through 62 )
50	X-RAY DIFFRACTION	50	chain 'G' and (resid 63 through 109 )
51	X-RAY DIFFRACTION	51	chain 'G' and (resid 110 through 126 )
52	X-RAY DIFFRACTION	52	chain 'H' and (resid 3 through 9 )
53	X-RAY DIFFRACTION	53	chain 'H' and (resid 10 through 19 )
54	X-RAY DIFFRACTION	54	chain 'H' and (resid 20 through 27 )
55	X-RAY DIFFRACTION	55	chain 'H' and (resid 28 through 35 )
56	X-RAY DIFFRACTION	56	chain 'H' and (resid 36 through 61 )
57	X-RAY DIFFRACTION	57	chain 'H' and (resid 62 through 74 )
58	X-RAY DIFFRACTION	58	chain 'H' and (resid 75 through 84 )
59	X-RAY DIFFRACTION	59	chain 'H' and (resid 85 through 98 )
60	X-RAY DIFFRACTION	60	chain 'H' and (resid 99 through 110 )
61	X-RAY DIFFRACTION	61	chain 'H' and (resid 111 through 117 )

-
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