PDB-9c6l: Yasminevirus c12orf29, a 5' to 3' RNA ligase

ID or keywords:

Entry

Database: PDB / ID: 9c6l

Title

Yasminevirus c12orf29, a 5' to 3' RNA ligase

Components

RNA ligase1

Keywords

LIGASE / ATP-grasp / T-RNA

Function / homology

Protein of unknown function DUF5565 / RNA ligase 1 / RNA ligase (ATP) activity / response to reactive oxygen species / ADENOSINE MONOPHOSPHATE / Uncharacterized protein

Function and homology information

Biological species

Yasminevirus sp. GU-2018

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Hu, Y. / Lopez, V.A. / Tagliabracci, V.S. / Tomchick, D.R.

Funding support

United States, 5items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	DP2GM137419	United States
Robert A. Welch Foundation	I-1911	United States
Robert A. Welch Foundation	I-2088	United States
Robert A. Welch Foundation	I-1961	United States
Howard Hughes Medical Institute (HHMI)		United States

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Biochemical and structural insights into a 5' to 3' RNA ligase reveal a potential role in tRNA ligation.
Authors: Hu, Y. / Lopez, V.A. / Xu, H. / Pfister, J.P. / Song, B. / Servage, K.A. / Sakurai, M. / Jones, B.T. / Mendell, J.T. / Wang, T. / Wu, J. / Lambowitz, A.M. / Tomchick, D.R. / Pawlowski, K. / Tagliabracci, V.S.

#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...

History

Deposition	Jun 7, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 2, 2024	Provider: repository / Type: Initial release
Revision 1.1	Mar 5, 2025	Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9c6l.cif.gz	997.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9c6l.ent.gz	698.1 KB	Display	PDB format
PDBx/mmJSON format	9c6l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c6/9c6l ftp://data.pdbj.org/pub/pdb/validation_reports/c6/9c6l	HTTPS FTP

-
Related structure data

Related structure data	9c6mC 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	#129 - Sep 2010 Isocitrate Dehydrogenase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #24 - Dec 2001 Glycogen Phosphorylase similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (1)

Deposited unit

A: RNA ligase1

B: RNA ligase1

C: RNA ligase1

D: RNA ligase1

E: RNA ligase1

F: RNA ligase1

hetero molecules

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

1

A: RNA ligase1

B: RNA ligase1

C: RNA ligase1

hetero molecules

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

2

D: RNA ligase1

E: RNA ligase1

F: RNA ligase1

hetero molecules

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

Unit cell

Length a, b, c (Å)	104.897, 84.221, 115.240
Angle α, β, γ (deg.)	90.000, 106.875, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

#1: Protein	RNA ligase1 Mass: 30619.793 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yasminevirus sp. GU-2018 / Gene: YASMINEVIRUS_1364 / Plasmid: ppSUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: A0A5K0UB63
#2: Chemical	ChemComp-AMP / ADENOSINE MONOPHOSPHATE Mass: 347.221 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₇P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H₂O
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: 2.65 Å³/Da / Density % sol: 53.61 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 1.85 M sodium malonate, 50 mM NaCl, 0.1 M Bis-Tris, 20% ethylene glycol

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97891 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.97891 Å / Relative weight: 1

Reflection

Resolution: 2.6→50 Å / Num. obs: 55600 / % possible obs: 98 % / Redundancy: 9.9 % / B_iso Wilson estimate: 45.3 Å² / CC_1/2: 0.963 / CC star: 0.991 / R_merge(I) obs: 0.19 / R_pim(I) all: 0.061 / R_rim(I) all: 0.2 / Χ²: 0.887 / Net I/σ(I): 4.7 / Num. measured all: 550364

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
2.6-2.64	6	1.229	2382	0.527	0.831	0.488	1.328	0.812	85
2.64-2.69	6.6	1.09	2521	0.653	0.889	0.412	1.17	0.778	90.8
2.69-2.74	7.2	1.093	2715	0.7	0.907	0.395	1.166	0.787	95.4
2.74-2.8	8	1.06	2729	0.731	0.919	0.367	1.125	0.797	97.2
2.8-2.86	8.5	0.91	2753	0.788	0.939	0.31	0.964	0.776	97.5
2.86-2.93	9.1	0.793	2736	0.861	0.962	0.264	0.837	0.791	96.6
2.93-3	10.3	0.736	2818	0.893	0.971	0.233	0.773	0.82	99.9
3-3.08	10.8	0.609	2829	0.914	0.977	0.19	0.639	0.838	100
3.08-3.17	11	0.497	2827	0.936	0.983	0.155	0.521	0.87	99.9
3.17-3.28	10.9	0.412	2822	0.948	0.986	0.129	0.432	0.912	100
3.28-3.39	10.7	0.341	2813	0.952	0.988	0.107	0.358	0.908	100
3.39-3.53	10.2	0.274	2818	0.958	0.989	0.088	0.288	0.946	99.9
3.53-3.69	10.5	0.223	2845	0.967	0.992	0.071	0.235	0.972	99.6
3.69-3.88	11.3	0.201	2841	0.969	0.992	0.062	0.21	1.013	99.9
3.88-4.13	11.2	0.171	2843	0.963	0.991	0.053	0.179	0.998	99.9
4.13-4.45	11	0.16	2815	0.964	0.991	0.05	0.167	1.006	99.9
4.45-4.89	10.4	0.149	2851	0.978	0.994	0.047	0.156	0.972	99.4
4.89-5.6	11.4	0.146	2845	0.963	0.991	0.045	0.153	0.932	99.9
5.6-7.05	10.6	0.132	2872	0.973	0.993	0.042	0.139	0.832	99.4
7.05-50	10.9	0.11	2925	0.974	0.994	0.035	0.116	0.771	99

-
Processing

Software

Name	Version	Classification
PHENIX	1.21.1_5286	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.7→46.41 Å / SU ML: 0.4135 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7905
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2749	1948	4.29 %
R_work	0.2322	43471	-
obs	0.2341	45419	85.58 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 54.38 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→46.41 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11230	0	149	34	11413

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	11623
X-RAY DIFFRACTION	f_angle_d	0.5433	15736
X-RAY DIFFRACTION	f_chiral_restr	0.0432	1738
X-RAY DIFFRACTION	f_plane_restr	0.0037	2006
X-RAY DIFFRACTION	f_dihedral_angle_d	13.6503	4311

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 (%)
2.7-2.77	0.368	65	0.3142	1480	X-RAY DIFFRACTION	41.31
2.77-2.84	0.3516	84	0.2997	1862	X-RAY DIFFRACTION	51.6
2.84-2.93	0.3546	99	0.2847	2190	X-RAY DIFFRACTION	60.51
2.93-3.02	0.3601	116	0.2884	2596	X-RAY DIFFRACTION	72.28
3.02-3.13	0.3318	137	0.2839	3050	X-RAY DIFFRACTION	84.36
3.13-3.25	0.3079	152	0.278	3406	X-RAY DIFFRACTION	94.35
3.25-3.4	0.3145	160	0.2533	3553	X-RAY DIFFRACTION	98.23
3.4-3.58	0.2803	158	0.2396	3524	X-RAY DIFFRACTION	98.34
3.58-3.81	0.2492	160	0.2266	3582	X-RAY DIFFRACTION	98.6
3.81-4.1	0.2774	163	0.21	3623	X-RAY DIFFRACTION	99.87
4.1-4.51	0.2273	161	0.1907	3630	X-RAY DIFFRACTION	99.82
4.51-5.16	0.2215	163	0.1913	3622	X-RAY DIFFRACTION	99.5
5.16-6.5	0.2692	165	0.2283	3678	X-RAY DIFFRACTION	99.92
6.5-46.41	0.2766	165	0.2386	3675	X-RAY DIFFRACTION	98.31

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	1.87735196563	0.997993779477	-0.48303378938	2.51840181419	-0.828255843972	5.83793162522	0.175021412133	-0.618035599978	-0.152071887124	0.397172732872	-0.230979485331	-0.463073235345	-0.713205608582	0.758085931929	0.0874225115555	0.522242108054	-0.219374508303	0.0169435215843	0.977409432171	0.31365274198	0.307053006875	-26.931493908	28.3864940903	-30.3148587282
2	1.89555820516	0.410076359622	0.242844121678	1.40358775245	-0.0505794088648	0.226362396905	0.00816754437403	0.455819364678	0.405959911453	-0.329365736301	-0.311059457643	-0.31636344637	-0.33549881245	0.384130482293	0.00714230582192	0.34289012811	-0.246916209899	0.000935438532182	0.889837034554	0.275487965288	0.483757251949	-21.9548020193	31.4396879722	-25.2323386768
3	0.0808428678341	-0.121436188896	-0.072492791731	0.176461765177	0.108178313377	0.0669808947636	-0.279379242725	0.360238076382	0.0998412451207	-0.388303462927	0.198567668812	0.324917625324	-0.0786874515427	-0.16074311774	-0.135557330729	0.500033567813	-0.452404521118	-0.235318953035	0.618000354677	0.215873572264	0.789053553708	-23.7071834605	40.0863539273	-25.2517721082
4	2.66093548763	1.02211037652	1.92987290912	2.18437434898	0.186101734471	1.93597170932	0.160858905224	0.26055367744	-0.222575368546	0.160409332737	-0.312555047678	-0.449793165158	-0.00390400821739	0.720141963433	0.0287235712673	0.243107846765	-0.115487075352	-0.0719361747969	0.553110077591	0.117747902403	0.311600523725	-17.9069409604	23.3273375693	-9.07665905279
5	0.4271899168	0.670116629593	-0.0115443960063	1.73092667884	0.330660215741	0.175167043889	-0.163473503222	1.32131284872	0.162981924772	-1.27380162424	0.194464821353	-0.441015384919	-0.320324315983	0.722381306341	-0.0499103876346	0.803214992624	0.134917074572	0.311664243125	0.921644311968	0.146618791643	0.28538907403	-28.8013984003	12.9974345147	-36.6111135892
6	3.67246743515	0.332331499672	-2.35655446114	5.29580277778	0.368800443956	2.58589039217	0.146337772862	0.45583047069	0.218421595297	-0.13464628739	-0.172568806125	-0.228561087011	0.12878697292	0.819600987633	0.0257856189406	0.252751060076	-0.0296258328107	-0.0548972212788	0.624397174074	0.0202191760143	0.213951611211	-28.4937264896	17.442280551	-24.2450470628
7	4.08720113585	2.19716107335	-0.421200145711	4.80103426773	-4.50207893223	9.46117358625	0.167908069253	0.0441713628871	0.012923677627	-0.149596885359	0.100496646344	0.743322485471	-0.22883993584	-0.0359045245473	-0.261395694807	0.326510976575	0.00611150666317	-0.114277019084	0.193079017398	-0.0307602030458	0.513645625788	-60.6189154542	-5.20449737758	-13.774019158
8	2.12898018601	1.40545043275	-0.132303202014	5.62963690541	-1.44068127906	1.72018588091	0.0184158211749	0.0533027981491	-0.0905470867621	-0.371270816376	0.287594968331	0.426827447619	0.212620262538	-0.413054255053	-0.180162176039	0.360632756081	-0.113898841311	-0.138166581959	0.197836600587	-0.0208515047303	0.339913916854	-59.6749660851	-0.887910160768	-22.8471323973
9	6.09135434628	-0.454484234958	-0.382737907397	5.86719603269	-2.15281349254	5.90680591324	-0.185552114788	-0.588555344814	0.524445999688	0.148264440327	0.405291540495	1.19881391816	-0.491700740226	-0.909507539872	-0.251958960592	0.285455283309	0.0299597264603	-0.118681523027	0.463695909551	0.122936030304	0.731466213712	-71.1985151642	10.5507400833	-22.9675224547
10	2.39303246254	0.211379311785	-1.95850807246	0.197362576608	-0.548433984748	2.37415446745	0.136303388307	0.500671263411	0.49350753442	-0.2392044097	-0.0208794891093	0.14263510589	-0.0206635809336	-0.0160490241677	-0.0999343817839	0.296195414704	-0.00950713156183	-0.147580864387	0.423064201041	0.0791865664008	0.403168189531	-51.7303832889	19.8664954469	-32.358840776
11	1.30948037401	0.134263208404	-0.389959061156	2.14932450956	-1.53560965923	2.82689151227	-0.202864982124	0.320109149071	0.0416228001403	-0.60634326927	0.150199163383	0.100037214969	0.296596428535	0.0948100637454	0.12114694587	0.283592304263	-0.0997385598775	-0.0843218015691	0.25023071679	-0.0194710509144	0.253092997171	-47.016940997	3.89092719992	-25.5706385349
12	5.33872823913	4.34804220956	0.362114437511	5.38556894955	0.386268151021	0.0283031481609	-0.511449055445	0.334806001012	-0.26822270143	-0.998811674382	0.260467408405	-0.536482625408	0.0308342143398	0.10069550307	0.0806996164059	0.501662455598	-0.118715399796	0.0846779398121	0.23276651414	-0.00858664327288	0.438561184075	-55.8809879896	-22.8539745573	-9.51194466259
13	3.07328350688	2.44376664622	0.249395612748	3.32729449097	-1.16365267005	1.33249337394	-0.294657613791	-0.0158703035267	0.288820494938	-0.229345851012	0.0527433683953	0.224159677354	0.103383472741	-0.0986348713693	0.226724170332	0.314182840698	0.0299411803976	-0.0367661691546	0.124121407458	-0.0424822978439	0.274684006314	-48.6242584819	-3.15346535443	-11.9870056418
14	5.84376025663	3.45017214713	-1.50244887083	4.08740853988	-1.58646562705	3.90799807491	0.149889040965	-0.284084493963	0.406642931245	0.450010765555	0.0656828269666	0.283896098278	-0.0301906040185	0.476158357684	-0.123709584599	0.422733482047	-0.00576417268807	-0.155063978466	0.321158521774	-0.121546046163	0.350306648551	-21.7896553905	12.3200307452	14.6806415571
15	6.28979461893	1.13824365524	-0.397111602462	1.70325923969	0.794456809475	2.73280873044	-0.193150239032	-0.272149299423	-0.678605638569	0.343302827097	-0.0648097585771	-0.173640259693	0.716838726238	0.273564142975	0.124823699856	0.67371563389	0.0107323936583	-0.122302844055	0.275697071758	0.00154887264068	0.294692316707	-28.2073349916	1.88533577005	16.1925053093
16	3.85310420822	-1.4034441607	0.346452098046	3.2561048984	-0.0613008408852	3.76468678087	-0.385599726014	-0.807826528679	0.472872951517	1.25982539149	0.0195827815231	0.355751677569	-0.41934952885	0.258116942421	0.42678582075	0.858359619017	-0.00442092967997	-0.143139239403	0.51526728048	0.0377954378359	0.353494250525	-42.0437856455	10.51735118	24.5948336451
17	2.94591326116	0.742523650886	-0.0633831011822	3.38059775357	0.00115543160946	4.06736500612	0.0670793956931	-0.0434011613859	-0.468112140361	0.700881478285	-0.112963334389	-0.105750073434	0.846258224212	-0.414289599352	0.0948430993924	0.589844757428	-0.0570259783907	0.00854315656949	0.134485775325	-0.0392019412506	0.279238244937	-43.5890974696	-2.35464921294	6.69208358457
18	2.79346485229	0.560080496465	0.79615772387	1.22576549372	-0.465639332221	1.51249668372	-0.0425572338446	0.203970157972	-0.481027171898	0.431858377506	0.227942807736	-0.335664933887	0.496791914869	0.743159059829	-0.085257759551	0.415108717913	0.186583657398	-0.122446744593	0.402342613916	-0.102569851568	0.345278286956	-21.8115247024	5.94003496201	4.45753757658
19	3.39738632109	0.662248874647	-0.0356369931056	0.595368329045	-0.536210595908	2.73424440842	0.231391955535	0.119201582941	0.0107241641622	-0.438293105991	0.247200237901	0.308233684902	-0.264574283511	-0.070052118415	-0.0244260023952	0.711569552803	-0.103956448133	-0.156195018179	0.242014139916	0.297068219408	0.44323463706	5.89669250563	9.97379691996	-67.2793480668
20	2.70258642735	0.19598250062	0.463391206006	4.03421930082	-0.0320514565426	4.25654867732	-0.671490383413	1.32438072935	-0.301603112839	-0.760684167687	0.562226700519	0.0597682125991	-0.557272126959	-0.0836312322657	0.00447988294665	0.50087284343	-0.186431602863	-0.138272320985	0.689478584266	0.0326183510417	0.373868534276	-9.7276381189	-10.5690767526	-70.4944478562
21	0.628015554896	1.23715249409	-0.240043283527	2.20461462309	-0.412573278797	1.23528932025	-0.260392590878	0.13354785223	0.410297237495	-0.364339012656	0.15909563425	0.327333754637	-0.290406179445	-0.130405445771	0.0942413954668	0.348139071217	0.0131628636301	-0.115828647605	0.262438102585	0.1149756231	0.475428576793	-1.69566397423	4.91907197974	-57.2729655005
22	4.7353802458	3.30464975316	-3.04052349304	5.19028901344	-3.890753338	6.35980650032	-0.362477339473	-0.771755529156	0.413814437877	-0.17434557005	0.116382618188	-0.132878577187	-0.301484584844	-0.014704588544	0.207694174027	0.406284503133	0.171710401547	-0.154110367153	0.476529471904	-0.0980328554179	0.305507222536	19.3747194118	-7.51473254754	-18.0196913343
23	2.06397738916	0.757216020257	0.611400247572	1.56501055839	-0.0455720034308	1.27963650505	-0.31258512864	0.0807107101826	0.650733668037	0.166399315726	-0.0879163239604	-0.324482439627	-0.105538079295	0.137216099778	-0.0269761977495	0.462696266119	-0.0969294538008	-0.300967562648	0.134282998692	0.0729292082607	0.681223439005	24.2285842936	0.288263662164	-32.5574796098
24	1.66404204245	0.0196277522008	1.43706781427	3.59139094294	0.732547308494	1.75476590151	-0.0695227506781	0.14915231493	0.115477338966	-0.199968007219	0.0103975724329	-0.786839786654	0.231332502472	0.483771015743	0.429280805335	0.836874513161	-0.184592501263	-0.411401523414	0.465837977714	0.234415595598	0.735957874949	36.2358881846	-10.1388958165	-33.5823580747
25	6.84204068758	-2.52429323185	0.145860154285	6.34108603224	-1.5470784313	2.27306749407	-0.198657010209	0.758325299311	0.178857688474	0.389969920132	-0.334865520023	-0.830669747584	-0.0125589730543	0.647942150152	0.451694488499	0.232124459484	-0.0458315943746	-0.0901896953445	0.47034018244	-0.00673806971834	0.384454083637	27.7408580154	-3.61958281746	-46.2600001094
26	6.19366516013	0.15622373741	-0.256158212393	5.3950847537	-0.595073087478	3.85744943456	0.0102052392604	0.592799971143	0.944786907441	0.247366051717	-0.193494326537	-0.757736671462	-0.825178047081	0.143408377526	0.13784697123	0.429627684311	0.0551714446566	-0.0561483209051	0.201092302345	0.243625107681	0.653537541363	20.2193744097	8.53931853908	-46.7794087174
27	0.910316102037	0.138879522136	0.571412335479	1.11057475645	-1.11678716886	4.4034986858	-0.210595267528	-0.106069107777	0.491469475319	0.269829491594	0.123157568724	-0.239495922663	-0.702044805517	0.216058795915	-0.00130700323594	0.339869796752	0.01514960148	-0.115668357175	0.158326257545	-0.0372004849113	0.425958518582	16.661648859	2.16655672969	-37.1058234129
28	7.36985257083	-0.529181676663	4.85268421692	4.40349022306	4.31670148831	8.43533862034	0.149921325152	-1.61206051257	0.44572341394	1.2900578822	0.233143576126	-0.670934602119	-0.677128864987	-1.32564290679	-0.330821563178	0.681663975709	0.137837423182	-0.0995198694747	0.853296943646	-0.134069912736	0.390988014678	9.45932059438	-1.88630385671	-6.28289051996
29	4.7925374777	0.100645451898	2.31342955379	0.395638456294	-0.923789478601	5.32245033682	-0.210967018025	-0.315957985943	0.0500171290443	-0.132396095707	0.375383366176	-0.303070683798	-0.296847715856	0.0523487374759	-0.151498418109	0.357309211296	0.113195871783	-0.0408556383083	0.22145290055	-0.0783903042856	0.380126231446	11.0158955301	-3.47139020412	-22.9738314697
30	2.42294048651	1.00195876886	0.731876710677	0.489227162908	0.891727269858	4.95689153134	0.0832978317475	-0.0134046095953	0.0858437538539	0.0547583598369	0.197606438854	-0.0203871644027	-0.0957953706411	-0.616235537976	-0.197033409682	0.260950696309	0.135551224063	-0.0148002735198	0.331524827932	-0.0610674950438	0.380536801606	6.27834411387	-6.87245692701	-32.517778045
31	2.11421710659	0.396914233655	1.81368670979	1.902171639	-1.16064269536	3.0481550244	0.24800620969	-0.293831432907	0.0935360545103	-0.164111910966	0.429215662795	0.929189431892	0.150513991984	0.415375198204	-0.631068822647	0.213002310573	-0.116175654277	-0.086020347638	0.894418227181	0.139158275381	0.765807865796	-23.1571889095	-23.1373809668	-39.4402197242
32	0.876625307523	0.529992877498	-0.21127093897	0.605535055594	-0.0109578774682	0.604199210652	-0.0139124351059	0.0470499257711	0.127136751252	0.0375605979297	0.227349117557	0.605468792917	-0.021740934889	-0.785353720298	-0.167541451412	0.114035918881	-0.118276494418	0.108998905609	1.11281547833	0.371074487346	0.548744893827	-22.6602446321	-21.0110319221	-33.3757827445
33	1.58213349058	0.58954430626	-0.679547310976	1.28184958799	-0.551261554677	0.87941205153	-0.074092870927	-0.00682777300439	-0.292429449736	-0.630121553963	0.404202542037	0.268999360449	0.394125897379	-0.36530896852	0.0498770687799	0.467968470473	-0.395900141114	-0.118511210899	0.661739132026	0.437716091986	0.504911461631	-10.0405355944	-34.8822999536	-28.6234081279
34	1.27032639332	-0.959299913739	0.116056248547	1.16574967546	-0.235412298141	0.0604394080673	-0.051448584585	-0.488581582186	-0.0336806915246	0.286157963608	-0.00235844541466	-0.211819397691	-0.00504423610653	-0.0100680410098	-0.090365432501	0.446884783594	-0.213272064764	-0.423535370007	0.807156842349	0.117742857574	0.397773190412	2.70035015062	-23.4034880267	-14.8156784609
35	1.50063938247	1.05211042469	-0.885591810453	2.18078686287	-0.573128837637	4.45346302523	-0.117336638092	-0.765977056786	-0.159048727753	0.567096067503	0.260699584103	0.527680670682	-0.223017571037	-0.842027545783	-0.115912236192	0.392156524255	0.117688695902	0.0213144445956	0.908524303565	0.144286659001	0.294418005714	-9.91515476498	-14.100359605	-21.9582331213
36	4.33455282006	2.16248263804	-1.14787330026	1.6020187903	-0.518972100228	2.5904831475	-0.0287577755172	-0.608739747912	-0.346033900693	0.103456814922	0.0680482907481	0.315029297982	-0.146465184086	-0.304919963248	0.125187534552	0.239352676439	0.102481077482	0.0797948683262	0.522641874802	0.0988222722446	0.398145627358	-7.01795479908	-16.4854742767	-31.562133878
37	2.54786957086	2.70088775366	0.420147460181	2.88632926323	0.491618412851	0.164057349755	0.184070201183	0.20981357787	1.29440379322	0.183957151347	-0.0564783654042	0.855774228713	0.366374003575	-0.79056792085	-0.0767710958886	0.396980232821	0.0885022250785	0.0519770962539	0.881932635768	0.105193500424	0.685142000993	-27.1875090736	-7.72024224858	-43.9822402781
38	3.73503687307	1.10949125981	-2.17481930894	2.87403798891	0.477273701477	1.82280264611	0.0013889528196	-0.8084906511	0.0339680928182	-0.203386428649	0.100622116201	0.302475651293	-0.0897132146593	-0.611523121179	-0.199476922117	0.233910839242	0.080510510894	-0.0301620873078	0.679985340121	0.184465696707	0.447702955772	-16.0788487826	-12.9451315975	-39.3536430041

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 16 through 48 )	A	A	16 - 48	1 - 20
2	2	chain 'A' and (resid 49 through 102 )	A	A	49 - 102	21 - 74
3	3	chain 'A' and (resid 103 through 117 )	A	A	103 - 117	75 - 89
4	4	chain 'A' and (resid 118 through 199 )	A	A	118 - 199	90 - 171
5	5	chain 'A' and (resid 200 through 232 )	A	A	200 - 232	172 - 198
6	6	chain 'A' and (resid 233 through 276 )	A	A	233 - 276	199 - 242
7	7	chain 'B' and (resid 14 through 55 )	B	G	14 - 55	1 - 28
8	8	chain 'B' and (resid 56 through 92 )	B	G	56 - 92	29 - 65
9	9	chain 'B' and (resid 93 through 119 )	B	G	93 - 119	66 - 89
10	10	chain 'B' and (resid 120 through 144 )	B	G	120 - 144	90 - 114
11	11	chain 'B' and (resid 145 through 205 )	B	G	145 - 205	115 - 175
12	12	chain 'B' and (resid 206 through 221 )	B	G	206 - 221	176 - 191
13	13	chain 'B' and (resid 222 through 276 )	B	G	222 - 276	192 - 246
14	14	chain 'C' and (resid 16 through 55 )	C	I	16 - 55	1 - 28
15	15	chain 'C' and (resid 56 through 89 )	C	I	56 - 89	29 - 62
16	16	chain 'C' and (resid 90 through 124 )	C	I	90 - 124	63 - 91
17	17	chain 'C' and (resid 125 through 190 )	C	I	125 - 190	92 - 157
18	18	chain 'C' and (resid 191 through 276 )	C	I	191 - 276	158 - 238
19	19	chain 'D' and (resid 16 through 73 )	D	L	16 - 73	1 - 44
20	20	chain 'D' and (resid 74 through 144 )	D	L	74 - 144	45 - 106
21	21	chain 'D' and (resid 145 through 276 )	D	L	145 - 276	107 - 238
22	22	chain 'E' and (resid 16 through 64 )	E	N	16 - 64	1 - 36
23	23	chain 'E' and (resid 65 through 89 )	E	N	65 - 89	37 - 61
24	24	chain 'E' and (resid 90 through 114 )	E	N	90 - 114	62 - 77
25	25	chain 'E' and (resid 115 through 133 )	E	N	115 - 133	78 - 96
26	26	chain 'E' and (resid 134 through 157 )	E	N	134 - 157	97 - 120
27	27	chain 'E' and (resid 158 through 205 )	E	N	158 - 205	121 - 168
28	28	chain 'E' and (resid 206 through 221 )	E	N	206 - 221	169 - 182
29	29	chain 'E' and (resid 222 through 255 )	E	N	222 - 255	183 - 216
30	30	chain 'E' and (resid 256 through 276 )	E	N	256 - 276	217 - 237
31	31	chain 'F' and (resid 16 through 48 )	F	P	16 - 48	1 - 20
32	32	chain 'F' and (resid 49 through 89 )	F	P	49 - 89	21 - 61
33	33	chain 'F' and (resid 90 through 130 )	F	P	90 - 130	62 - 95
34	34	chain 'F' and (resid 131 through 144 )	F	P	131 - 144	96 - 109
35	35	chain 'F' and (resid 145 through 176 )	F	P	145 - 176	110 - 141
36	36	chain 'F' and (resid 177 through 199 )	F	P	177 - 199	142 - 164
37	37	chain 'F' and (resid 200 through 232 )	F	P	200 - 232	165 - 191
38	38	chain 'F' and (resid 233 through 276 )	F	P	233 - 276	192 - 235

-
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