PDB-5jmc: Receptor binding domain of Botulinum neurotoxin A in complex with...

ID or keywords:

Entry

Database: PDB / ID: 5jmc

Title

Receptor binding domain of Botulinum neurotoxin A in complex with rat SV2C

Components

Botulinum neurotoxin type A
Synaptic vesicle glycoprotein 2C

Keywords

HYDROLASE

Function / homology

Function and homology information

host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / dopaminergic synapse / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / neurotransmitter transport / regulation of synaptic vesicle exocytosis / protein transmembrane transporter activity ...
Similarity search - Function

Biological species

Clostridium botulinum (bacteria)

Rattus norvegicus (Norway rat)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.64 Å

Authors

Yao, G. / Zhang, S. / Mahrhold, S. / Lam, K. / Stern, D. / Bagramyan, K. / Perry, K. / Kalkum, M. / Rummel, A. / Dong, M. / Jin, R.

Funding support

United States, 1items

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2016
Title: N-linked glycosylation of SV2 is required for binding and uptake of botulinum neurotoxin A.
Authors: Yao, G. / Zhang, S. / Mahrhold, S. / Lam, K.H. / Stern, D. / Bagramyan, K. / Perry, K. / Kalkum, M. / Rummel, A. / Dong, M. / Jin, R.

History

Deposition	Apr 28, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 15, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 3, 2016	Group: Database references
Revision 1.2	Sep 27, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3	Dec 11, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Sep 27, 2023	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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5jmc.cif.gz	845.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5jmc.ent.gz	709.9 KB	Display	PDB format
PDBx/mmJSON format	5jmc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5jmc_validation.pdf.gz	496.9 KB	Display	wwPDB validaton report
Full document	5jmc_full_validation.pdf.gz	548.7 KB	Display
Data in XML	5jmc_validation.xml.gz	76.1 KB	Display
Data in CIF	5jmc_validation.cif.gz	103.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jm/5jmc ftp://data.pdbj.org/pub/pdb/validation_reports/jm/5jmc	HTTPS FTP

-
Related structure data

Related structure data	5jlvC 3fuoS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4jra-2 5mfc-1 5jlv-1 2w68-d 3tg1-d 6kr1-4 1o20-d 4biz-3 6kr1-3 6kr1-1 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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5jlvC

3fuoS

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#208 - Apr 2017 Glucose Transporters similarity (8) #39 - Mar 2003 lac Repressor similarity (6) #95 - Nov 2007 Multidrug Resistance Transporters similarity (5)

Deposited unit

A: Botulinum neurotoxin type A

B: Synaptic vesicle glycoprotein 2C

C: Botulinum neurotoxin type A

D: Synaptic vesicle glycoprotein 2C

E: Botulinum neurotoxin type A

F: Synaptic vesicle glycoprotein 2C

G: Botulinum neurotoxin type A

H: Synaptic vesicle glycoprotein 2C

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

1

A: Botulinum neurotoxin type A

B: Synaptic vesicle glycoprotein 2C

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

2

C: Botulinum neurotoxin type A

D: Synaptic vesicle glycoprotein 2C

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

3

E: Botulinum neurotoxin type A

F: Synaptic vesicle glycoprotein 2C

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

4

G: Botulinum neurotoxin type A

H: Synaptic vesicle glycoprotein 2C

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

Unit cell

Length a, b, c (Å)	88.662, 143.989, 110.917
Angle α, β, γ (deg.)	90.00, 93.62, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Botulinum neurotoxin type A / BoNT/A / Bontoxilysin-A / BOTOX Mass: 50472.195 Da / Num. of mol.: 4 / Fragment: UNP residues 872-1296 / Mutation: A1158T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, atx, bna / Production host: Escherichia coli (E. coli) References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Protein	Synaptic vesicle glycoprotein 2C / Synaptic vesicle protein 2C Mass: 14522.051 Da / Num. of mol.: 4 / Fragment: UNP residues 455-577 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Sv2c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z2I6
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.74 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 100 mM sodium cacodylate, pH 6.5, 13% polyethylene glycol (PEG) 3350, 200 mM NaCl

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 2.64→87.76 Å / Num. obs: 81176 / % possible obs: 99.44 % / Redundancy: 3.4 % / R_merge(I) obs: 0.151 / Net I/σ(I): 9.09
Reflection shell	Resolution: 2.64→2.73 Å / Redundancy: 3.1 % / R_merge(I) obs: 1.132 / Mean I/σ(I) obs: 1.43 / % possible all: 99.2

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3FUO

3fuo

Resolution: 2.64→87.759 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.95

	R_factor	Num. reflection	% reflection
R_free	0.2747	4058	5.01 %
R_work	0.2395	-	-
obs	0.2413	80958	99.3 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.64→87.759 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16825	0	0	162	16987

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	17189
X-RAY DIFFRACTION	f_angle_d	1.219	23213
X-RAY DIFFRACTION	f_dihedral_angle_d	13.652	6319
X-RAY DIFFRACTION	f_chiral_restr	0.064	2487
X-RAY DIFFRACTION	f_plane_restr	0.005	2977

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 (%)
2.64-2.6711	0.3941	134	0.3788	2625	X-RAY DIFFRACTION	99
2.6711-2.7036	0.4212	154	0.3721	2630	X-RAY DIFFRACTION	99
2.7036-2.7379	0.3964	136	0.3579	2601	X-RAY DIFFRACTION	100
2.7379-2.7739	0.3823	140	0.3424	2719	X-RAY DIFFRACTION	99
2.7739-2.8119	0.3299	126	0.3394	2637	X-RAY DIFFRACTION	100
2.8119-2.8521	0.3878	137	0.3331	2655	X-RAY DIFFRACTION	100
2.8521-2.8946	0.376	145	0.333	2606	X-RAY DIFFRACTION	99
2.8946-2.9399	0.383	140	0.3122	2675	X-RAY DIFFRACTION	99
2.9399-2.9881	0.352	133	0.2955	2658	X-RAY DIFFRACTION	100
2.9881-3.0396	0.3186	143	0.2974	2662	X-RAY DIFFRACTION	100
3.0396-3.0949	0.2959	125	0.2988	2638	X-RAY DIFFRACTION	100
3.0949-3.1544	0.3109	129	0.29	2702	X-RAY DIFFRACTION	100
3.1544-3.2188	0.3336	119	0.277	2659	X-RAY DIFFRACTION	100
3.2188-3.2888	0.3039	161	0.2696	2660	X-RAY DIFFRACTION	100
3.2888-3.3653	0.2976	134	0.2622	2678	X-RAY DIFFRACTION	100
3.3653-3.4495	0.301	140	0.2515	2628	X-RAY DIFFRACTION	100
3.4495-3.5427	0.2721	160	0.2422	2650	X-RAY DIFFRACTION	100
3.5427-3.647	0.2446	121	0.2352	2657	X-RAY DIFFRACTION	100
3.647-3.7647	0.2407	152	0.2292	2664	X-RAY DIFFRACTION	100
3.7647-3.8992	0.273	145	0.2288	2646	X-RAY DIFFRACTION	100
3.8992-4.0554	0.266	135	0.2175	2675	X-RAY DIFFRACTION	100
4.0554-4.2399	0.2104	153	0.1939	2662	X-RAY DIFFRACTION	99
4.2399-4.4635	0.2449	133	0.1866	2651	X-RAY DIFFRACTION	99
4.4635-4.7431	0.2017	129	0.171	2659	X-RAY DIFFRACTION	99
4.7431-5.1093	0.224	162	0.1869	2637	X-RAY DIFFRACTION	99
5.1093-5.6234	0.2688	143	0.195	2649	X-RAY DIFFRACTION	99
5.6234-6.4369	0.2378	136	0.2131	2658	X-RAY DIFFRACTION	99
6.4369-8.1089	0.2259	143	0.2211	2655	X-RAY DIFFRACTION	98
8.1089-87.8076	0.2478	150	0.1961	2604	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	1.9922	0.234	-0.0414	5.3686	-0.309	3.3993	-0.0749	0.0149	0.1877	-0.101	-0.0025	-0.1815	-0.5377	0.082	0.0629	0.3459	0.0134	-0.0071	0.2726	-0.0154	0.2284	93.8624	61.2761	-4.4941
2	2.4823	0.7646	0.4663	6.9768	-1.0914	3.5692	-0.0458	0.2952	0.1666	-0.6779	-0.1009	0.1018	-0.0639	-0.6623	0.075	0.3616	-0.0214	-0.024	0.4405	-0.0919	0.2776	84.7617	44.26	-15.0119
3	1.6998	0.9164	0.3955	3.5439	2.5327	4.7775	-0.2637	0.6351	-0.3989	-0.6075	-0.0609	0.1908	1.0268	-1.0123	0.2622	0.8515	-0.2436	0.0937	0.7042	-0.082	0.509	80.6	28.4306	-18.761
4	4.2579	-0.158	-0.2565	9.6191	-1.4999	6.8043	-0.2644	0.3885	0.0024	-0.4913	0.3032	0.7692	0.0981	-1.6515	-0.0641	0.6253	-0.0553	-0.0582	0.6433	-0.0437	0.4585	76.3563	36.5178	-15.2541
5	3.3251	-0.3889	-0.7559	7.6971	-2.0916	4.204	-0.1892	0.683	-0.3188	0.1005	-0.0424	-0.7064	0.5785	0.0497	0.1699	0.5339	-0.0901	0.0289	0.3823	-0.0018	0.4543	92.1091	32.4683	-2.0045
6	5.7321	1.0214	5.4818	3.049	4.1732	8.8644	0.265	-0.3491	-1.0069	2.0805	0.1084	-0.2321	1.682	-0.1949	-0.4215	0.925	-0.0418	-0.0026	0.5945	0.0591	0.9011	95.7093	15.0581	17.3165
7	4.4075	0.3658	0.7253	5.5193	-0.8431	2.6183	0.2275	-0.2937	-0.0153	0.1588	-0.18	-0.9711	0.279	0.3825	-0.032	0.6607	-0.1148	-0.0366	0.4497	0.0981	0.3554	93.3397	19.1543	16.3518
8	4.9386	-0.5186	2.4921	3.9016	0.9351	4.8549	0.3288	-0.2679	0.2812	0.6548	-0.1877	-0.4558	-0.2636	-0.1089	-0.0783	0.9265	-0.047	0.0892	0.2921	0.0168	0.46	92.0976	23.7541	17.1429
9	4.916	1.5875	-0.834	7.508	-1.3811	4.7469	-0.0797	-0.4386	-0.0687	0.7624	-0.0613	0.443	0.0496	-0.3187	0.1483	0.5018	-0.0416	0.0431	0.3898	0.0251	0.2873	85.2945	25.9904	16.053
10	3.5433	3.6184	4.6309	3.9611	4.3016	8.9692	0.4363	1.1005	0.8436	-0.5421	-0.0501	1.7033	0.1344	-0.0664	-0.1672	0.8604	0.0033	0.0397	0.5744	0.0571	0.7841	83.2276	27.0438	6.4781
11	1.9182	-0.4121	-0.0699	7.7024	1.8584	2.9269	0.05	0.083	-0.0254	-0.8467	-0.1948	0.6535	-0.3016	-0.1671	0.1342	0.4729	0.0614	-0.0455	0.3014	-0.0194	0.3357	38.6919	47.6762	5.5566
12	1.9063	-0.196	0.5527	4.5378	-1.8041	4.5363	0.1067	-0.2777	-0.3514	0.5558	-0.0811	0.117	0.678	0.5709	0.0007	0.7133	0.1019	0.0323	0.3661	-0.0268	0.5094	46.9434	18.1001	13.9933
13	4.9126	-0.4173	-1.3727	4.4085	-0.1152	1.9587	0.1527	-0.7562	-0.062	0.7957	-0.0276	-0.0675	1.0436	0.985	-0.0356	1.1917	0.3119	-0.076	0.7267	-0.0215	0.4961	56.7125	15.3813	25.2822
14	8.442	-2.9683	-3.1964	8.0595	-3.7599	9.4733	0.5713	-1.4136	0.3523	1.6466	0.8359	-0.5863	-0.4147	0.9128	-1.3526	1.367	0.1124	-0.0286	0.7819	-0.0586	0.6885	60.1728	24.5489	17.9613
15	0.5685	-0.0925	1.4976	4.4129	-1.8664	4.5554	0.018	0.1553	0.5567	1.515	0.2456	0.0995	0.2995	-0.0686	-0.0924	0.2571	0.0071	-0.0602	0.4938	-0.1462	0.4889	48.4655	22.6091	13.6823
16	3.1761	-2.3448	0.0913	5.388	-5.3247	8.072	0.9935	-0.2745	0.4063	-1.4146	-0.022	1.4597	-0.933	-1.3879	-0.7874	0.7334	0.0971	-0.1023	0.469	-0.1068	0.6328	39.559	25.0112	3.5052
17	3.6651	1.9171	-3.4489	1.0008	-1.8035	3.2534	-0.4167	0.02	-1.5794	-1.2054	0.0201	0.0036	2.055	-0.0044	0.3432	0.7701	-0.0505	-0.0441	0.3107	0.0232	0.6604	40.9649	15.1248	0.2829
18	2.2381	0.4007	-0.0318	3.8368	-2.5382	3.6648	0.0331	0.6089	-0.2434	-0.2055	-0.1534	0.5457	0.7078	-0.1391	0.1135	0.6392	0.0095	-0.0104	0.6698	-0.1934	0.5974	36.4947	4.0752	-17.5723
19	6.0782	-2.6867	1.0419	6.1751	-1.0806	6.0068	-0.0305	0.7427	-0.0516	-0.4362	-0.2405	0.0111	0.3661	-0.037	0.2914	0.7121	-0.0137	0.0128	0.3228	-0.0467	0.3928	42.1386	6.5224	-16.8878
20	2.5127	1.622	0.2178	1.5096	1.3708	3.5569	0.0181	0.0009	0.2732	0.4431	-0.0677	-0.1177	-0.4994	0.1374	0.0272	0.8103	0.0426	0.075	0.3342	-0.0309	0.4504	46.877	12.4743	-13.6109
21	6.338	0.3004	-4.175	1.6256	-1.5538	5.4958	-0.2776	-1.058	0.0459	0.3292	-0.0081	-0.1592	0.1469	0.7233	0.2616	0.6603	0.0394	-0.0827	0.5233	-0.0392	0.4054	57.2343	5.5284	-35.7133
22	2.1581	0.0863	0.0398	6.0291	-0.7214	3.2691	-0.0127	0.1366	-0.0591	-0.5535	-0.0352	-0.0558	0.1262	0.087	0.0535	0.4128	-0.0096	0.0319	0.3007	0.0004	0.1978	51.2718	7.2734	-51.4007
23	1.5404	0.2996	0.0008	1.5896	2.0581	2.9045	0.0749	-0.2679	0.4383	0.0918	-0.3644	0.2596	-0.6324	-0.847	0.0743	0.9304	0.109	0.083	0.3915	-0.0021	0.504	41.2126	35.6362	-45.7663
24	3.7248	0.4965	1.632	2.328	-0.0848	3.6509	-0.1558	-0.4759	0.5038	0.4295	0.0675	0.5241	-0.8	-0.7206	0.1323	1.4105	0.1987	0.1426	0.6521	-0.1191	0.6977	38.37	39.267	-30.5531
25	1.2008	-0.0119	1.0511	2.2862	-3.0609	4.9614	0.1442	-0.3085	0.1089	0.7446	0.9947	1.2347	-1.4918	-1.8943	-0.8817	1.2369	0.4283	0.1719	1.4351	-0.0909	0.8067	25.5686	38.2704	-37.1221
26	4.8979	1.0527	-3.2107	9.8095	1.8567	2.9309	0.313	-2.5304	1.8573	1.6832	0.5871	0.3466	-0.6843	-0.0716	-0.9032	1.4388	0.2517	0.2282	1.3471	-0.0851	1.0358	26.3728	29.862	-40.8418
27	7.5288	1.3863	-2.7074	2.4317	0.2444	5.6792	-1.196	-0.0988	-0.7298	0.3995	0.4021	0.0914	0.5213	0.1744	0.854	0.6398	-0.0546	0.1245	0.273	0.0028	0.4773	44.3365	31.2038	-44.9229
28	8.0075	6.0232	0.8491	9.2743	-0.1733	0.2318	0.1709	-0.8911	0.5516	-0.2818	-0.1219	0.4798	-1.389	0.54	0.0544	1.1063	-0.0692	0.2232	0.3857	-0.072	0.4794	49.5341	37.1547	-54.681
29	7.2902	2.4382	-2.7398	6.8106	1.5531	4.4502	-0.0049	0.0445	-0.0735	0.0043	0.0365	-1.1094	-1.0319	1.7145	-0.0467	0.4396	-0.0465	-0.067	0.5345	0.0988	0.4963	61.0101	49.4039	-67.9324
30	3.9843	3.1588	0.0685	3.0954	-0.5676	4.7591	-0.1486	0.5431	0.7426	-0.1016	0.1315	0.3231	-1.112	0.1998	-0.0952	0.6015	0.0624	0.0333	0.5269	0.0682	0.5778	54.8949	50.5478	-71.8444
31	8.8227	-1.4014	-1.5818	0.4338	0.5043	3.147	0.576	1.0028	0.2499	0.0647	-0.5527	0.5417	-1.2187	-0.5045	0.007	0.9675	0.0402	0.0557	0.3452	0.0665	0.3835	48.5177	50.6367	-75.574
32	4.7499	0.8414	0.8844	1.6617	-1.6881	4.4856	0.0221	-0.0067	-0.0303	0.381	-0.1798	-0.0697	-0.0487	-0.002	0.1063	0.7052	0.0133	0.0518	0.338	-0.0151	0.4027	49.9086	43.844	-71.5615
33	3.4815	-0.0514	-0.1098	3.2194	-2.2992	6.9153	-0.1967	-0.0937	-0.0982	1.3922	0.4469	-0.0097	-0.4058	-1.005	-0.1886	0.9133	0.0205	0.207	0.3315	-0.0649	0.6026	44.4856	43.9849	-65.3171
34	2.8041	-0.6447	0.7061	4.8233	-0.4147	4.6474	-0.0098	-0.3022	-0.2183	0.6178	-0.1039	0.1324	0.6878	-0.2933	0.1745	0.8422	-0.0758	0.0622	0.4475	-0.0423	0.6541	45.2993	37.9828	-69.5976
35	1.7159	0.1078	0.1917	4.9306	0.2719	1.8696	-0.1037	0.0253	-0.1696	0.1859	-0.0247	0.3624	0.6592	-0.2037	0.1083	0.7028	-0.1168	0.0736	0.386	-0.005	0.3176	80.5681	20.0183	49.4688
36	2.0781	0.6186	-1.0937	3.8191	-1.0596	4.3597	-0.0793	0.3399	0.4677	-0.5965	0.1097	-0.0134	-0.3695	0.2704	-0.0153	0.5659	-0.089	-0.0185	0.3514	0.0221	0.3816	91.849	51.5529	40.1609
37	4.588	0.5391	-0.3758	1.7567	0.3494	0.1318	-0.011	0.4811	0.0502	-0.4164	0.0262	-0.2648	0.4039	0.6719	0.0621	0.8813	-0.1837	0.106	0.6919	0.1018	0.473	103.3774	48.3409	34.457
38	7.3278	-2.0832	4.6025	7.6945	-0.4666	2.976	-0.3209	1.1825	-0.1678	-0.0819	-0.1769	-0.3078	0.2697	0.86	0.4574	0.5293	0.0092	0.0802	0.434	0.0756	0.3357	97.5271	44.231	41.9188
39	4.5687	1.6518	1.2574	4.3598	3.5876	4.7363	-0.2177	0.1714	0.3847	0.8532	0.1216	0.9279	-0.7614	-0.1101	0.035	0.8465	-0.0739	0.0551	0.3677	0.0025	0.484	82.0833	48.7505	53.0222
40	1.4999	-1.7049	-0.6874	5.5644	-4.0489	6.7904	0.1628	0.1537	0.0579	0.3104	0.017	0.5124	-1.603	-0.8193	0.0152	0.9623	0.1446	0.041	0.7104	-0.0956	0.6772	75.8501	66.1655	70.5395
41	4.8491	1.0362	2.4762	5.3727	1.2988	4.1439	0.0949	-0.2563	0.5475	-0.0528	-0.531	0.928	-0.4456	-0.9929	0.6065	0.7103	0.0645	0.0843	0.4216	-0.0954	0.4966	78.8867	62.6303	71.7182
42	4.412	-1.4335	-0.4576	2.1516	-0.4635	1.046	0.1505	-0.2699	-1.0089	0.8291	-0.2989	1.1283	0.3609	-0.5875	0.2185	0.5859	-0.0778	0.1794	0.4886	-0.0843	0.4684	77.8346	56.1676	75.5272
43	3.8349	1.1522	1.1799	6.1081	0.815	5.306	0.2386	-0.1555	0.0374	0.0091	-0.1161	-0.4598	-0.5008	-0.0949	-0.0727	0.4961	-0.001	0.0286	0.2888	-0.0467	0.3417	86.1509	55.2857	69.8113

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 868 through 1080 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 1081 through 1121 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 1122 through 1270 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 1276 through 1285 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 1286 through 1298 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 476 through 490 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 491 through 508 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 509 through 523 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 524 through 558 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 559 through 566 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 868 through 1091 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 1092 through 1194 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 1195 through 1270 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 1277 through 1281 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 1282 through 1286 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 1287 through 1291 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 1292 through 1297 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 476 through 499 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 500 through 518 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 519 through 564 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 868 through 903 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 904 through 1091 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 1092 through 1164 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 1165 through 1245 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 1246 through 1270 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 1276 through 1280 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 1281 through 1290 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 1291 through 1297 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 476 through 483 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 484 through 503 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 504 through 513 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 514 through 538 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 539 through 548 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 549 through 564 )
35	X-RAY DIFFRACTION	35	chain 'G' and (resid 868 through 1092 )
36	X-RAY DIFFRACTION	36	chain 'G' and (resid 1093 through 1224 )
37	X-RAY DIFFRACTION	37	chain 'G' and (resid 1225 through 1270 )
38	X-RAY DIFFRACTION	38	chain 'G' and (resid 1277 through 1285 )
39	X-RAY DIFFRACTION	39	chain 'G' and (resid 1286 through 1298 )
40	X-RAY DIFFRACTION	40	chain 'H' and (resid 476 through 489 )
41	X-RAY DIFFRACTION	41	chain 'H' and (resid 490 through 509 )
42	X-RAY DIFFRACTION	42	chain 'H' and (resid 510 through 518 )
43	X-RAY DIFFRACTION	43	chain 'H' and (resid 519 through 564 )

-
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