PDB-7xgg: Crystal structure of BCL-xL in complex with computationally desig...

ID or keywords:

Entry

Database: PDB / ID: 7xgg

Title

Crystal structure of BCL-xL in complex with computationally designed inhibitor protein

Components

BCL-xL and MCL-1 dual inhibitor
Bcl-2-like protein 1

Keywords

APOTOSIS / DE NOVO PROTEIN / computational design

Function / homology

Function and homology information

apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway ...apoptotic process in bone marrow cell / The NLRP1 inflammasome / dendritic cell apoptotic process / dendritic cell proliferation / SARS-CoV-1-mediated effects on programmed cell death / positive regulation of mononuclear cell proliferation / BH3-only proteins associate with and inactivate anti-apoptotic BCL-2 members / negative regulation of dendritic cell apoptotic process / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / negative regulation of execution phase of apoptosis / regulation of mitochondrial membrane permeability / fertilization / regulation of growth / Bcl-2 family protein complex / NFE2L2 regulating tumorigenic genes / response to cycloheximide / STAT5 activation downstream of FLT3 ITD mutants / hepatocyte apoptotic process / cellular response to alkaloid / negative regulation of release of cytochrome c from mitochondria / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of reproductive process / negative regulation of developmental process / apoptotic mitochondrial changes / germ cell development / BH3 domain binding / negative regulation of anoikis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / ectopic germ cell programmed cell death / negative regulation of protein localization to plasma membrane / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ovarian follicle development / response to cytokine / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of autophagy / release of cytochrome c from mitochondria / epithelial cell proliferation / regulation of cytokinesis / regulation of mitochondrial membrane potential / cellular response to amino acid stimulus / cellular response to gamma radiation / male gonad development / endocytosis / intrinsic apoptotic signaling pathway in response to DNA damage / RAS processing / synaptic vesicle membrane / channel activity / neuron apoptotic process / Interleukin-4 and Interleukin-13 signaling / spermatogenesis / nuclear membrane / defense response to virus / in utero embryonic development / negative regulation of neuron apoptotic process / mitochondrial outer membrane / mitochondrial inner membrane / positive regulation of apoptotic process / mitochondrial matrix / centrosome / protein kinase binding / negative regulation of apoptotic process / endoplasmic reticulum / mitochondrion / identical protein binding / cytosol / cytoplasm
Similarity search - Function

Biological species

Homo sapiens (human)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.9 Å

Authors

Oh, B.-H. / Kim, S.

Funding support

1items

Citation

Journal: Comput Struct Biotechnol J / Year: 2022
Title: Computational design of an apoptogenic protein that binds BCL-xL and MCL-1 simultaneously and potently.
Authors: Kim, S. / Park, H.S. / Oh, B.H.

History

Deposition	Apr 4, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 20, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 23, 2024	Group: Data collection / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7xgg.cif.gz	389.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7xgg.ent.gz	319.7 KB	Display	PDB format
PDBx/mmJSON format	7xgg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7xgg_validation.pdf.gz	480.7 KB	Display	wwPDB validaton report
Full document	7xgg_full_validation.pdf.gz	498.3 KB	Display
Data in XML	7xgg_validation.xml.gz	40 KB	Display
Data in CIF	7xgg_validation.cif.gz	58 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xg/7xgg ftp://data.pdbj.org/pub/pdb/validation_reports/xg/7xgg	HTTPS FTP

-
Related structure data

Related structure data	7xgeC 7xgfC 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	#70 - Oct 2005 Designer Proteins similarity (1) #177 - Sep 2014 Apoptosomes similarity (12)

Deposited unit

B: Bcl-2-like protein 1

A: BCL-xL and MCL-1 dual inhibitor

F: Bcl-2-like protein 1

D: BCL-xL and MCL-1 dual inhibitor

C: Bcl-2-like protein 1

E: Bcl-2-like protein 1

117 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: Bcl-2-like protein 1

A: BCL-xL and MCL-1 dual inhibitor

C: Bcl-2-like protein 1

defined by author&software
Evidence: gel filtration
58.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Bcl-2-like protein 1

D: BCL-xL and MCL-1 dual inhibitor

E: Bcl-2-like protein 1

defined by author&software
58.3 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	60.612, 68.539, 80.517
Angle α, β, γ (deg.)	100.890, 110.570, 108.730
Int Tables number	1
Space group name H-M	P1

#1: Protein	Bcl-2-like protein 1 / Bcl2-L-1 / Apoptosis regulator Bcl-X Mass: 19827.191 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: BCL2L1, BCL2L, BCLX / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07817
#2: Protein	BCL-xL and MCL-1 dual inhibitor Mass: 18600.221 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.61 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 4% PEG 3,000(w/v), 0.1M Sodium acetate(pH4.5)

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 5C (4A) / Wavelength: 0.97403 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 28, 2019

Radiation

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

Radiation wavelength

Wavelength: 0.97403 Å / Relative weight: 1

Reflection

Resolution: 1.6→50 Å / Num. obs: 162032 / % possible obs: 96.7 % / Redundancy: 1.8 % / R_merge(I) obs: 0.073 / R_pim(I) all: 0.073 / R_rim(I) all: 0.103 / Χ²: 2.045 / Net I/σ(I): 3.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.9-1.93	3.1	0.322	3987	0.871	0.217	0.391	0.524	95.3
1.93-1.97	3.3	0.285	4039	0.906	0.188	0.344	0.565	95.9
1.97-2.01	3.3	0.247	4109	0.921	0.16	0.295	0.612	96.3
2.01-2.05	3.6	0.225	4038	0.953	0.137	0.264	0.672	96.1
2.05-2.09	3.7	0.196	4083	0.965	0.117	0.229	0.751	96.1
2.09-2.14	3.7	0.169	4110	0.972	0.101	0.197	0.85	96.5
2.14-2.19	3.7	0.153	4013	0.977	0.091	0.178	0.931	96.4
2.19-2.25	3.7	0.14	4087	0.98	0.083	0.163	0.997	96.4
2.25-2.32	3.7	0.125	4109	0.981	0.075	0.146	1.105	96.8
2.32-2.39	3.7	0.115	4039	0.986	0.069	0.134	1.238	96.1
2.39-2.48	3.7	0.111	4085	0.984	0.067	0.13	1.403	96.8
2.48-2.58	3.7	0.103	4071	0.987	0.062	0.12	1.522	96.6
2.58-2.7	3.7	0.097	4136	0.987	0.058	0.113	1.798	97
2.7-2.84	3.7	0.093	4018	0.986	0.056	0.109	2.117	96
2.84-3.02	3.5	0.086	4130	0.987	0.053	0.102	2.543	96.8
3.02-3.25	3.4	0.082	4072	0.986	0.052	0.098	3.053	96.7
3.25-3.58	3	0.074	4092	0.986	0.052	0.092	4.394	96.6
3.58-4.09	3.5	0.069	4115	0.989	0.044	0.082	5.001	97.7
4.09-5.16	3.9	0.065	4182	0.993	0.038	0.075	5.141	99.3
5.16-50	3.9	0.065	4218	0.996	0.038	0.076	5.119	99.5

-
Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
HKL-2000		data scaling
PDB_EXTRACT	3.27	data extraction
AutoSol		phasing
HKL-2000		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.9→38.13 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 19.16 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1967	3973	2.45 %
R_work	0.1657	158046	-
obs	0.1665	162019	95.37 %

Solvent computation

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

Displacement parameters

B_iso max: 115.08 Å² / B_iso mean: 32.9394 Å² / B_iso min: 8.07 Å²

Refinement step

Cycle: final / Resolution: 1.9→38.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7318	0	0	536	7854
B_iso mean	-	-	-	40.12	-
Num. residues	-	-	-	-	910

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 28

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9-1.92	0.2838	117	0.2315	4710	4827	80
1.92-1.95	0.2723	145	0.2239	5716	5861	95
1.95-1.97	0.2389	136	0.2083	5446	5582	95
1.97-2	0.2482	141	0.1931	5673	5814	95
2-2.03	0.1925	145	0.1861	5703	5848	96
2.03-2.06	0.2062	143	0.1787	5636	5779	95
2.06-2.09	0.2453	142	0.174	5684	5826	96
2.09-2.13	0.2069	141	0.1687	5565	5706	96
2.13-2.16	0.1626	144	0.1591	5752	5896	96
2.16-2.2	0.1864	141	0.1527	5621	5762	95
2.2-2.25	0.182	144	0.1503	5676	5820	96
2.25-2.29	0.2112	145	0.1464	5736	5881	96
2.29-2.34	0.2026	141	0.1499	5627	5768	95
2.34-2.4	0.1905	141	0.1527	5644	5785	96
2.4-2.46	0.1993	142	0.1593	5711	5853	96
2.46-2.52	0.1798	143	0.1561	5686	5829	96
2.52-2.6	0.2173	141	0.1525	5619	5760	96
2.6-2.68	0.1752	144	0.1539	5598	5742	95
2.68-2.78	0.1817	144	0.1623	5666	5810	95
2.78-2.89	0.1691	140	0.1539	5705	5845	96
2.89-3.02	0.1691	144	0.1613	5735	5879	96
3.02-3.18	0.2196	140	0.166	5588	5728	96
3.18-3.38	0.1952	143	0.1678	5686	5829	96
3.38-3.64	0.1798	141	0.1575	5606	5747	95
3.64-4	0.1575	142	0.1551	5706	5848	97
4-4.58	0.1629	148	0.1544	5855	6003	99
4.58-5.77	0.2668	148	0.1815	5880	6028	99
5.77-38.13	0.219	147	0.1895	5816	5963	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	3.4471	0.6117	-0.0682	3.134	1.4631	1.2182	-0.0562	-0.0763	0.239	0.0807	-0.1925	0.1809	-0.558	-0.4498	0.2364	0.1774	0.0366	-0.0223	0.1649	0.0004	0.167	21.6264	40.4252	-13.9051
2	1.6728	-1.9775	-2.4125	4.379	4.6833	5.6498	0.1284	-0.4892	0.484	0.7916	-0.3527	0.9908	-0.3488	-1.2453	0.7125	0.407	0.0073	0.0501	0.5281	-0.0748	0.3986	15.4684	38.4673	-19.3748
3	1.9652	0.265	-0.4165	2.0709	0.7913	2.6041	0.0462	0.1711	0.0992	-0.1386	-0.1064	0.0473	-0.3183	-0.0731	0.08	0.1344	0.0116	-0.0226	0.152	0.0356	0.1064	32.495	39.0753	-16.8515
4	2.0241	0.6973	0.9883	1.7284	0.2397	2.2393	-0.0178	0.0281	-0.2247	0.08	0.0238	-0.0111	0.0562	-0.1421	0.0154	0.083	0.0189	0.027	0.1241	-0.0106	0.1264	28.0287	27.8961	-10.1718
5	2.2371	1.0894	1.0947	2.3932	0.9887	4.1724	-0.0245	0.0093	0.003	-0.0129	-0.0931	0.1846	0.0355	-0.2246	0.096	0.0993	0.0135	0.0462	0.2063	0.0009	0.1825	19.0823	29.8009	-10.2788
6	4.036	1.439	-0.9151	7.5079	0.2908	4.7678	-0.0107	-0.2124	0.2997	0.3225	-0.1795	-0.0958	-0.8367	-0.1463	-0.0375	0.2368	0.0082	-0.066	0.1331	-0.0226	0.1322	30.9831	40.8926	3.1003
7	5.9327	0.1011	-0.6757	8.152	-0.2723	3.4567	0.1626	0.0279	0.346	-0.1723	-0.079	-0.3503	-0.5466	0.1869	-0.0375	0.2168	0.0173	-0.0177	0.0953	-0.008	0.179	34.3598	47.7655	-6.3087
8	3.0208	-0.8521	0.1567	3.6563	-0.4019	1.7737	0.1501	0.1359	-0.2433	-0.3313	-0.1367	0.1475	0.1356	0.0495	-0.0184	0.1076	0.0486	-0.0258	0.1755	-0.0125	0.1757	47.7286	15.8189	-13.6639
9	5.5327	1.6833	0.4533	3.1171	1.2014	2.1251	0.3677	-0.4429	-0.0594	0.671	-0.3689	0.0851	-0.0248	-0.0309	-0.0239	0.1477	0.0485	-0.0321	0.1888	0.0524	0.1937	45.3207	22.9038	-4.7249
10	3.5961	-1.132	0.4781	3.5551	0.1775	2.6558	0.1923	-0.1308	-0.6943	0.051	-0.107	-0.0249	0.2878	-0.2195	0.0582	0.0856	0.0102	-0.0125	0.1412	0.0121	0.2027	34.8362	21.2485	-10.4965
11	2.9121	0.352	-1.0044	2.7286	-1.3808	4.52	0.092	-0.131	-0.4841	0.1006	-0.1718	0.2902	0.6175	-0.4011	0.1184	0.3504	-0.0909	-0.0502	0.2197	0.0044	0.25	27.3808	28.1714	16.1455
12	5.1827	-2.937	1.9504	2.4913	-0.8514	2.9251	0.0616	0.1113	0.4453	-0.0327	-0.1204	-0.3851	0.0225	-0.0152	0.1268	0.2877	-0.0235	0.0046	0.1405	0.0071	0.2083	36.0887	37.3082	21.0687
13	3.418	-1.5562	-1.1189	3.7418	0.9313	4.9153	0.078	-0.2168	0.2216	0.2463	0.0274	-0.1492	0.4621	0.0194	-0.0806	0.1761	-0.037	-0.0185	0.1109	-0.0144	0.1154	34.5576	36.7957	24.6478
14	4.8426	-1.0922	-0.571	3.4678	0.508	3.6136	0.1899	-0.2166	-0.0485	0.175	-0.1684	0.4457	0.4461	-0.5055	-0.0177	0.2893	-0.1092	-0.0284	0.2126	0.0081	0.1891	28.5246	32.1309	25.3216
15	4.0264	0.0036	0.5752	3.8854	0.2369	2.0924	0.1171	0.0827	-0.2417	0.2532	-0.0436	-0.1339	0.1419	0.021	-0.0433	0.1772	-0.0125	-0.0023	0.1122	-0.0304	0.1153	38.006	48.5287	31.3673
16	5.3117	-0.4533	0.2508	3.7034	-0.3378	3.3112	0.1526	0.7567	-0.2221	-0.3439	-0.1342	-0.1988	0.0751	0.2119	0.141	0.2209	-0.023	0.0609	0.163	-0.0397	0.1666	38.3042	54.7084	22.5711
17	6.4306	-1.0331	0.4885	4.4274	-0.4358	2.5366	-0.1471	0.0409	0.0539	0.0745	-0.0098	-0.4972	-0.0213	0.2384	0.0393	0.1027	-0.0216	0.0125	0.1175	0.0074	0.153	43.1944	61.9904	28.6719
18	4.2466	0.0105	-2.7041	4.5359	0.7745	6.791	0.0722	0.1765	-0.0797	-0.1997	0.0121	-0.612	0.0158	0.6385	-0.0286	0.1306	0.0363	0.0073	0.2545	-0.0134	0.1713	68.141	8.5149	-0.2488
19	2.8914	0.6736	-1.1018	4.8055	-0.1847	4.286	0.1016	0.0781	-0.294	0.3314	-0.1009	-0.9396	0.7132	0.6926	0.1322	0.3424	0.0716	-0.0586	0.3487	-0.0323	0.3192	67.7665	0.8962	7.4357
20	2.3797	1.4744	-1.9251	5.8365	-0.566	5.7196	0.1382	-0.1287	-0.4264	0.4471	-0.2137	-0.0955	-0.5641	0.3688	0.1007	0.2164	-0.0051	-0.0137	0.2194	-0.0073	0.1397	65.1937	17.5732	0.2132
21	2.1409	1.4931	0.415	4.194	1.6007	4.6026	-0.3704	-0.3223	1.1786	1.264	-0.0154	1.1644	-1.227	-0.1683	0.4041	0.5076	-0.0002	-0.0599	0.3615	-0.0417	0.5889	47.7643	8.2861	-0.1246
22	1.3901	0.7904	-0.2753	7.5346	-4.2514	4.0198	0.0742	0.2227	-0.0993	-0.454	-0.0453	0.4657	0.4913	0.1312	0.0024	0.2106	0.0213	-0.0127	0.1484	-0.0367	0.1818	54.8974	-1.5926	-9.7634
23	0.7321	0.5888	-0.8001	4.3166	-2.9927	5.6432	-0.0189	0.1239	-0.0081	-0.0909	0.0882	0.2049	0.2077	-0.0661	-0.1607	0.073	0.0113	0.0065	0.1498	-0.0054	0.1354	57.7806	8.6679	-7.0834
24	2.0923	1.2899	-0.6181	4.2463	-1.5058	3.1703	-0.054	0.008	-0.1391	0.1339	-0.0697	-0.2774	0.0661	0.1369	0.0272	0.1707	0.0807	0.0016	0.169	-0.0402	0.1696	63.0335	-0.7962	-4.5718
25	3.5021	2.305	0.9046	5.6427	-0.575	3.104	-0.0385	0.0716	0.332	-0.1988	0.0021	0.1622	-0.2971	0.1931	-0.0228	0.0968	-0.0361	0.0344	0.2783	0.0213	0.2327	68.2175	18.7945	-12.0792
26	3.8763	-0.5642	1.3644	2.6855	0.0551	2.0461	-0.1398	0.1939	0.3557	-0.1818	-0.1142	-0.2749	-0.9042	0.167	0.2144	0.3026	-0.028	-0.0378	0.1275	-0.0134	0.1923	43.9967	84.3038	30.9849
27	3.0859	0.2349	-2.0255	4.0275	-3.0952	3.5201	-0.2602	0.0086	0.714	0.1115	0.1483	-0.2819	-0.6374	0.2559	0.1802	0.287	-0.0793	-0.0437	0.2931	0.0366	0.2503	49.9877	83.6669	40.7134
28	2.2906	-0.3478	1.9496	0.3077	-1.1091	4.3685	-0.4404	0.2209	1.0388	-0.4195	-0.0527	0.0821	-1.3404	0.6231	0.5517	0.7836	-0.0416	-0.074	0.3816	0.0112	0.5299	50.0038	89.8475	32.6413
29	1.8846	0.1801	-0.0902	4.0586	-1.7404	3.1671	0.0024	-0.0494	0.165	0.1978	-0.0452	0.0743	-0.6157	-0.0932	0.0027	0.1723	0.0072	-0.0076	0.1313	-0.0266	0.0799	34.573	77.4462	33.6874
30	7.9181	2.5019	-1.783	1.8128	-2.1178	4.8642	0.2771	-0.5852	-0.1823	0.3113	0.2312	-0.4702	0.0088	0.2739	0.1063	0.2502	-0.0012	0.0067	0.245	-0.0213	0.1792	43.2092	66.796	39.5374
31	1.5332	0.1249	0.4491	0.7151	-0.6783	0.8824	0.2258	-0.9106	-0.2429	0.4234	0.0149	-0.3293	-0.2838	1.1259	0.1641	0.526	0.0259	-0.2082	0.6074	-0.0683	0.3819	55.6504	67.1017	34.146
32	7.6646	0.867	2.3356	3.4879	0.9477	5.9506	-0.3793	0.2987	0.0843	-0.2054	0.1029	-0.6656	-0.0476	0.7469	-0.0003	0.1901	0.0094	0.0286	0.2574	0.0439	0.2145	50.2143	67.5852	24.4529
33	2.1152	0.3757	1.2818	0.9889	0.6331	4.3174	-0.0252	0.0024	-0.1391	-0.0082	-0.0001	-0.1123	-0.1326	0.2125	0.0556	0.1153	-0.0072	0.0112	0.093	0.0159	0.0999	42.6261	72.3063	27.9833
34	2.3884	-0.3203	1.5245	1.5817	0.2039	4.8726	-0.1816	0.1793	0.0613	0.0025	-0.0682	-0.2522	-0.415	0.8178	0.1092	0.1858	-0.0974	0.0041	0.2981	0.0726	0.1793	52.6124	77.1794	27.8813
35	4.588	-1.6354	0.7	4.3375	-1.2905	5.7437	-0.0551	0.1731	0.1658	-0.116	-0.0322	0.1453	-0.6368	-0.2235	0.1793	0.2502	0.0267	-0.0388	0.1819	-0.0068	0.1072	36.5422	78.891	14.4236
36	4.8346	0.3418	-0.1275	5.5584	-1.023	4.0955	-0.0018	0.0685	0.0642	0.2723	-0.0435	0.5252	-0.8511	-0.6086	0.1357	0.2756	0.1023	-0.0263	0.1591	-0.0203	0.1522	29.5846	82.2449	23.8796

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 6 through 23 )	B	6 - 23
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 24 through 42 )	B	24 - 42
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 43 through 74 )	B	43 - 74
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 75 through 119 )	B	75 - 119
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 120 through 140 )	B	120 - 140
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 141 through 149 )	B	141 - 149
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 150 through 160 )	B	150 - 160
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 4 through 78 )	A	4 - 78
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 79 through 120 )	A	79 - 120
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 121 through 165 )	A	121 - 165
11	X-RAY DIFFRACTION	11	chain 'F' and (resid 1 through 44 )	F	1 - 44
12	X-RAY DIFFRACTION	12	chain 'F' and (resid 45 through 93 )	F	45 - 93
13	X-RAY DIFFRACTION	13	chain 'F' and (resid 94 through 119 )	F	94 - 119
14	X-RAY DIFFRACTION	14	chain 'F' and (resid 120 through 160 )	F	120 - 160
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 4 through 78 )	D	4 - 78
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 79 through 124 )	D	79 - 124
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 125 through 165 )	D	125 - 165
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 4 through 23 )	C	4 - 23
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 24 through 43 )	C	24 - 43
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 44 through 62 )	C	44 - 62
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 63 through 75 )	C	63 - 75
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 76 through 93 )	C	76 - 93
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 94 through 119 )	C	94 - 119
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 120 through 140 )	C	120 - 140
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 141 through 159 )	C	141 - 159
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 6 through 22 )	E	6 - 22
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 23 through 29 )	E	23 - 29
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 30 through 44 )	E	30 - 44
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 45 through 68 )	E	45 - 68
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 69 through 74 )	E	69 - 74
31	X-RAY DIFFRACTION	31	chain 'E' and (resid 75 through 81 )	E	75 - 81
32	X-RAY DIFFRACTION	32	chain 'E' and (resid 82 through 93 )	E	82 - 93
33	X-RAY DIFFRACTION	33	chain 'E' and (resid 94 through 119 )	E	94 - 119
34	X-RAY DIFFRACTION	34	chain 'E' and (resid 120 through 140 )	E	120 - 140
35	X-RAY DIFFRACTION	35	chain 'E' and (resid 141 through 149 )	E	141 - 149
36	X-RAY DIFFRACTION	36	chain 'E' and (resid 150 through 160 )	E	150 - 160

-
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