PDB-8j54: Crystal structure of RXR/DR2 complex

ID or keywords:

Entry

Database: PDB / ID: 8j54

Title

Crystal structure of RXR/DR2 complex

Components

DNA (5'-D(*CP*AP*TP*GP*AP*CP*CP*TP*AP*CP*TP*GP*AP*CP*CP*TP*AP*G)-3')
DNA (5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*GP*TP*AP*GP*GP*TP*CP*AP*TP*G)-3')
Retinoic acid receptor RXR

Keywords

DNA/DNA BINDING PROTEIN / retinoid-related orphan receptor / DR2 / DNA BINDING PROTEIN / DNA-DNA BINDING PROTEIN complex

Function / homology

Function and homology information

nuclear steroid receptor activity / sequence-specific DNA binding / DNA-binding transcription factor activity / DNA-templated transcription / zinc ion binding / nucleus
Similarity search - Function

Biological species

Homo sapiens (human)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.72 Å

Authors

Chen, Y. / Jiang, L.

Funding support

China, 1items

Citation

Journal: Structure / Year: 2024
Title: Structural characterization of the DNA binding mechanism of retinoic acid-related orphan receptor gamma.
Authors: Jiang, L. / Liu, X. / Liang, X. / Dai, S. / Wei, H. / Guo, M. / Chen, Z. / Xiao, D. / Chen, Y.

History

Deposition	Apr 21, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	Feb 14, 2024	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Apr 17, 2024	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8j54.cif.gz	224 KB	Display	PDBx/mmCIF format
PDB format	pdb8j54.ent.gz	177.7 KB	Display	PDB format
PDBx/mmJSON format	8j54.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8j54_validation.pdf.gz	478.1 KB	Display	wwPDB validaton report
Full document	8j54_full_validation.pdf.gz	482.9 KB	Display
Data in XML	8j54_validation.xml.gz	14.5 KB	Display
Data in CIF	8j54_validation.cif.gz	19.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j5/8j54 ftp://data.pdbj.org/pub/pdb/validation_reports/j5/8j54	HTTPS FTP

-
Related structure data

Related structure data	7xvnC 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	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (4) #139 - Jul 2011 DNA Methyltransferase similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#67 - Jul 2005
TATA-Binding Protein
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#255 - Mar 2021
Cisplatin and DNA
similarity (1)
#91 - Jul 2007
Thymine Dimers
similarity (1)
#122 - Feb 2010
Enhanceosome
similarity (1)
#172 - Apr 2014
RecA and Rad51
similarity (1)
#181 - Jan 2015
Cascade and CRISPR
similarity (1)
#253 - Jan 2021
Expressome
similarity (1)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (1)
#135 - Mar 2011
Integrase
similarity (1)
#150 - Jun 2012
Sliding Clamps
similarity (1)
#180 - Dec 2014
TAL Effectors
similarity (1)
#227 - Nov 2018
Telomerase
similarity (1)
#48 - Dec 2003
Catabolite Activator Protein
similarity (1)
#84 - Dec 2006
Transposase
similarity (1)
#155 - Nov 2012
Vitamin D Receptor
similarity (4)
#139 - Jul 2011
DNA Methyltransferase
similarity (1)
#3 - Mar 2000
DNA Polymerase
similarity (1)
#40 - Apr 2003
RNA Polymerase
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#87 - Mar 2007
Zinc Fingers
similarity (1)
#119 - Nov 2009
Designed DNA Crystal
similarity (1)
#125 - May 2010
Parvoviruses
similarity (1)
#131 - Nov 2010
Inteins
similarity (1)
#160 - Apr 2013
Actinomycin
similarity (1)
#190 - Oct 2015
Two-component Systems
similarity (1)
#23 - Nov 2001
DNA
similarity (1)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (1)
#257 - May 2021
Fetal Hemoglobin
similarity (1)
#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (1)
#31 - Jul 2002
p53 Tumor Suppressor
similarity (1)
#33 - Sep 2002
HIV Reverse Transcriptase
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)
#45 - Sep 2003
Estrogen Receptor
similarity (1)
#55 - Jul 2004
DNA Ligase
similarity (1)
#7 - Jul 2000
Nucleosome
similarity (1)
#8 - Aug 2000
Restriction Enzymes
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (1)
#241 - Jan 2020
Twenty Years of Molecules
similarity (1)

Deposited unit

A: DNA (5'-D(*CP*AP*TP*GP*AP*CP*CP*TP*AP*CP*TP*GP*AP*CP*CP*TP*AP*G)-3')

B: DNA (5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*GP*TP*AP*GP*GP*TP*CP*AP*TP*G)-3')

C: Retinoic acid receptor RXR

D: Retinoic acid receptor RXR

E: Retinoic acid receptor RXR

F: Retinoic acid receptor RXR

N: DNA (5'-D(*CP*AP*TP*GP*AP*CP*CP*TP*AP*CP*TP*GP*AP*CP*CP*TP*AP*G)-3')

P: DNA (5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*GP*TP*AP*GP*GP*TP*CP*AP*TP*G)-3')

hetero molecules

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

1

A: DNA (5'-D(*CP*AP*TP*GP*AP*CP*CP*TP*AP*CP*TP*GP*AP*CP*CP*TP*AP*G)-3')

B: DNA (5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*GP*TP*AP*GP*GP*TP*CP*AP*TP*G)-3')

C: Retinoic acid receptor RXR

D: Retinoic acid receptor RXR

hetero molecules

defined by author&software
31 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Retinoic acid receptor RXR

F: Retinoic acid receptor RXR

N: DNA (5'-D(*CP*AP*TP*GP*AP*CP*CP*TP*AP*CP*TP*GP*AP*CP*CP*TP*AP*G)-3')

P: DNA (5'-D(*CP*TP*AP*GP*GP*TP*CP*AP*GP*TP*AP*GP*GP*TP*CP*AP*TP*G)-3')

hetero molecules

defined by author&software
31 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	36.239, 63.646, 244.649
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: DNA chain	DNA (5'-D(CPAPTPGPAPCPCPTPAPCPTPGPAPCPCPTPAPG)-3') Mass: 5460.556 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: DNA chain	DNA (5'-D(CPTPAPGPGPTPCPAPGPTPAPGPGPTPCPAPTPG)-3') Mass: 5571.614 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein	Retinoic acid receptor RXR / ROR gamma / Nuclear receptor subfamily 2 group B member Mass: 9849.454 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rxra, RXR alpha / Production host: Escherichia coli (E. coli) / References: UniProt: Q6LC96
#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.41 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion, hanging drop Details: 0.1 M Bis-Tris6.5, 0.01 mM CaCl2, 18-23% PEG2000MME

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
Detector	Type: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 23, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.979 Å / Relative weight: 1
Reflection	Resolution: 2.7→38.79 Å / Num. obs: 28366 / % possible obs: 96.77 % / Redundancy: 12.3 % / CC_1/2: 0.998 / Net I/σ(I): 16.5
Reflection shell	Resolution: 2.7→2.82 Å / Num. unique obs: 1554 / CC_1/2: 0.978

-
Processing

Software

Name	Version	Classification
PHENIX	(1.19.2_4158: ???)	refinement
HKL-2000		data reduction
autoPROC		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.72→38.79 Å / SU ML: 0.38 / Cross valid method: NONE / σ(F): 1.44 / Phase error: 36.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2729	2840	10.01 %
R_work	0.217	-	-
obs	0.2225	28366	96.89 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.72→38.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2488	1461	8	0	3957

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	4156
X-RAY DIFFRACTION	f_angle_d	0.496	5863
X-RAY DIFFRACTION	f_dihedral_angle_d	24.66	1064
X-RAY DIFFRACTION	f_chiral_restr	0.031	619
X-RAY DIFFRACTION	f_plane_restr	0.002	508

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 (%)
2.72-2.77	0.4333	146	0.3393	1288	X-RAY DIFFRACTION	96
2.77-2.82	0.3959	148	0.3352	1311	X-RAY DIFFRACTION	99
2.82-2.87	0.3478	135	0.3258	1274	X-RAY DIFFRACTION	99
2.87-2.93	0.3818	155	0.3255	1321	X-RAY DIFFRACTION	99
2.93-3	0.375	146	0.3418	1304	X-RAY DIFFRACTION	99
3-3.07	0.4502	141	0.3249	1288	X-RAY DIFFRACTION	99
3.07-3.14	0.3344	137	0.3144	1239	X-RAY DIFFRACTION	96
3.14-3.23	0.3803	140	0.2993	1302	X-RAY DIFFRACTION	95
3.23-3.32	0.3344	146	0.2833	1267	X-RAY DIFFRACTION	95
3.32-3.43	0.3163	128	0.2919	1177	X-RAY DIFFRACTION	93
3.43-3.55	0.4053	137	0.2773	1266	X-RAY DIFFRACTION	95
3.55-3.69	0.3258	113	0.2505	995	X-RAY DIFFRACTION	74
3.7-3.86	0.3252	143	0.2402	1295	X-RAY DIFFRACTION	99
3.86-4.07	0.2921	150	0.2236	1336	X-RAY DIFFRACTION	100
4.07-4.32	0.2407	144	0.2094	1274	X-RAY DIFFRACTION	100
4.32-4.65	0.2555	144	0.1985	1322	X-RAY DIFFRACTION	100
4.65-5.12	0.2282	151	0.1983	1332	X-RAY DIFFRACTION	100
5.12-5.86	0.2434	143	0.1872	1296	X-RAY DIFFRACTION	100
5.86-7.37	0.2646	151	0.1917	1336	X-RAY DIFFRACTION	100
7.38-38.79	0.1982	142	0.1553	1303	X-RAY DIFFRACTION	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	5.384	-0.3314	-2.979	4.961	-2.0405	7.1519	0.0571	-2.0538	-1.204	0.6266	-0.0902	-0.6564	0.0204	-0.6008	0.1429	0.8163	0.0614	0.0289	1.7337	0.1507	0.6304	-5.9477	-21.8408	62.773
2	3.524	-2.5488	-0.5501	1.8523	1.044	6.9085	1.2236	0.0009	0.3618	-0.6257	0.4215	-0.8457	0.0607	1.3138	-0.9642	0.7708	0.0505	0.1056	1.2431	0.0427	0.924	0.9888	-24.1243	46.515
3	8.1324	1.2921	-0.7864	6.2762	-0.5447	5.5894	-0.5689	1.8719	1.2527	-1.3264	0.6579	-0.351	-0.7943	0.1519	-0.3866	1.2306	0.1371	0.0906	0.8986	-0.0132	0.7383	-7.9127	-19.7649	29.2578
4	8.2249	-1.8994	-1.0986	2.4986	0.8878	7.4616	1.9191	1.0418	-0.3777	-0.7541	0.3343	-0.0896	-0.137	-0.8472	-1.8797	1.4915	-0.1452	0.0916	1.9892	-0.0376	0.8292	-1.5605	-23.5522	14.2008
5	7.9324	2.3979	-3.8916	2.2627	1.0391	4.66	0.1439	0.5555	-0.5383	0.0836	0.3338	-0.0223	-0.2345	0.5354	-0.4084	0.7773	0.1749	-0.0349	0.6469	-0.0267	0.6243	-4.3554	-23.8875	35.5556
6	2.8883	0.1272	-4.0065	6.5738	-0.4987	5.5806	0.5453	0.2393	2.1556	2.0853	-0.489	-0.4449	-1.3459	0.5633	-0.3542	1.042	-0.1071	-0.0317	2.0664	0.1249	1.0837	1.282	-23.9564	67.4349
7	5.5561	0.8748	-0.1943	2.4442	3.3873	5.2688	1.0749	-0.6675	-0.2829	-1.8589	-0.9573	-1.0653	-1.2665	-1.6751	0.1237	1.058	0.1058	0.114	1.0111	-0.0579	0.6729	-8.7222	-9.3374	51.3085
8	7.3523	1.3217	-1.5923	6.8245	-0.454	6.7928	0.6574	-0.2178	-0.836	-1.3145	-0.4356	-0.8118	1.0586	0.9403	-0.1699	0.9043	0.1755	0.0707	1.1747	-0.0294	0.5593	-12.9478	-21.3429	55.8685
9	4.1645	0.4616	-2.9318	2.0571	0.2079	2.0163	0.4608	-2.1912	0.4193	1.1525	-0.654	0.4021	-0.6031	-0.0791	0.1052	1.3453	0.0235	0.0754	1.7342	-0.3369	1.0229	-17.9874	-12.1418	65.9314
10	2.5533	-2.1386	-2.4531	4.3017	1.0867	3.621	0.4399	-0.7869	0.3069	-0.7771	-0.4016	-0.442	0.3086	-1.965	-0.2053	0.5007	-0.0637	0.0907	1.4216	-0.2211	0.7691	-17.9519	-17.5825	54.7542
11	7.3512	5.4577	-1.2889	6.211	-2.4859	5.9031	-0.932	3.2183	0.6057	-1.1533	1.8344	-0.9095	0.7826	0.8361	-0.6016	0.6625	0.0752	-0.1703	0.9945	-0.0794	0.5267	-19.7727	-26.0145	24.0658
12	6.7031	-4.5164	-0.6392	7.5796	-1.2205	3.3437	0.9229	2.098	-1.6402	-2.1584	-0.0727	0.1643	0.9729	0.3953	-0.5969	0.7734	-0.041	0.0033	0.7906	-0.2793	0.8593	-9.5818	-31.0961	29.7302
13	4.4814	-0.4394	4.0829	0.0408	-0.3388	3.7731	0.5128	-0.7153	-3.1064	1.084	-0.2419	0.6365	0.6314	-1.705	0.5368	0.8313	0.4445	0.1351	1.0968	-0.058	1.3208	-18.0789	-36.0777	41.5005
14	4.5167	-0.0788	0.0123	6.0818	2.0231	2.9768	-0.2416	-1.4668	-1.1698	3.3104	0.1222	1.3243	0.9838	-0.0474	-0.0837	1.2171	0.061	0.0294	0.61	0.0626	0.8513	-18.2913	-31.8578	37.0902
15	5.3718	-3.5853	0.3499	5.1824	-3.7405	4.5048	1.4086	0.8495	-0.9702	-0.2255	0.4382	0.2021	1.0083	0.366	0.0231	0.7288	0.0852	-0.1323	0.9342	-0.6452	1.0384	-11.4349	-37.7462	23.9963
16	1.7324	1.5069	-0.7873	2.6348	-4.0231	9.0656	-0.6315	0.0862	0.1393	-0.9118	0.2937	0.211	0.7633	-1.082	0.2175	1.1621	0.3046	-0.2024	0.164	-0.1381	0.6354	5.9155	16.0506	35.4934
17	2.556	1.4533	1.9132	4.6913	-1.6207	4.9692	0.1733	0.4385	-0.87	0.8782	0.3408	0.1981	1.0222	-0.4553	-0.9024	0.8286	0.1547	0.0247	0.6096	-0.0389	0.7865	12.8135	7.6876	33.8367
18	1.1538	0.6153	1.5359	5.5943	-0.2173	2.9416	-0.2798	1.1436	0.8876	-1.8731	0.1559	-2.297	-0.8625	-0.2804	-0.1201	1.2816	0.3479	0.5949	1.3231	0.0488	1.28	19.8607	11.6295	20.6729
19	5.4393	0.3241	-0.8165	5.1866	3.4344	5.2184	0.4224	0.5964	0.0588	-0.2202	0.4464	-0.4714	-0.2932	0.6795	-0.6563	0.9528	0.0395	-0.0013	1.0611	0.0191	0.8136	15.6624	10.4154	29.6882
20	5.7388	-1.7316	0.4613	3.5668	2.615	4.7446	0.416	-0.5484	0.0159	-0.3784	-0.1277	0.1357	0.1838	-0.3037	-0.3573	0.4841	0.0545	0.0271	0.5256	-0.0059	0.615	-3.3286	0.3787	7.606
21	6.2897	-1.5071	0.5499	6.3085	-0.4097	4.0646	0.0033	1.5652	0.6918	-2.2629	0.2757	0.4491	-0.1183	-0.1503	-0.2772	1.0992	-0.0909	-0.0946	0.8288	0.14	0.9819	-3.3703	7.0815	-0.8551
22	3.1504	-3.058	0.9395	4.5122	-0.3117	5.6864	0.9918	-0.1239	0.2403	-0.9304	-0.3228	0.1343	1.1144	1.1495	-0.3647	1.1968	0.0256	0.1572	0.8848	-0.1507	0.7402	5.0018	-4.4739	-1.7219
23	0.5543	-1.2323	-0.4778	5.4273	4.3697	5.0193	-0.0273	-0.1535	-0.3344	1.8122	1.3994	-1.1521	1.7017	1.8345	-1.0175	1.218	0.1143	-0.0895	1.2248	-0.2094	0.8666	8.6456	-7.6235	15.7614
24	2.9022	0.8182	-0.8444	4.9015	-2.5479	7.0445	0.0999	-0.4338	0.4251	0.8023	0.7316	0.932	1.241	-0.305	-0.6871	1.2501	0.1548	-0.011	0.9584	-0.0143	0.8023	2.1792	2.9541	31.3687
25	9.9852	-5.1862	9.0445	3.1669	-4.584	8.2491	0.9259	-5.0827	-1.3827	0.0364	1.5392	-0.2027	0.1889	-0.9265	-2.1811	1.5054	0.0595	-0.1007	1.7025	-0.0615	1.0123	4.4933	-2.7313	47.6251
26	9.0068	-0.4816	-0.7383	9.5066	5.7881	3.5617	1.0915	-0.6289	0.4583	-0.5946	-0.5426	-0.3428	0.219	-2.9669	-0.5422	1.2295	0.1308	-0.1161	1.0247	-0.1823	0.7007	8.8365	3.0774	42.3592
27	9.6805	2.887	5.5516	1.7399	2.109	3.3996	1.3431	0.8695	-0.1527	0.0346	0.2812	0.0038	3.319	1.2702	-1.6804	1.5443	0.0699	-0.0291	0.9638	0.0431	0.9582	1.2947	-3.7044	26.054
28	3.6349	1.0095	-1.6515	4.6167	5.0447	9.2647	0.128	1.0951	-0.0784	0.1632	0.8892	-1.7032	1.1914	-0.3357	-1.0539	0.8793	0.0644	0.0208	0.8597	-0.2227	0.8872	10.0499	-2.8154	9.4773
29	4.3368	-0.0334	2.6925	1.661	0.6899	4.1547	0.7659	-0.612	-2.4883	-1.4624	1.1127	0.7982	0.3449	0.29	-0.5431	1.5578	0.1057	-0.0161	1.9784	-0.1333	1.2103	8.0442	-12.0579	-4.9065

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 620 through 624 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 625 through 629 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 630 through 634 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 635 through 637 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 611 through 625 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 626 through 628 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 136 through 156 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 157 through 169 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 170 through 189 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 190 through 213 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 136 through 155 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 156 through 169 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 170 through 184 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 185 through 201 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 202 through 212 )
16	X-RAY DIFFRACTION	16	chain 'E' and (resid 136 through 150 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 151 through 168 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 169 through 183 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 184 through 213 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 136 through 168 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 169 through 213 )
22	X-RAY DIFFRACTION	22	chain 'N' and (resid 620 through 624 )
23	X-RAY DIFFRACTION	23	chain 'N' and (resid 625 through 629 )
24	X-RAY DIFFRACTION	24	chain 'N' and (resid 630 through 634 )
25	X-RAY DIFFRACTION	25	chain 'N' and (resid 635 through 637 )
26	X-RAY DIFFRACTION	26	chain 'P' and (resid 611 through 615 )
27	X-RAY DIFFRACTION	27	chain 'P' and (resid 616 through 620 )
28	X-RAY DIFFRACTION	28	chain 'P' and (resid 621 through 625 )
29	X-RAY DIFFRACTION	29	chain 'P' and (resid 626 through 628 )

-
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

-
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