PDB-4ejf: Allosteric peptides that bind to a caspase zymogen and mediate ca...

ID or keywords:

Entry

Database: PDB / ID: 4ejf

Title

Allosteric peptides that bind to a caspase zymogen and mediate caspase tetramerization

Components

Caspase-6
phage-derived peptide 419

Keywords

HYDROLASE / Caspase-6 / zymogen / C163A / Caspase / protease

Function / homology

Function and homology information

caspase-6 / Breakdown of the nuclear lamina / regulation of programmed cell death / positive regulation of necroptotic process / cellular response to staurosporine / cysteine-type endopeptidase activity involved in execution phase of apoptosis / cysteine-type endopeptidase activity involved in apoptotic process / hepatocyte apoptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / Apoptotic cleavage of cellular proteins ...
Similarity search - Function

Biological species

Homo sapiens (human)
synthetic (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.6465 Å

Authors

Murray, J.M.

Citation

Journal: Nat.Chem.Biol. / Year: 2012
Title: Allosteric peptides bind a caspase zymogen and mediate caspase tetramerization.
Authors: Stanger, K. / Steffek, M. / Zhou, L. / Pozniak, C.D. / Quan, C. / Franke, Y. / Tom, J. / Tam, C. / Elliott, J.M. / Lewcock, J.W. / Zhang, Y. / Murray, J. / Hannoush, R.N.

History

Deposition	Apr 6, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 20, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 18, 2012	Group: Derived calculations
Revision 1.2	Sep 5, 2012	Group: Database references
Revision 1.3	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4ejf.cif.gz	426.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4ejf.ent.gz	353.3 KB	Display	PDB format
PDBx/mmJSON format	4ejf.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4ejf_validation.pdf.gz	508.5 KB	Display	wwPDB validaton report
Full document	4ejf_full_validation.pdf.gz	526.2 KB	Display
Data in XML	4ejf_validation.xml.gz	40.4 KB	Display
Data in CIF	4ejf_validation.cif.gz	55.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ej/4ejf ftp://data.pdbj.org/pub/pdb/validation_reports/ej/4ejf	HTTPS FTP

-
Related structure data

Related structure data	3nr2S S: Starting model for refinement
Similar structure data	5hy5-d 1x0c-d 6tfs-d 5w58-1 2z8g-d 4bmm-1 6v3r-2 6b8l-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#56 - Aug 2004 Caspases similarity (16) #224 - Aug 2018 Legumain similarity (12) #177 - Sep 2014 Apoptosomes similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #213 - Sep 2017 Sirtuins similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #19 - Jul 2001 Actin similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#56 - Aug 2004
Caspases
similarity (16)
#224 - Aug 2018
Legumain
similarity (12)
#177 - Sep 2014
Apoptosomes
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#213 - Sep 2017
Sirtuins
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#221 - May 2018
Human Papillomavirus and Vaccines
similarity (1)
#234 - Jun 2019
MDM2 and Cancer
similarity (1)
#19 - Jul 2001
Actin
similarity (1)

Deposited unit

A: Caspase-6

B: Caspase-6

C: Caspase-6

D: Caspase-6

E: phage-derived peptide 419

F: phage-derived peptide 419

G: phage-derived peptide 419

H: phage-derived peptide 419

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	128.299, 105.692, 91.924
Angle α, β, γ (deg.)	90.000, 106.610, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.181619, -0.007389, 0.983341), (-0.005804, -0.999946, -0.008586), (0.983352, -0.007267, 0.181566)	7.62406, -73.454498, -8.27234
2	given	(-0.999997, 0.0012, 0.001894), (0.001271, 0.999279, 0.037935), (-0.001847, 0.037937, -0.999278)	51.153, -1.91358, 45.631199
3	given	(-0.956126, -0.292951, 0.001682), (-0.2929, 0.955817, -0.024969), (0.005707, -0.024366, -0.999687)	46.112301, 7.81898, 44.403198
4	given	(-0.190634, 0.069836, 0.979174), (-0.000554, -0.997474, 0.071033), (0.981661, 0.012999, 0.190191)	13.9373, -75.587097, -5.83303
5	given	(0.122646, 0.218388, -0.968124), (-0.005248, -0.975332, -0.220679), (-0.992437, 0.032146, -0.118475)	56.855099, -68.173103, 52.1763

#1: Protein	Caspase-6 / CASP-6 / Apoptotic protease Mch-2 / Caspase-6 subunit p18 / Caspase-6 subunit p11 Mass: 32055.627 Da / Num. of mol.: 4 / Mutation: C163A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CASP6, MCH2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P55212, caspase-6
#2: Protein/peptide	phage-derived peptide 419 Mass: 2232.581 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic (others)
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.18 Å³/Da / Density % sol: 43.51 %
Crystal grow	Temperature: 292.15 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 20% (w/v) PEG3350, 0.2 M NaThiocyanate pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 292.15K

-
Data collection

Diffraction

Mean temperature: 80 K

Diffraction source

Source:

SYNCHROTRON / Site:

SSRL

/ Beamline: BL7-1 / Wavelength: 0.979 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 5, 2009

Radiation

Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Resolution: 2.64→80.148 Å / Num. all: 34281 / Num. obs: 34281 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / B_iso Wilson estimate: 35.28 Å² / R_sym value: 0.086 / Net I/σ(I): 11.1

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.64-2.79	3.8	0.456	1.7	18785	4993	0.456	99.8
2.79-2.96	3.8	0.298	2.6	17793	4732	0.298	99.8
2.96-3.16	3.7	0.2	3.9	16510	4410	0.2	99.8
3.16-3.42	3.7	0.124	6.2	15553	4155	0.124	99.8
3.42-3.74	3.7	0.075	10.1	14085	3780	0.075	99.8
3.74-4.18	3.7	0.057	13.2	12853	3469	0.057	99.9
4.18-4.83	3.7	0.043	17.3	11168	3047	0.043	99.6
4.83-5.92	3.6	0.045	16.4	9302	2572	0.045	99.5
5.92-8.37	3.7	0.039	18.6	7521	2006	0.039	99.8
8.37-80.148	3.6	0.021	26.6	4052	1117	0.021	99.3

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
SCALA	3.3.16	data scaling
PHASER		phasing
PHENIX	dev_713	refinement
PDB_EXTRACT	3.11	data extraction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3NR2

3nr2

Resolution: 2.6465→58.933 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.72 / σ(F): 1.35 / Phase error: 26.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2391	1718	5.02 %
R_work	0.1882	-	-
obs	0.1907	34192	99.43 %

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 36.754 Å² / k_sol: 0.356 e/Å³

Displacement parameters

B_iso max: 202.79 Å² / B_iso mean: 44.3314 Å² / B_iso min: 13.27 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-9.5681 Å²	-0 Å²	6.5607 Å²
2-	-	-2.8825 Å²	-0 Å²
3-	-	-	12.4506 Å²

Refinement step

Cycle: LAST / Resolution: 2.6465→58.933 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8196	0	10	279	8485

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8359
X-RAY DIFFRACTION	f_angle_d	0.726	11259
X-RAY DIFFRACTION	f_chiral_restr	0.049	1223
X-RAY DIFFRACTION	f_plane_restr	0.003	1428
X-RAY DIFFRACTION	f_dihedral_angle_d	14.343	3044

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.6465-2.7244	0.3104	153	0.2564	2675	2828	100
2.7244-2.8123	0.3388	132	0.2511	2734	2866	100
2.8123-2.9128	0.3	151	0.2341	2666	2817	100
2.9128-3.0295	0.2877	145	0.2226	2689	2834	99
3.0295-3.1673	0.2645	128	0.2103	2715	2843	100
3.1673-3.3343	0.2634	130	0.2004	2717	2847	100
3.3343-3.5432	0.2644	152	0.19	2699	2851	100
3.5432-3.8167	0.2344	162	0.1707	2688	2850	100
3.8167-4.2007	0.219	142	0.1516	2727	2869	100
4.2007-4.8083	0.1669	133	0.1386	2712	2845	99
4.8083-6.057	0.1893	133	0.1785	2735	2868	99
6.057-58.9471	0.2311	157	0.2025	2717	2874	98

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	2.5292	0.4548	-0.0818	2.9108	0.0533	2.1369	0.3052	-0.1428	0.2648	0.0341	0.0718	0.0539	-0.3748	-0.037	-0.2233	0.1598	0.0131	0.0372	0.3536	0.018	0.2989	5.2128	-21.248	36.9841
2	3.1286	-0.9833	-1.4845	1.3922	0.8895	4.4374	0.7275	0.4006	1.5457	-0.0382	0.2511	1.624	-0.8935	-0.0888	-0.0857	0.0987	0.089	-0.4516	0.5808	0.3042	-0.3623	-1.7404	-19.5321	24.8695
3	1.9122	0.1129	-0.3972	1.562	-0.4403	1.7972	0.0979	-0.1164	0.4807	-0.1069	-0.0557	-0.0785	-0.4219	-0.0372	-0.029	0.2039	0.0204	0.0198	0.336	-0.0072	0.2828	8.68	-15.4861	34.6382
4	1.6863	-0.4444	-1.0473	1.6777	-0.0552	3.9248	-0.0371	0.047	0.0058	-0.1024	-0.1293	-0.4415	0.3337	0.5469	0.1885	0.2315	-0	0.0798	0.3707	-0.0003	0.3488	15.5191	-23.0803	33.8508
5	3.3499	0.2847	0.556	2.3271	1.0721	2.5895	0.0784	0.5398	0.1098	-0.4725	0.0473	0.1644	0.1103	0.01	0.0476	0.2687	-0.0015	-0.0268	0.3433	0.0134	0.3287	5.9253	-29.7109	25.3829
6	2.3866	0.6288	0.6117	1.9356	-0.1237	2.3962	0.1015	0.2069	-0.1502	-0.1048	0.1936	0.2802	0.1846	-0.3104	-0.2375	0.1934	-0.0039	-0.0316	0.3819	0.0518	0.272	-3.3835	-31.4397	30.5529
7	1.8299	0.3443	-1.7035	4.6394	0.7818	2.5884	0.2726	1.2101	-0.6215	-1.0244	-0.0293	0.8073	1.0224	-0.9722	-0.1367	0.5162	-0.1896	-0.2107	0.8157	-0.1113	0.3697	-4.789	-37.6687	19.4716
8	5.0504	0.2504	0.9917	2.6034	-1.5456	3.6344	-0.0791	-0.6931	-0.0979	-0.1782	0.4114	0.1537	0.0924	-0.7672	-0.0622	0.3371	-0.0598	0.0832	0.3371	-0.0748	0.159	-0.8892	-27.2852	47.8214
9	3.4411	-3.0372	-0.6025	7.0307	-1.131	1.9397	0.0255	0.4316	-0.5866	-0.3394	0.2323	0.6797	-0.0794	-0.4032	-0.1314	0.2398	-0.0013	0.0307	0.4937	0.0494	0.4206	-10.4011	-49.3394	38.7954
10	8.101	0.7033	-1.2094	1.6685	0.0686	2.2717	-0.094	0.5009	-0.5964	-0.4327	0.4479	-0.8399	-0.0639	0.7392	-0.0623	0.1827	0.1422	-0.0123	0.2988	0.2092	0.5277	22.6584	-58.207	37.7347
11	6.8747	1.2583	-0.2508	2.0763	-0.2446	1.7168	-0.06	-0.6622	-0.4579	0.4158	0.0839	-0.3015	0.0284	0.2321	-0.0167	0.3482	-0.0054	-0.0781	0.369	0.0819	0.2821	17.0131	-55.8652	47.769
12	1.8332	-1.0184	-0.8203	1.153	0.6054	1.2741	-0.0141	-0.1893	-0.3131	-0.2234	0.0059	-0.0246	0.0937	-0.0558	-0.0541	0.2295	-0.0458	-0.048	0.2522	0.096	0.272	12.4646	-58.3515	34.7917
13	2.0481	1.495	-0.8884	3.1211	-0.4939	1.6803	-0.2881	1.3293	0.5189	-0.8648	0.4762	0.3968	0.2441	-0.0162	-0.1139	0.3648	0.0137	-0.033	0.4488	0.0979	0.2992	7.7006	-53.1859	26.8241
14	2.5415	0.6968	0.3133	1.7385	0.3518	1.5228	-0.1799	0.054	0.3528	-0.0028	-0.0002	-0.4105	0.1262	0.2808	0.1475	0.2114	0.0173	-0.0148	0.3016	0.1125	0.3246	15.6814	-46.3739	39.1345
15	2.0347	-0.1265	0.2963	1.1462	0.3707	1.4286	-0.0719	-0.3043	0.1765	0.0648	0.113	0.0718	-0.0648	0.1106	-0.0113	0.2745	-0.0521	-0.0359	0.4207	0.0919	0.2	11.3502	-43.7454	48.3052
16	3.4618	0.2486	-0.7072	3.9537	0.2196	2.0865	0.1801	-0.8154	0.3347	0.4668	0.0378	-0.1689	-0.1256	0.7311	-0.1274	0.2267	-0.0767	-0.0399	0.6596	-0.0049	0.0617	12.049	-41.1368	47.375
17	2.7329	-1.2439	-0.9385	7.9132	2.696	3.5768	0.1322	0.538	-0.0231	-0.7386	-0.1115	-0.1721	-0.1236	-0.0248	-0.1508	0.363	-0.0289	0.086	0.3212	-0.0496	0.2601	49.4655	-24.401	-9.2901
18	3.6693	0.3609	-3.0478	2.4494	-2.3275	8.1968	0.7393	-0.2379	0.7701	1.1565	0.3637	-0.119	-0.0994	-0.2854	-0.172	0.192	-0.0717	0.1146	0.3532	-0.2243	0.4578	42.365	-15.6809	22.8073
19	2.6088	0.5839	-1.8139	1.3716	-0.485	5.621	0.4101	-0.1734	0.8786	0.6929	0.6082	-0.8025	-0.8997	0.4707	-0.2469	0.2988	0.0148	-0.1163	0.4837	-0.2589	0.5501	53.077	-17.8305	19.3567
20	0.9013	-0.3493	-0.0524	1.0853	1.527	1.729	0.1613	-0.1747	0.373	0.0798	-0.0827	-0.1047	-0.2556	0.0923	-0.0736	0.2798	-0.0097	-0.0029	0.2399	-0.069	0.3836	41.2906	-15.5131	12.4642
21	2.5498	1.1361	-2.0268	3.1615	-1.0315	4.7182	-0.3322	0.327	0.1612	-0.3599	0.4265	0.278	0.6009	-1.2082	0.0375	0.2553	-0.0291	0.003	0.2614	-0.0421	0.2837	34.3805	-20.7903	6.3408
22	2.1234	-0.3052	0.4635	1.9391	-1.0724	4.2763	0.0265	-0.4117	-0.0293	0.355	0.0739	-0.25	0.1381	0.1573	-0.08	0.2566	-0.0129	-0.0392	0.2426	-0.115	0.2449	45.5737	-27.1411	16.8537
23	1.4182	-0.349	0.3462	1.5995	-0.5636	3.0116	-0.0314	-0.2887	0.0168	0.06	0.0276	-0.3656	0.2145	0.4336	-0.0037	0.2204	0.0311	-0.0115	0.3892	-0.1208	0.3104	54.5581	-29.9111	13.5963
24	2.8848	-0.1912	-1.4251	4.1849	-1.2171	1.1534	0.7301	-1.0934	-0.6234	1.1072	0.0151	-0.6487	1.2307	1.0965	-0.082	0.4833	0.2218	-0.2267	1.0085	-0.0117	0.4066	55.4127	-36.0106	24.1201
25	6.181	0.2147	0.0654	2.2068	1.218	3.2366	0.2171	0.1081	-0.0072	-1.0515	-0.2401	-0.616	-0.3428	0.5273	-0.0801	0.3197	0.0337	0.0612	0.3133	-0.0245	0.3252	51.9907	-25.4679	-3.672
26	3.7222	0.8037	-1.0962	5.1796	-0.3343	1.7632	-0.6221	-0.6295	-0.7161	-0.4877	-0.0958	-0.6656	-1.1563	0.5658	0.0012	-0.1293	0.11	0.2006	0.2688	-0.1231	0.572	61.3496	-47.7433	4.9989
27	5.9309	-0.7438	-1.3683	2.0826	-0.7137	2.5587	-0.3602	0.3336	-0.3409	-0.2276	0.1854	0.2972	0.1329	-0.3473	0.1448	0.2623	-0.0181	-0.0091	0.1888	-0.036	0.2427	31.6455	-55.1147	0.1148
28	2.0428	1.0406	0.0602	0.9604	-0.3015	0.7735	-0.1792	-0.3726	-0.1948	0.1757	0.048	-0.1485	0.1534	-0.0629	0.1489	0.2931	0.0406	0.0192	0.2478	-0.0064	0.2677	38.6405	-56.859	8.5929
29	6.299	-1.3109	-0.9735	2.7661	0.5464	0.8116	-0.1076	-1.7377	0.2761	0.4714	0.2659	-0.0972	-0.2834	0.0876	0.13	0.3559	0.1296	0.0312	0.5248	0.0242	0.3389	43.4129	-51.8745	16.7852
30	1.9338	-0.9174	-0.2963	1.8436	-0.3343	1.9388	-0.0327	-0.1696	0.4778	-0.1743	-0.0742	0.1501	-0.065	-0.37	0.0918	0.2392	0.029	-0.0293	0.1711	-0.0463	0.2894	35.3903	-44.7162	4.7032
31	3.0981	0.4127	0.0729	1.8419	-0.9629	1.8213	-0.2533	0.1854	0.2553	-0.295	0.187	-0.0517	-0.1594	-0.0858	0.04	0.2914	0.0221	0.0069	0.1847	-0.0469	0.2159	39.7342	-41.8103	-4.3877
32	2.9209	-0.4839	-0.6869	3.8233	0.6377	2.2699	0.0663	0.3231	0.491	-0.397	-0.0683	0.3191	0.0073	-0.6932	-0.0505	0.2636	-0.0207	0.0267	0.3462	0.0627	0.1806	38.9281	-39.1743	-3.3458
33	3.1333	0.7809	-0.819	3.7524	1.1162	5.1717	0.108	-0.0093	0.5624	0.3141	0.0648	0.1642	0.1315	0.046	-0.0064	0.2822	0.0384	0.0191	0.4785	-0.0475	0.2797	24.8824	-15.5355	24.5506
34	2.9587	-0.3286	-0.3052	3.0736	0.2715	4.1886	-0.086	0.0024	0.3303	-0.0926	-0.4271	-0.6095	-0.1238	0.0068	0.0642	0.3406	0.0238	-0.0301	0.3801	0.0212	0.2264	27.1961	-15.1484	22.3052
35	1.6315	0.8029	-0.8748	3.6814	0.3432	2.7511	0.5819	-0.5468	0.2019	0.1802	-0.331	-0.5308	-0.0407	0.4226	-0.1272	0.3029	0.0141	0.0264	0.4917	-0.0369	0.4505	28.8115	-58.8968	22.2528
36	3.4789	-1.1478	-0.8536	4.8996	0.0537	3.397	-0.0412	-0.3135	0.1811	0.3828	0.0944	-0.603	0.388	-0.5811	-0.0924	0.2963	-0.0667	0.0095	0.3381	0.03	0.1728	22.9922	-58.9444	22.3789

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 31:59)	A	31 - 59
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 60:80)	A	60 - 80
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 81:121)	A	81 - 121
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 122:155)	A	122 - 155
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 156:205)	A	156 - 205
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 206:257)	A	206 - 257
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 258:280)	A	258 - 280
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 281:292)	A	281 - 292
9	X-RAY DIFFRACTION	9	chain 'B' and (resseq 30:44)	B	30 - 44
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 45:59)	B	45 - 59
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 60:80)	B	60 - 80
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 81:132)	B	81 - 132
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 133:151)	B	133 - 151
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 152:205)	B	152 - 205
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 206:258)	B	206 - 258
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 259:291)	B	259 - 291
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 30:44)	C	30 - 44
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 45:59)	C	45 - 59
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 60:80)	C	60 - 80
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 81:132)	C	81 - 132
21	X-RAY DIFFRACTION	21	chain 'C' and (resseq 133:151)	C	133 - 151
22	X-RAY DIFFRACTION	22	chain 'C' and (resseq 152:205)	C	152 - 205
23	X-RAY DIFFRACTION	23	chain 'C' and (resseq 206:257)	C	206 - 257
24	X-RAY DIFFRACTION	24	chain 'C' and (resseq 258:280)	C	258 - 280
25	X-RAY DIFFRACTION	25	chain 'C' and (resseq 281:292)	C	281 - 292
26	X-RAY DIFFRACTION	26	chain 'D' and (resseq 30:44)	D	30 - 44
27	X-RAY DIFFRACTION	27	chain 'D' and (resseq 45:80)	D	45 - 80
28	X-RAY DIFFRACTION	28	chain 'D' and (resseq 81:132)	D	81 - 132
29	X-RAY DIFFRACTION	29	chain 'D' and (resseq 133:151)	D	133 - 151
30	X-RAY DIFFRACTION	30	chain 'D' and (resseq 152:205)	D	152 - 205
31	X-RAY DIFFRACTION	31	chain 'D' and (resseq 206:258)	D	206 - 258
32	X-RAY DIFFRACTION	32	chain 'D' and (resseq 259:291)	D	259 - 291
33	X-RAY DIFFRACTION	33	chain 'E'	E	39 - 50
34	X-RAY DIFFRACTION	34	chain 'F'	F	39 - 49
35	X-RAY DIFFRACTION	35	chain 'G'	G	39 - 50
36	X-RAY DIFFRACTION	36	chain 'H'	H	39 - 50

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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