PDB-5lv2: Crystal structure of mouse CARM1 in complex with inhibitor LH1246

ID or keywords:

Entry

Database: PDB / ID: 5lv2

Title

Crystal structure of mouse CARM1 in complex with inhibitor LH1246

Components

Histone-arginine methyltransferase CARM1

Keywords

TRANSFERASE / PROTEIN ARGININE METHYLTRANSFERASE / CATALYTIC DOMAIN / CHROMATIN REGULATOR / MRNA PROCESSING / MRNA SPLICING / NUCLEUS / S-ADENOSYL-L-METHIONINE / TRANSCRIPTION / TRANSCRIPTION REGULATION

Function / homology

Function and homology information

regulation of growth plate cartilage chondrocyte proliferation / histone H3R26 methyltransferase activity / histone H3R17 methyltransferase activity / endochondral bone morphogenesis / histone H3R2 methyltransferase activity / RMTs methylate histone arginines / Regulation of lipid metabolism by PPARalpha / Cytoprotection by HMOX1 / protein-arginine omega-N asymmetric methyltransferase activity / type I protein arginine methyltransferase ...
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.29 Å

Authors

Cura, V. / Marechal, N. / Troffer-Charlier, N. / Halby, L. / Arimondo, P. / Bonnefond, L. / Cavarelli, J.

Citation

Journal: Philos.Trans.R.Soc.Lond.B Biol.Sci. / Year: 2018
Title: Hijacking DNA methyltransferase transition state analogues to produce chemical scaffolds for PRMT inhibitors.
Authors: Halby, L. / Marechal, N. / Pechalrieu, D. / Cura, V. / Franchini, D.M. / Faux, C. / Alby, F. / Troffer-Charlier, N. / Kudithipudi, S. / Jeltsch, A. / Aouadi, W. / Decroly, E. / Guillemot, J. ...

History

Deposition	Sep 12, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 17, 2024	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_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5lv2.cif.gz	1.5 MB	Display	PDBx/mmCIF format
PDB format	pdb5lv2.ent.gz	1.3 MB	Display	PDB format
PDBx/mmJSON format	5lv2.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5lv2_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	5lv2_full_validation.pdf.gz	2.5 MB	Display
Data in XML	5lv2_validation.xml.gz	106.7 KB	Display
Data in CIF	5lv2_validation.cif.gz	148.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lv/5lv2 ftp://data.pdbj.org/pub/pdb/validation_reports/lv/5lv2	HTTPS FTP

-
Related structure data

Related structure data	5lv3C 5lv4C 5lv5C 5tbhC 5tbiC 5tbjC 5ih3S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5lv3-d 5tbi-d 6s7a-d 6s77-d 5is6-d 5dwq-d 2y1w-d 5tbj-d 5k8x-d 6s71-d 6s79-d 2y1x-d 5isa-d 6s7c-d 5k8v-d 5is7-d 6s70-d 6arj-d 5tbh-d 5isg-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#122 - Feb 2010 Enhanceosome similarity (3) #155 - Nov 2012 Vitamin D Receptor similarity (2) #63 - Mar 2005 T-Cell Receptor similarity (1)

Deposited unit

A: Histone-arginine methyltransferase CARM1

B: Histone-arginine methyltransferase CARM1

C: Histone-arginine methyltransferase CARM1

D: Histone-arginine methyltransferase CARM1

E: Histone-arginine methyltransferase CARM1

F: Histone-arginine methyltransferase CARM1

G: Histone-arginine methyltransferase CARM1

H: Histone-arginine methyltransferase CARM1

hetero molecules

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

1

A: Histone-arginine methyltransferase CARM1

B: Histone-arginine methyltransferase CARM1

C: Histone-arginine methyltransferase CARM1

D: Histone-arginine methyltransferase CARM1

hetero molecules

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

2

E: Histone-arginine methyltransferase CARM1

F: Histone-arginine methyltransferase CARM1

G: Histone-arginine methyltransferase CARM1

H: Histone-arginine methyltransferase CARM1

hetero molecules

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

Unit cell

Length a, b, c (Å)	98.684, 74.832, 206.639
Angle α, β, γ (deg.)	90.00, 90.53, 90.00
Int Tables number	4
Space group name H-M	P12₁1

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	Histone-arginine methyltransferase CARM1 / Coactivator-associated arginine methyltransferase 1 / Protein arginine N-methyltransferase 4 Mass: 40850.457 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Carm1, Prmt4 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q9WVG6, type I protein arginine methyltransferase

#1: Protein

Histone-arginine methyltransferase CARM1 / Coactivator-associated arginine methyltransferase 1 / Protein arginine N-methyltransferase 4

Mass: 40850.457 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Carm1, Prmt4 / Production host:

Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9WVG6, type I protein arginine methyltransferase

-
Non-polymers , 9 types, 1197 molecules

#2: Chemical	ChemComp-SAO / 5'-S-[(3S)-3-azaniumyl-3-carboxypropyl]-5'-thioadenosine / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 385.419 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₂₁N₆O₅S
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-LHB / 5-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]methyl]-4-azanyl-1-(methoxymethyl)pyrimidin-2-one Mass: 433.422 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₇H₂₃N₉O₅
#5: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#6: Chemical	ChemComp-M2M / 1-METHOXY-2-(2-METHOXYETHOXY)ETHANE Mass: 134.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₃
#7: Chemical	ChemComp-DXE / 1,2-DIMETHOXYETHANE Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₂
#8: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#9: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#10: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1166 / 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: 2.33 Å³/Da / Density % sol: 47.31 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Tris-HCl pH 8.0 100 mM PEG 2000 MME 17 % NaCl 100 mM

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97857 Å / Relative weight: 1
Reflection	Resolution: 2.29→49.34 Å / Num. obs: 134100 / % possible obs: 99.1 % / Redundancy: 3.4 % / B_iso Wilson estimate: 31.6 Å² / CC_1/2: 0.985 / R_merge(I) obs: 0.158 / Net I/σ(I): 5.5
Reflection shell	Resolution: 2.29→2.33 Å / Redundancy: 3.2 % / R_merge(I) obs: 1.162 / Mean I/σ(I) obs: 1 / CC_1/2: 0.412 / % possible all: 90.9

-
Processing

Software

Name	Version	Classification
PHENIX	dev_1980	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5IH3

5ih3

Resolution: 2.29→49.34 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / Phase error: 26.01

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.238	12853	4.91 %	Random selection
R_work	0.2051	-	-	-
obs	0.2067	134021	98.96 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.29→49.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21990	0	365	1166	23521

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	22974
X-RAY DIFFRACTION	f_angle_d	0.912	31095
X-RAY DIFFRACTION	f_dihedral_angle_d	13.734	8422
X-RAY DIFFRACTION	f_chiral_restr	0.042	3387
X-RAY DIFFRACTION	f_plane_restr	0.004	4090

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 (%)
2.2938-2.3199	0.3433	401	0.3426	7046	X-RAY DIFFRACTION	86
2.3199-2.3472	0.3256	390	0.3295	8479	X-RAY DIFFRACTION	99
2.3472-2.3758	0.3569	373	0.319	8336	X-RAY DIFFRACTION	100
2.3758-2.4059	0.3334	472	0.327	8383	X-RAY DIFFRACTION	99
2.4059-2.4375	0.3652	449	0.3244	8206	X-RAY DIFFRACTION	99
2.4375-2.4709	0.3454	393	0.3099	8473	X-RAY DIFFRACTION	100
2.4709-2.5062	0.3172	494	0.2995	8238	X-RAY DIFFRACTION	100
2.5062-2.5436	0.3626	410	0.2863	8352	X-RAY DIFFRACTION	100
2.5436-2.5834	0.3395	440	0.2856	8467	X-RAY DIFFRACTION	99
2.5834-2.6257	0.3313	426	0.2766	8204	X-RAY DIFFRACTION	99
2.6257-2.671	0.2804	393	0.2742	8487	X-RAY DIFFRACTION	99
2.671-2.7195	0.289	426	0.2548	8276	X-RAY DIFFRACTION	100
2.7195-2.7718	0.2972	401	0.2554	8393	X-RAY DIFFRACTION	100
2.7718-2.8284	0.2389	412	0.2524	8302	X-RAY DIFFRACTION	99
2.8284-2.8899	0.3089	421	0.246	8464	X-RAY DIFFRACTION	99
2.8899-2.9571	0.278	395	0.2345	8226	X-RAY DIFFRACTION	99
2.9571-3.0311	0.2503	477	0.2247	8348	X-RAY DIFFRACTION	100
3.0311-3.113	0.2896	376	0.2279	8485	X-RAY DIFFRACTION	99
3.113-3.2046	0.2601	464	0.2092	8187	X-RAY DIFFRACTION	99
3.2046-3.308	0.2588	369	0.2072	8437	X-RAY DIFFRACTION	99
3.308-3.4262	0.2376	515	0.2031	8276	X-RAY DIFFRACTION	99
3.4262-3.5634	0.2288	397	0.1755	8372	X-RAY DIFFRACTION	99
3.5634-3.7255	0.2008	459	0.1648	8284	X-RAY DIFFRACTION	99
3.7255-3.9218	0.1911	433	0.1587	8331	X-RAY DIFFRACTION	99
3.9218-4.1674	0.183	435	0.1428	8373	X-RAY DIFFRACTION	100
4.1674-4.489	0.1792	461	0.1378	8345	X-RAY DIFFRACTION	100
4.489-4.9404	0.1643	447	0.1266	8331	X-RAY DIFFRACTION	100
4.9404-5.6544	0.1517	397	0.1472	8406	X-RAY DIFFRACTION	100
5.6544-7.1205	0.2165	479	0.1852	8332	X-RAY DIFFRACTION	100
7.1205-49.3513	0.1928	448	0.1832	8220	X-RAY DIFFRACTION	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	0.5709	0.3095	0.2664	1.6187	-0.1723	1.0569	0.0428	-0.0101	-0.0335	0.0576	-0.0673	-0.185	-0.0395	0.1321	-0	0.3478	0.007	-0.0309	0.3983	-0.0176	0.298	16.3265	-17.6917	29.4067
2	0.2945	-0.005	0.1894	0.3741	-0.0289	0.0557	0.0202	0.0014	-0.1242	-0.0589	0.0264	0.1026	0.0039	-0.0363	-0	0.2927	-0.0137	0.0072	0.3666	-0.0147	0.3077	-16.5799	-5.7386	12.0218
3	0.7065	-0.1671	0.3508	0.9046	0.5054	0.4231	0.033	0.0728	-0.1842	0.0323	-0.0811	0.1311	0.0816	-0.0071	-0	0.3773	0.0198	0.0297	0.3342	-0.0609	0.3213	-4.425	-23.4693	16.16
4	0.2955	-0.2652	0.3491	0.5897	-0.2941	0.2453	-0.0184	-0.142	-0.2111	-0.2235	0.0695	-0.1032	0.0509	0.1775	0	0.3461	0.0061	0.0138	0.4403	-0.079	0.3405	1.4562	7.9944	14.556
5	0.1849	0.0741	0.2448	0.0269	-0.0254	0.1431	-0.1228	-0.2076	0.1093	0.1621	0.1557	0.5449	-0.1178	-0.4513	0.0035	0.4455	-0.011	0.065	0.3802	-0.0548	0.4402	-18.6143	21.1498	16.7478
6	0.3733	0.4106	0.0914	0.5085	0.4216	0.8152	-0.0614	0.1037	0.028	-0.1668	0.0303	0.018	-0.1222	0.0681	0	0.3897	-0.084	0.0428	0.3652	0.0176	0.2972	-9.0212	18.878	4.4066
7	0.521	0.1855	0.2201	-0.0777	-0.0182	0.0337	-0.0596	-0.0199	0.0582	0.0548	0.1399	0.099	0.0007	-0.0488	-0.0002	0.4716	-0.0423	0.0393	0.3762	-0.0391	0.3038	-2.7821	19.6428	25.4318
8	0.1752	-0.4145	0.2488	0.2057	-0.3789	0.2877	-0.0094	-0.2366	0.1055	0.3141	0.1092	0.0263	-0.0154	-0.013	-0	0.5774	-0.0816	0.0135	0.4813	-0.0441	0.3578	3.1614	-0.1111	42.8759
9	0.2501	-0.3232	0.4696	0.0988	-0.2082	0.3835	-0.1469	0.0721	-0.013	0.0848	0.0762	-0.0012	-0.6104	0.0181	-0.0059	0.5242	-0.0049	0.0694	0.388	-0.0215	0.3477	0.3772	26.3749	33.1163
10	-0.196	0.0936	0.3881	0.4309	-0.0586	0.2406	0.0066	-0.0452	0.0948	0.1145	-0.0537	0.1677	-0.0469	-0.0172	0	0.4177	0.0028	0.0333	0.4153	-0.0348	0.3204	-7.4256	18.5387	36.2317
11	0.3197	-0.2868	0.1091	0.2951	-0.3842	0.5724	-0.0006	0.1544	-0.1657	0.1089	-0.1197	0.1093	0.088	-0.0854	-0.0015	0.4488	-0.0296	0.0384	0.4264	-0.0568	0.379	5.2306	13.6913	36.1047
12	0.0715	0.01	-0.1446	0.0212	-0.0302	0.2259	-0.3612	-0.2443	-0.5915	0.2509	0.1957	-0.0744	-0.2245	-0.1109	-0.0036	0.342	0.0286	0.0513	0.2859	0.0171	0.3413	13.869	5.4375	88.6529
13	0.4455	-0.2556	-0.0174	0.9176	0.0927	1.0128	-0.0319	0.0522	-0.0296	-0.1482	0.0124	-0.1486	0.0149	0.0875	0.0001	0.216	-0.0671	0.0679	0.2264	-0.0362	0.2285	14.9683	16.7696	71.9935
14	-0.1691	-0.0032	-0.0451	1.0784	-0.4283	0.3433	-0.0303	0.1368	-0.0022	0.071	0.1796	0.0883	-0.0818	-0.0934	0.1105	0.1211	-0.0274	0.0208	0.1513	-0.0234	0.2374	-13.0513	6.9478	88.6611
15	1.0321	-0.0205	-0.0981	0.2848	0.2098	0.5409	-0.002	-0.0242	0.1637	0.0029	-0.0147	0.0156	-0.0858	-0.0891	0.0002	0.2139	-0.0347	0.0096	0.2063	-0.0399	0.2485	-6.377	22.5894	87.2125
16	0.3737	0.1918	-0.118	0.4333	-0.1476	0.1564	-0.0848	0.2002	-0.153	-0.1632	0.0891	0.0246	0.2633	-0.0274	0.1181	0.2403	-0.0707	-0.0016	0.212	-0.0832	0.2397	-8.3618	9.3853	87.6238
17	0.5707	0.167	-0.3446	0.7246	-0.7167	1.3308	0.4	0.0544	0.138	-0.0416	-0.0034	-0.0869	-0.1426	0.2562	0.3883	0.1656	-0.0044	-0.0121	0.3049	-0.1239	0.2957	2.3725	-9.431	88.2395
18	0.0318	-0.0642	0.0231	0.0402	0.0359	0.144	-0.0524	0.4492	0.3778	0.2015	0.215	-0.0171	0.043	0.0599	0	0.2005	-0.0337	-0.0174	0.3388	0.0639	0.3356	-16.3762	-13.5331	83.0139
19	0.6012	-0.2415	-0.1714	0.3261	-0.0352	1.4093	-0.0374	-0.1236	-0.0457	0.1136	0.2076	0.0479	0.1546	0.0642	0.0339	0.1855	0.0357	-0.028	0.1731	0.0035	0.2742	-10.4806	-21.6076	96.5913
20	0.6838	0.1087	-0.4615	0.2573	0.1355	0.7473	-0.0239	-0.0362	-0.0832	-0.1036	0.1877	0.027	0.237	0.2195	0.2022	0.2559	0.0461	-0.0667	0.2305	-0.0496	0.3046	-2.184	-22.937	80.5143
21	0.2983	0.0266	-0.0235	0.3055	-0.1696	0.0583	-0.0246	0.3553	-0.1567	-0.2101	0.1918	0.1714	0.0731	0.125	0.0154	0.4804	-0.0891	0.0338	0.3678	-0.0968	0.2872	7.7363	4.6085	58.7024
22	0.5324	0.193	-0.7201	0.3988	-0.0897	1.1325	-0.111	0.1525	-0.057	-0.1475	0.0786	-0.0872	0.2454	0.2183	0.0034	0.3683	0.0131	-0.059	0.315	-0.0762	0.3959	0.1002	-23.4276	68.8267
23	-0.0499	-0.0732	-0.0156	0.8746	-0.0061	1.1023	-0.014	0.0374	0.039	-0.0981	0.1207	0.0391	0.0512	0.0974	0.0004	0.2396	-0.0287	-0.0289	0.2332	-0.0561	0.2454	-1.2358	-20.268	65.7745
24	0.114	0.0221	-0.0695	0.0303	-0.0325	0.1608	-0.0244	-0.6217	0.0556	0.1438	0.2598	0.1312	-0.2257	-0.1518	0	0.2913	0.0388	-0.0027	0.3237	-0.0845	0.5849	-5.0716	-6.2246	70.3105
25	0.3586	0.3339	-0.0258	0.3021	-0.015	0.1804	-0.2149	-0.1416	0.5114	0.13	-0.0545	0.0247	-0.0215	-0.3637	-0.0044	0.2922	-0.0464	-0.0507	0.2729	-0.0083	0.2969	-65.6266	-9.7309	89.0256
26	0.092	-0.0059	-0.168	0.1511	0.0716	0.1288	-0.0232	-0.0584	0.1267	0.0067	-0.0752	0.0057	-0.2149	0.3897	-0.0024	0.2929	-0.0518	-0.0652	0.363	0.0735	0.281	-58.312	-8.1971	73.7634
27	0.6202	-0.3531	0.2483	1.2018	0.1649	0.8961	0.01	0.0764	-0.0273	-0.125	-0.055	0.1459	0.0705	-0.1285	-0.1308	0.2073	-0.071	-0.0657	0.259	-0.0072	0.2199	-66.1615	-22.8585	72.1717
28	0.0122	-0.0533	-0.2401	1.0776	0.09	-0.0363	-0.0599	0.0646	-0.0006	0.1225	0.2078	-0.1698	0.0547	0.0644	0.0424	0.1159	-0.0297	-0.0186	0.1654	0.0012	0.2416	-33.3791	-8.9678	88.9945
29	0.4705	0.2241	0.0551	0.1737	-0.4479	0.783	0.0113	-0.1461	-0.2916	0.0347	0.0046	0.0003	0.174	-0.0697	0.0046	0.191	-0.0616	-0.0343	0.1504	0.0335	0.3292	-50.341	-30.2259	90.2537
30	1.0079	0.1794	-0.0239	0.2403	-0.4067	0.5028	-0.0607	0.0039	-0.1856	-0.1471	-0.0471	-0.195	-0.0306	0.1363	-0.0422	0.187	-0.0204	-0.0285	0.2262	0.0193	0.2357	-42.2318	-26.5559	83.2148
31	0.4383	0.3543	0.2739	0.5593	0.4878	0.3974	0.0358	-0.0347	0.0632	-0.0733	-0.0922	0.0152	0.0062	0.0869	-0.0265	0.1758	-0.0285	0.008	0.2223	0.0882	0.2481	-44.5793	-17.4242	92.2857
32	0.354	0.4508	0.354	0.5629	0.1776	0.5156	0.224	-0.0328	-0.0281	0.058	0.0994	0.0388	0.1581	-0.1451	0.187	0.1464	-0.0299	0.0166	0.2952	0.0886	0.3137	-52.6986	6.1689	88.0556
33	0.0855	-0.1302	0.2925	0.1239	-0.0059	0.3441	0.0129	0.2259	-0.1076	0.1476	0.2216	-0.0231	-0.1224	0.1715	0.0083	0.2428	-0.0316	0.0302	0.2083	-0.0226	0.2867	-33.621	20.1797	86.4112
34	0.4755	-0.3197	0.3558	0.5793	-0.0922	1.0471	-0.0617	-0.101	0.0073	0.1142	0.1924	-0.1354	-0.1794	-0.1637	0.0185	0.179	0.0601	0.0262	0.1947	0.0179	0.2346	-42.9836	17.4468	98.4901
35	0.19	0.1138	0.2266	0.3405	-0.1693	0.269	0.0118	0.0548	0.0598	-0.1905	0.1127	-0.0562	-0.1336	-0.1568	0.0349	0.2322	0.0199	0.0328	0.2553	0.0277	0.2574	-51.7881	9.3708	71.5267
36	0.1184	-0.1381	-0.1401	0.5311	0.1453	0.342	0.2834	0.5762	0.3699	-0.0257	0.0326	0.2853	0.5333	0.3177	0.1776	0.3462	0.0129	-0.0361	0.3929	0.1152	0.3086	-55.2665	1.4561	63.9768
37	0.2936	0.0755	0.7762	0.8624	0.059	1.4179	-0.0825	0.0856	0.0533	-0.1807	0.1217	-0.0403	-0.1706	0.0696	0.0021	0.2676	-0.0007	0.0435	0.2346	0.0379	0.2783	-46.2503	19.4969	67.9707
38	0.0259	0.1944	-0.2062	0.567	0.6416	0.7536	-0.0887	-0.0332	-0.1648	-0.1364	0.1284	0.0414	0.0721	-0.0475	0.0013	0.2759	-0.0076	0.0081	0.3057	0.0438	0.3636	-56.0563	13.1648	65.0046
39	0.8747	0.1414	-0.3174	1.1335	-0.0053	0.9269	0.0066	-0.0068	-0.0176	0.0512	-0.0409	0.1059	0.0352	-0.1606	-0.0001	0.3318	0.0089	0.01	0.3503	0.0351	0.2564	-66.1468	13.8477	29.1398
40	0.5567	-0.1326	-0.1509	0.4491	0.2199	-0.113	-0.0159	0.0574	0.1833	-0.1358	0.0923	-0.1494	-0.0596	0.0337	0.0004	0.3199	-0.0135	-0.0108	0.3253	0.0078	0.3211	-33.2919	5.0901	13.9666
41	1.1002	-0.1022	-0.2731	0.5472	-0.285	0.4412	0.0156	0.079	0.1649	0.058	0.0211	-0.117	-0.0636	-0.0586	0.0003	0.3718	0.024	-0.0063	0.3105	0.0552	0.3093	-46.13	19.4382	15.4915
42	0.2912	-0.2116	-0.3498	0.594	0.4441	0.6384	-0.0361	-0.0602	0.2553	-0.0986	0.194	0.1145	-0.1052	-0.1163	0.0724	0.319	0.022	-0.0186	0.3845	0.0823	0.2891	-50.2955	-11.518	14.7473
43	0.0969	0.0971	-0.0038	0.1597	0.0355	0.2465	-0.0373	-0.1181	-0.0526	0.1056	0.095	-0.1451	-0.1406	0.1609	-0.0015	0.3919	-0.0287	0.0123	0.3391	0.0325	0.4328	-30.8394	-24.2814	17.3085
44	0.5011	0.5166	-0.1731	0.4295	0.0221	0.8925	-0.1253	0.1837	-0.0752	-0.1336	0.0815	-0.0964	0.1005	0.0431	-0	0.3579	-0.0798	-0.0066	0.3177	-0.0159	0.2645	-40.3491	-22.9316	4.5787
45	-0.0003	0.0845	0.084	0.1098	-0.1664	0.2092	-0.0839	-0.0687	-0.1884	0.0472	0.1373	-0.105	0.1348	-0.1267	0	0.3837	-0.0312	-0.0246	0.3564	0.0242	0.3468	-47.1229	-26.2006	21.966
46	0.203	-0.3765	-0.0697	0.3373	-0.3932	0.4286	-0.003	-0.1581	-0.1468	0.196	0.0009	-0.0488	-0.1324	0.073	-0.0005	0.5499	-0.0635	-0.0351	0.4579	0.0377	0.3676	-52.2638	-4.1083	43.3295
47	0.0206	-0.0577	-0.3991	0.4306	0.5296	1.0033	-0.1061	0.0009	-0.0596	0.0736	0.0146	-0.1045	0.1968	-0.0039	0.0001	0.4189	0.0077	-0.056	0.3867	0.0498	0.3276	-47.8923	-24.5468	35.5624
48	0.2114	-0.0131	0.1351	0.202	0.1529	0.1459	-0.0155	-0.0836	0.3247	-0.1602	-0.1573	0.1503	0.1965	0.0846	0.0019	0.4772	0.0205	-0.0612	0.414	0.0395	0.6885	-52.9705	-12.3976	35.5909

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 136:293)
2	X-RAY DIFFRACTION	2	(chain A and resid 294:341)
3	X-RAY DIFFRACTION	3	(chain A and resid 342:478)
4	X-RAY DIFFRACTION	4	(chain B and resid 135:164)
5	X-RAY DIFFRACTION	5	(chain B and resid 165:183)
6	X-RAY DIFFRACTION	6	(chain B and resid 184:258)
7	X-RAY DIFFRACTION	7	(chain B and resid 259:306)
8	X-RAY DIFFRACTION	8	(chain B and resid 307:350)
9	X-RAY DIFFRACTION	9	(chain B and resid 351:381)
10	X-RAY DIFFRACTION	10	(chain B and resid 382:438)
11	X-RAY DIFFRACTION	11	(chain B and resid 439:477)
12	X-RAY DIFFRACTION	12	(chain C and resid 136:149)
13	X-RAY DIFFRACTION	13	(chain C and resid 150:282)
14	X-RAY DIFFRACTION	14	(chain C and resid 283:342)
15	X-RAY DIFFRACTION	15	(chain C and resid 343:462)
16	X-RAY DIFFRACTION	16	(chain C and resid 463:478)
17	X-RAY DIFFRACTION	17	(chain D and resid 136:161)
18	X-RAY DIFFRACTION	18	(chain D and resid 162:168)
19	X-RAY DIFFRACTION	19	(chain D and resid 169:248)
20	X-RAY DIFFRACTION	20	(chain D and resid 249:306)
21	X-RAY DIFFRACTION	21	(chain D and resid 307:335)
22	X-RAY DIFFRACTION	22	(chain D and resid 336:378)
23	X-RAY DIFFRACTION	23	(chain D and resid 379:471)
24	X-RAY DIFFRACTION	24	(chain D and resid 472:477)
25	X-RAY DIFFRACTION	25	(chain E and resid 136:148)
26	X-RAY DIFFRACTION	26	(chain E and resid 149:162)
27	X-RAY DIFFRACTION	27	(chain E and resid 163:293)
28	X-RAY DIFFRACTION	28	(chain E and resid 294:349)
29	X-RAY DIFFRACTION	29	(chain E and resid 350:380)
30	X-RAY DIFFRACTION	30	(chain E and resid 381:439)
31	X-RAY DIFFRACTION	31	(chain E and resid 440:478)
32	X-RAY DIFFRACTION	32	(chain F and resid 135:163)
33	X-RAY DIFFRACTION	33	(chain F and resid 164:183)
34	X-RAY DIFFRACTION	34	(chain F and resid 184:258)
35	X-RAY DIFFRACTION	35	(chain F and resid 259:327)
36	X-RAY DIFFRACTION	36	(chain F and resid 328:342)
37	X-RAY DIFFRACTION	37	(chain F and resid 343:430)
38	X-RAY DIFFRACTION	38	(chain F and resid 431:477)
39	X-RAY DIFFRACTION	39	(chain G and resid 136:293)
40	X-RAY DIFFRACTION	40	(chain G and resid 294:351)
41	X-RAY DIFFRACTION	41	(chain G and resid 352:478)
42	X-RAY DIFFRACTION	42	(chain H and resid 136:164)
43	X-RAY DIFFRACTION	43	(chain H and resid 165:182)
44	X-RAY DIFFRACTION	44	(chain H and resid 183:258)
45	X-RAY DIFFRACTION	45	(chain H and resid 259:300)
46	X-RAY DIFFRACTION	46	(chain H and resid 301:350)
47	X-RAY DIFFRACTION	47	(chain H and resid 351:462)
48	X-RAY DIFFRACTION	48	(chain H and resid 463:476)

-
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

-
Protein , 1 types, 8 molecules ABCDEFGH

-
Non-polymers , 9 types, 1197 molecules

-
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

-Protein , 1 types, 8 molecules ABCDEFGH

-Non-polymers , 9 types, 1197 molecules

-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

-
Protein , 1 types, 8 molecules ABCDEFGH

-
Non-polymers , 9 types, 1197 molecules

-
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