PDB-8zrs: Crystal structure of Skd3, AAA+ only

ID or keywords:

Entry

Database: PDB / ID: 8zrs

Title

Crystal structure of Skd3, AAA+ only

Components

Caseinolytic peptidase B protein homolog

Keywords

CHAPERONE / Disaggregase

Function / homology

Function and homology information

head development / thigmotaxis / anatomical structure morphogenesis / cerebellum development / cellular response to heat / ATP hydrolysis activity / mitochondrion / ATP binding / cytoplasm
Similarity search - Function

Biological species

Danio rerio (zebrafish)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.39 Å

Authors

Lee, S. / Lee, C.

Funding support

Korea, Republic Of, 2items

Citation

Journal: To Be Published
Title: Crystal structure of Skd3, AAA+ only
Authors: Lee, S. / Lee, C.

History

Deposition	Jun 5, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jun 11, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8zrs.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb8zrs.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	8zrs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zr/8zrs ftp://data.pdbj.org/pub/pdb/validation_reports/zr/8zrs	HTTPS FTP

-
Related structure data

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	#32 - Aug 2002 Chaperones similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (4) #176 - Aug 2014 Dynein similarity (4) #150 - Jun 2012 Sliding Clamps similarity (1) #250 - Oct 2020 Capsaicin Receptor TRPV1 similarity (1) #223 - Jul 2018 Piezo1 Mechanosensitive Channel similarity (1)

Deposited unit

A: Caseinolytic peptidase B protein homolog

B: Caseinolytic peptidase B protein homolog

C: Caseinolytic peptidase B protein homolog

D: Caseinolytic peptidase B protein homolog

E: Caseinolytic peptidase B protein homolog

F: Caseinolytic peptidase B protein homolog

G: Caseinolytic peptidase B protein homolog

H: Caseinolytic peptidase B protein homolog

I: Caseinolytic peptidase B protein homolog

J: Caseinolytic peptidase B protein homolog

K: Caseinolytic peptidase B protein homolog

L: Caseinolytic peptidase B protein homolog

hetero molecules

501 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	140.857, 172.407, 140.866
Angle α, β, γ (deg.)	90.00, 120.00, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Caseinolytic peptidase B protein homolog Mass: 41651.566 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Danio rerio (zebrafish) / Gene: clpb / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8M3AT32
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.96 Å³/Da / Density % sol: 58.5 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 8% PEG 3350, 100 mM HEPES pH 7.5, 100 mM ammonium sulfate

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site: PAL/PLS

/ Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å

Detector

Type: ADSC QUANTUM 270 / Detector: CCD / Date: May 15, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 3.39→50 Å / Num. obs: 79613 / % possible obs: 98.9 % / Redundancy: 6.8 % / CC_1/2: 1 / CC star: 1 / R_merge(I) obs: 0.112 / R_pim(I) all: 0.046 / R_rim(I) all: 0.122 / Χ²: 0.701 / Net I/σ(I): 5.2

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²	% possible all
3.4-3.46	6.1	0.614	3862	0.917	0.978	0.261	0.669	0.445	96.2
3.46-3.52	6.4	0.548	3942	0.946	0.986	0.231	0.597	0.451	98.3
3.52-3.59	6.5	0.454	3981	0.968	0.992	0.191	0.494	0.461	98.9
3.59-3.66	6.8	0.408	3916	0.978	0.994	0.168	0.442	0.462	99
3.66-3.74	6.8	0.349	3981	0.98	0.995	0.144	0.378	0.48	99.1
3.74-3.83	6.7	0.31	3966	0.98	0.995	0.128	0.336	0.481	99.1
3.83-3.92	6.6	0.272	4014	0.984	0.996	0.114	0.296	0.516	99
3.92-4.03	6.2	0.201	3976	0.987	0.997	0.089	0.22	0.552	99.3
4.03-4.15	6.5	0.16	4035	0.992	0.998	0.068	0.175	0.571	99.3
4.15-4.28	6.6	0.144	3940	0.992	0.998	0.061	0.157	0.615	99.3
4.28-4.44	7.2	0.125	3974	0.995	0.999	0.05	0.135	0.633	99.2
4.44-4.61	7.4	0.105	3974	0.996	0.999	0.041	0.113	0.689	99.2
4.61-4.82	7.4	0.104	3957	0.997	0.999	0.041	0.112	0.732	99.1
4.82-5.08	7.4	0.098	4075	0.996	0.999	0.039	0.105	0.744	99.4
5.08-5.4	7.3	0.107	3924	0.997	0.999	0.042	0.115	0.746	99.2
5.4-5.81	7.2	0.102	3993	0.996	0.999	0.04	0.11	0.728	99.5
5.81-6.4	7.1	0.096	4033	0.996	0.999	0.038	0.103	0.8	98.9
6.4-7.32	6.6	0.08	3995	0.996	0.999	0.033	0.087	0.931	99.1
7.32-9.21	6.3	0.05	3979	0.998	0.999	0.021	0.055	1.202	98.5
9.21-50	7.2	0.045	4096	0.998	1	0.018	0.048	1.608	98.6

-
Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data scaling
HKL-2000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 3.39→14.904 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 34.84 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2837	1943	2.49 %
R_work	0.2293	-	-
obs	0.2307	78005	97.75 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.39→14.904 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28227	0	60	0	28287

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	27609
X-RAY DIFFRACTION	f_angle_d	1.42	37401
X-RAY DIFFRACTION	f_dihedral_angle_d	14.954	9756
X-RAY DIFFRACTION	f_chiral_restr	0.06	4402
X-RAY DIFFRACTION	f_plane_restr	0.007	4768

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
3.3904-3.4741	0.3403	132	0.3143	5045	X-RAY DIFFRACTION	91
3.4741-3.5668	0.4137	144	0.2994	5340	X-RAY DIFFRACTION	98
3.5668-3.6703	0.4295	144	0.2891	5448	X-RAY DIFFRACTION	98
3.6703-3.7869	0.2891	134	0.2718	5443	X-RAY DIFFRACTION	98
3.7869-3.9198	0.3221	133	0.2647	5498	X-RAY DIFFRACTION	98
3.9198-4.0737	0.301	142	0.243	5394	X-RAY DIFFRACTION	99
4.0737-4.255	0.3486	138	0.2202	5511	X-RAY DIFFRACTION	99
4.255-4.4736	0.1994	133	0.2051	5457	X-RAY DIFFRACTION	99
4.4736-4.7453	0.2467	152	0.1864	5546	X-RAY DIFFRACTION	99
4.7453-5.0981	0.2531	133	0.1997	5433	X-RAY DIFFRACTION	99
5.0981-5.5864	0.302	141	0.2285	5517	X-RAY DIFFRACTION	98
5.5864-6.3397	0.2773	136	0.2576	5471	X-RAY DIFFRACTION	98
6.3397-7.7925	0.2578	146	0.2512	5493	X-RAY DIFFRACTION	98
7.7925-14.904	0.2358	135	0.1817	5466	X-RAY DIFFRACTION	97

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	5.0808	-1.9453	0.4715	5.2973	-0.7467	1.5661	-0.0576	-1.0022	0.0838	0.2743	0.2768	-0.0681	1.3654	1.2059	-0.2897	0.9494	0.3991	0.0433	1.609	-0.0934	0.7604	140.19	64.332	-29.595
2	6.5326	1.1763	1.2307	1.9074	-1.4348	2.2977	-1.0859	-1.8002	0.8612	0.202	1.5606	-0.7748	0.5314	1.5436	-0.2456	1.1282	0.4128	-0.0757	2.0908	-0.3175	0.9216	149.225	69.089	-26.674
3	3.933	0.4032	-4.074	1.5187	-0.6406	7.1909	0.3771	-0.0663	0.282	0.0735	0.0203	-0.0503	-0.5188	0.4401	-0.3285	0.5835	0.0411	-0.0135	1.0173	-0.1664	0.7841	125.409	72.266	-11.016
4	5.445	1.382	2.2599	4.4164	1.2732	5.3954	-0.0162	0.1979	-0.8094	-0.3422	-0.1225	-0.1088	0.2401	-0.3965	0.1247	0.6251	-0.0271	0.0306	0.6591	-0.051	0.7987	172.11	64.906	29.126
5	5.5201	1.4716	2.1503	4.5935	0.9697	5.5414	-0.1253	-0.2689	0.1561	0.2295	-0.0523	-0.2362	-0.3422	-0.0745	0.1124	0.4541	0.058	0.0454	0.4513	0.021	0.5218	171.512	78.227	34.108
6	8.1213	-2.5825	1.2564	2.7839	0.5113	4.1958	-0.1279	-0.4659	0.7526	0.1863	-0.0415	-0.3499	0.328	0.7951	0.2247	0.6116	0.028	0.0059	0.9427	0.088	0.7195	206.632	70.524	41.449
7	2.8634	2.2055	-1.0139	4.6738	1.3768	9.3527	0.0047	0.07	0.9241	0.3629	-0.2782	0.0274	-0.5423	-0.0851	0.2623	0.5692	0.0649	-0.0667	0.8153	-0.0617	0.701	180.228	116.683	39.386
8	7.0751	-1.4942	-2.4694	1.265	-1.2989	4.245	0.1569	0.8535	0.7647	-0.8348	-0.1645	0.0592	0.0189	-0.2955	0.0207	0.8158	-0.0736	-0.0007	0.6927	0.1994	0.8526	179.786	117.412	21.619
9	2.2957	0.934	-2.7686	3.8239	-3.6361	5.2136	0.2436	0.4255	0.1781	-0.0473	-0.2459	0.4755	-0.0018	-0.0225	-0.5677	0.6241	-0.7551	0.2625	-0.9949	0.2061	0.6898	183.847	118.717	25.796
10	8.2369	-2.1932	-1.2559	1.5315	0.5711	1.51	-0.1845	-0.3753	-0.4519	0.2299	0.0356	0.3108	0.0376	-0.4215	0.1775	0.6324	0.0167	-0.0182	0.7451	-0.0417	0.6381	157.845	107.576	39.508
11	8.3065	1.1536	-1.8481	4.3522	-1.3517	4.3902	-0.2086	0.4902	-0.2697	-0.17	0.1753	0.118	0.6789	-0.7692	0.173	0.7483	-0.0935	0.0715	0.7271	-0.1295	0.611	204.772	65.091	14.161
12	4.1104	3.4128	0.8387	2.485	0.7823	1.9296	0.9124	1.7444	-0.0632	0.952	-0.4639	-0.3622	0.0694	-0.2674	-0.143	0.7426	-0.0379	0.0497	0.3964	-0.113	0.9104	200.96	64.359	16.008
13	2.0046	-0.359	-1.5991	5.7986	0.3958	4.5787	0.2297	-0.009	0.9074	0.0086	0.0455	-0.4679	-0.1631	0.5579	-0.3152	0.6422	0.1982	0.1643	0.3587	0.0016	0.9215	211.222	82.288	17.558
14	6.1065	-1.7349	-1.4427	2.4276	1.5909	6.1698	0.6184	0.2295	0.4995	-0.2584	-0.2632	-0.2721	-0.5142	-0.1455	-0.3925	0.6069	0.0102	0.0987	0.5378	-0.007	0.7723	232.952	70.834	-9.425
15	1.9945	-1.8773	2.0986	5.8173	-2.0688	4.4678	-0.1677	1.8266	0.0435	-0.2473	-0.2662	-1.2481	-1.349	0.9465	0.1638	0.9522	0.2147	0.0477	1.2413	0.0564	0.8458	219.496	118.21	-32.901
16	1.3801	-1.4107	-0.1147	2.7501	-0.2196	0.9413	-0.0922	-1.789	-0.3007	0.7326	0.9226	0.4931	-2.5167	-2.0862	0.8405	0.8734	0.7722	-0.1215	2.5836	0.3676	0.7955	207.893	118.023	-27.529
17	3.1057	-2.8391	2.4857	4.362	-0.7261	3.3517	-0.4389	-2.2347	-0.7205	0.622	0.5183	1.4286	-0.9623	-2.0526	-0.5585	1.1778	0.7392	0.0025	2.4578	0.065	1.2861	196.327	119.931	-22.442
18	6.5964	-3.9179	2.2795	4.4153	0.3401	4.6117	0.072	-2.7052	-1.7255	-0.0262	-0.0016	1.2264	-1.0229	-1.3119	0.1303	1.135	0.4551	0.0814	2.2585	0.2252	0.992	198.384	116.453	-30.119
19	5.314	1.2087	4.7676	3.9868	1.4486	6.9701	0.2899	-0.1196	-1.4054	-0.3571	0.4544	0.3563	0.7209	-0.971	-0.5872	0.9201	-0.2347	-0.1845	1.5703	0.3006	1.1757	210.397	101.232	-31.068
20	5.4821	1.8049	3.621	3.7021	2.8812	7.2025	0.2994	0.3015	-0.1004	0.2247	-0.031	-0.1871	0.3797	-0.1573	-0.3031	0.5783	0.012	0.0166	0.8383	0.1867	0.665	233.703	111.71	-3.788
21	2.3022	0.5076	-0.8993	4.343	-2.4122	6.7632	0.569	-0.337	0.5863	0.5387	-0.199	-0.7617	-1.0089	1.2339	-0.1165	0.6918	0.0128	-0.0309	1.2341	0.098	0.8206	220.388	117.844	17.356
22	1.55	-0.7381	0.4782	4.7068	0.036	2.4631	0.2816	0.9366	0.4769	-0.2544	-0.0947	0.5995	-0.289	-0.7148	-0.2691	0.6241	0.1615	0.02	1.1573	0.2742	0.6912	209.151	117.551	9.774
23	1.6985	-2.1297	0.2484	6.2378	0.3288	0.1308	0.3695	-0.0359	-0.6405	-0.8817	-0.2828	1.814	-0.3391	-0.3316	-0.6495	-0.0406	1.7775	-0.2768	2.565	1.5685	1.432	197.165	122.36	-0.07
24	4.9853	0.012	0.5326	5.3085	0.8394	5.46	-0.2228	-0.2335	0.4201	-0.0313	-0.2795	1.3618	-0.1776	-0.3757	-0.021	0.6829	0.3039	-0.0003	1.0921	0.2938	1.0206	203.358	116.025	6.07
25	3.9112	-0.067	0.9974	6.2725	0.0127	4.2412	0.0346	0.3216	0.0023	-0.1798	0.3684	0.2268	0.7253	-0.463	-0.4398	0.5965	-0.0307	0.0676	0.9252	0.0147	0.6166	212.738	104.859	8.68
26	5.4349	-0.7983	0.3564	3.1722	3.3032	8.3394	-0.1804	-0.921	0.2838	0.6091	-0.3221	0.1471	0.5885	-0.1162	0.5066	0.7031	-0.1156	0.0648	0.8856	0.0202	0.6579	202.733	111.809	44.216
27	1.2665	0.0891	-1.1653	1.5864	0.882	7.18	-0.7176	-2.0497	1.1313	0.1539	0.585	-0.412	-0.0645	0.6647	0.0855	0.8773	0.2489	-0.1114	2.3454	-0.3036	1.0903	174.078	118.961	-48.686
28	0.9604	-0.5019	1.4693	2.2929	1.5406	4.9644	0.143	-0.8221	1.2448	1.2618	1.3999	-0.2889	0.8584	-0.3019	-0.7114	1.0582	0.5245	0.0475	2.8474	-0.6166	1.6276	174.009	117.813	-37.767
29	4.5627	-1.6219	-0.1855	3.975	0.366	8.288	-1.3704	-2.162	-0.5734	1.1268	0.6283	0.578	1.8319	0.0615	0.6354	0.9728	0.2594	0.0778	2.2351	0.3916	1.2719	172.633	107.046	-44.367
30	3.2594	-3.3814	-2.2801	4.6414	2.3527	7.0427	-0.783	-1.7264	-1.0147	0.2372	-0.1418	1.1406	1.0652	0.1828	1.2097	1.1062	0.1489	0.228	2.2093	0.3727	1.5544	168.821	103.745	-45.145
31	5.8387	0.1293	-0.5027	4.566	-0.9417	5.3746	-0.0115	-0.17	-1.0182	-0.0555	0.0677	0.0117	-0.2236	-0.7346	-0.205	0.687	0.199	0.0038	1.1196	0.0849	0.7352	207.447	112.19	-55.048
32	3.4027	1.8559	-1.4836	3.7589	-1.5677	5.8509	0.0896	0.3461	-0.2479	0.0269	0.4518	0.5602	-0.1887	-2.2036	-0.5492	0.7177	0.034	0.0223	1.355	0.2374	0.8251	210.115	64.009	-23.723
33	1.4048	0.6147	0.9286	4.989	-1.4815	5.3286	-0.0687	0.3201	0.462	0.2888	0.4555	0.5991	-1.388	-0.7051	-0.39	1.1433	0.2238	0.2031	0.967	0.0742	0.8398	211.542	75.774	-20.745
34	5.4366	-0.4583	2.4162	0.7997	-0.2562	5.5485	-0.4425	-0.3384	-0.0812	-0.1406	-0.0488	0.0522	-0.6936	-0.1943	0.4545	0.8943	0.1193	0.0973	1.2664	0.2135	0.8836	202.01	70.451	-57.852
35	8.5984	2.0894	2.1489	4.899	0.2776	5.1419	-0.3346	0.1383	0.3169	-0.127	0.0759	-0.3209	-0.9389	0.8914	0.2575	0.706	-0.0721	-0.1252	0.8689	0.1206	0.659	147.135	117.156	14.305
36	3.2481	0.7244	-0.525	5.1541	-1.0979	3.9563	-0.2371	0.0084	-0.5952	-0.3077	0.3323	0.2273	-0.0167	-0.3753	-0.1582	0.6281	0.2258	-0.1319	0.479	-0.0352	0.8034	143.242	103.231	17.254
37	6.7139	-0.7322	2.4578	3.5874	-1.8869	7.6523	0.4958	-0.0449	-0.5332	-0.282	-0.1585	0.2086	0.582	-0.2856	-0.3587	0.5761	0.0012	-0.0478	0.4789	-0.0358	0.7223	119.199	111.305	-9.368
38	5.9124	0.063	0.5077	4.8487	1.8924	3.3478	0.054	0.3632	0.1663	0.1492	0.5789	-0.4766	0.0492	2.1501	-0.6141	0.7078	-0.0156	-0.0084	1.4418	-0.1871	0.7295	142.827	117.826	-22.09
39	4.4503	2.3968	0.1137	4.3242	-0.2544	3.5128	-0.0941	0.7254	-0.7364	0.3589	0.2184	-0.0187	1.4223	0.644	-0.1715	1.2055	0.3009	-0.1662	0.8731	-0.102	0.8324	139.584	104.954	-22.334
40	5.182	1.1624	-0.9115	3.6515	-2.1316	8.4059	-0.34	-0.0501	-0.135	-0.0031	0.1486	0.1268	0.669	-0.3554	0.2888	0.8178	0.1259	-0.0104	1.1897	-0.2036	0.768	149.764	111.917	-57.67
41	2.9949	-0.536	4.5354	2.8766	-0.4577	7.0093	-0.5219	0.0257	-2.3572	-0.9946	0.8538	0.5134	0.489	-0.7645	0.0586	0.8478	0.0127	0.1702	1.5895	0.0549	1.217	176.998	63.924	-56.783
42	2.5469	1.1365	-0.5194	1.4311	-1.1244	7.5918	-1.4252	-2.3222	-1.1117	0.179	0.8265	0.2164	0.5023	-0.6052	0.5737	0.8786	0.3104	0.0812	2.5241	0.4314	1.1452	178.446	62.643	-43.466
43	4.6671	0.2122	0.4649	4.2278	1.8017	5.1687	-1.1293	-2.049	-0.6493	1.1889	2.2238	-1.2321	-0.7455	-0.0869	-0.8684	1.309	0.6047	0.1661	3.4547	0.098	1.3012	183.824	65.443	-35.331
44	2.8615	-0.9859	2.2944	7.0386	-5.4955	5.3799	-1.0647	-0.5847	0.596	-0.2236	0.4603	0.17	-1.1927	-0.7223	0.4851	1.5288	0.3245	-0.2913	1.6332	-0.3429	1.2196	175.89	77.879	-48.916
45	1.5944	1.6763	-2.5558	2.9344	-1.0136	6.1453	-0.6481	-1.129	1.0952	0.4004	-0.4948	-0.1981	-0.9962	0.1215	0.4593	1.1008	0.2977	-0.3479	1.9981	-0.1697	1.5574	183.379	78.46	-45.131
46	8.9761	0.304	1.7658	2.573	-0.7177	3.9729	-0.3171	0.2013	0.8887	-0.0168	0.2473	-0.0672	-0.0761	0.8879	-0.0255	0.8103	0.2376	-0.0199	1.1818	-0.0981	0.7465	144.556	70.242	-55.03
47	2.7796	1.3103	1.2155	3.3547	1.556	5.5734	0.4494	-0.0981	0.0445	0.6367	-0.2711	0.8378	0.9978	-0.8539	0.1139	0.716	0.0576	-0.0471	0.96	-0.1122	0.8584	131.598	64.377	17.41
48	0.591	-1.8073	-0.5414	5.8376	1.4217	4.2212	0.4612	0.706	-0.5885	-0.221	-0.2814	-0.6125	0.4479	0.9609	-0.43	0.6784	0.1872	0.0113	1.1132	-0.26	0.6315	142.888	64.912	9.708
49	2.6374	0.0946	-1.3344	3.2595	-0.9572	1.6399	0.8055	0.377	0.4467	-1.3665	-0.3655	-1.5255	-0.1989	0.5936	-0.2243	0.6572	1.0889	0.4754	2.8789	-1.0762	1.1452	154.894	59.974	-0.046
50	2.2951	-1.5773	-2.3193	7.8494	-1.5723	9.2321	0.4633	-0.2239	-0.3749	-0.2906	-0.2611	-1.2613	0.7486	1.3143	-0.0685	0.7062	0.1336	0.0719	0.9687	-0.2685	0.918	145.92	66.263	2.611
51	4.3002	0.6941	0.0847	8.5201	1.6597	7.6895	0.196	0.114	0.5199	-0.2641	0.139	0.531	-1.228	0.2881	-0.427	0.6496	-0.0417	0.0127	0.9344	0.0798	0.6473	137.099	81.964	11.943
52	5.3996	2.046	-2.3727	4.4382	-1.396	9.3397	-0.0854	-0.2023	-0.1774	0.4475	-0.6365	0.0359	-0.4675	-0.0258	0.6014	0.5797	-0.1016	0.0623	0.7591	0.0352	0.5646	146.002	70.451	38.414
53	8.8727	-2.1475	4.8829	4.1481	-2.0991	2.9825	-0.3464	0.0546	0.2827	0.6806	-1.169	-0.1885	-0.5095	1.4885	1.581	0.6814	-0.214	-0.001	1.4208	0.0458	0.5981	155.299	70.531	39.582
54	5.4669	-1.7074	-4.5697	3.1135	-1.884	9.8798	-0.1123	-0.9798	0.0038	0.6851	0.1361	-0.5308	-0.2689	0.3593	-0.151	0.9713	-0.0826	-0.1254	1.2118	0.1023	0.8432	150.542	70.067	55.034

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 RESID 294:373 )	A	294 - 373
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 374:494 )	A	374 - 494
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 495:641 )	A	495 - 641
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 294:430 )	B	294 - 430
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 431:529 )	B	431 - 529
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 530:640 )	B	530 - 640
7	X-RAY DIFFRACTION	7	( CHAIN C AND RESID 294:343 )	C	294 - 343
8	X-RAY DIFFRACTION	8	( CHAIN C AND RESID 344:430 )	C	344 - 430
9	X-RAY DIFFRACTION	9	( CHAIN C AND RESID 431:455 )	C	431 - 455
10	X-RAY DIFFRACTION	10	( CHAIN C AND RESID 456:641 )	C	456 - 641
11	X-RAY DIFFRACTION	11	( CHAIN D AND RESID 294:430 )	D	294 - 430
12	X-RAY DIFFRACTION	12	( CHAIN D AND RESID 431:455 )	D	431 - 455
13	X-RAY DIFFRACTION	13	( CHAIN D AND RESID 456:529 )	D	456 - 529
14	X-RAY DIFFRACTION	14	( CHAIN D AND RESID 530:641 )	D	530 - 641
15	X-RAY DIFFRACTION	15	( CHAIN E AND RESID 294:323 )	E	294 - 323
16	X-RAY DIFFRACTION	16	( CHAIN E AND RESID 324:371 )	E	324 - 371
17	X-RAY DIFFRACTION	17	( CHAIN E AND RESID 372:417 )	E	372 - 417
18	X-RAY DIFFRACTION	18	( CHAIN E AND RESID 418:455 )	E	418 - 455
19	X-RAY DIFFRACTION	19	( CHAIN E AND RESID 456:529 )	E	456 - 529
20	X-RAY DIFFRACTION	20	( CHAIN E AND RESID 530:641 )	E	530 - 641
21	X-RAY DIFFRACTION	21	( CHAIN F AND RESID 294:323 )	F	294 - 323
22	X-RAY DIFFRACTION	22	( CHAIN F AND RESID 324:373 )	F	324 - 373
23	X-RAY DIFFRACTION	23	( CHAIN F AND RESID 374:402 )	F	374 - 402
24	X-RAY DIFFRACTION	24	( CHAIN F AND RESID 403:417 )	F	403 - 417
25	X-RAY DIFFRACTION	25	( CHAIN F AND RESID 418:529 )	F	418 - 529
26	X-RAY DIFFRACTION	26	( CHAIN F AND RESID 530:640 )	F	530 - 640
27	X-RAY DIFFRACTION	27	( CHAIN G AND RESID 294:401 )	G	294 - 401
28	X-RAY DIFFRACTION	28	( CHAIN G AND RESID 405:417 )	G	405 - 417
29	X-RAY DIFFRACTION	29	( CHAIN G AND RESID 418:494 )	G	418 - 494
30	X-RAY DIFFRACTION	30	( CHAIN G AND RESID 495:529 )	G	495 - 529
31	X-RAY DIFFRACTION	31	( CHAIN G AND RESID 530:641 )	G	530 - 641
32	X-RAY DIFFRACTION	32	( CHAIN H AND RESID 294:417 )	H	294 - 417
33	X-RAY DIFFRACTION	33	( CHAIN H AND RESID 418:529 )	H	418 - 529
34	X-RAY DIFFRACTION	34	( CHAIN H AND RESID 530:641 )	H	530 - 641
35	X-RAY DIFFRACTION	35	( CHAIN I AND RESID 294:430 )	I	294 - 430
36	X-RAY DIFFRACTION	36	( CHAIN I AND RESID 431:529 )	I	431 - 529
37	X-RAY DIFFRACTION	37	( CHAIN I AND RESID 530:641 )	I	530 - 641
38	X-RAY DIFFRACTION	38	( CHAIN J AND RESID 294:430 )	J	294 - 430
39	X-RAY DIFFRACTION	39	( CHAIN J AND RESID 431:529 )	J	431 - 529
40	X-RAY DIFFRACTION	40	( CHAIN J AND RESID 530:640 )	J	530 - 640
41	X-RAY DIFFRACTION	41	( CHAIN K AND RESID 294:323 )	K	294 - 323
42	X-RAY DIFFRACTION	42	( CHAIN K AND RESID 324:401 )	K	324 - 401
43	X-RAY DIFFRACTION	43	( CHAIN K AND RESID 405:430 )	K	405 - 430
44	X-RAY DIFFRACTION	44	( CHAIN K AND RESID 431:494 )	K	431 - 494
45	X-RAY DIFFRACTION	45	( CHAIN K AND RESID 495:529 )	K	495 - 529
46	X-RAY DIFFRACTION	46	( CHAIN K AND RESID 530:641 )	K	530 - 641
47	X-RAY DIFFRACTION	47	( CHAIN L AND RESID 294:323 )	L	294 - 323
48	X-RAY DIFFRACTION	48	( CHAIN L AND RESID 324:373 )	L	324 - 373
49	X-RAY DIFFRACTION	49	( CHAIN L AND RESID 374:402 )	L	374 - 402
50	X-RAY DIFFRACTION	50	( CHAIN L AND RESID 403:455 )	L	403 - 455
51	X-RAY DIFFRACTION	51	( CHAIN L AND RESID 456:529 )	L	456 - 529
52	X-RAY DIFFRACTION	52	( CHAIN L AND RESID 530:574 )	L	530 - 574
53	X-RAY DIFFRACTION	53	( CHAIN L AND RESID 575:596 )	L	575 - 596
54	X-RAY DIFFRACTION	54	( CHAIN L AND RESID 597:640 )	L	597 - 640

-
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