PDB-7cux: Crystal structure of human Schlafen 5 N'-terminal domain (SLFN5-N...

ID or keywords:

Entry

Database: PDB / ID: 7cux

Title

Crystal structure of human Schlafen 5 N'-terminal domain (SLFN5-N) involved in ssRNA cleaving and DNA binding

Components

Schlafen family member 5

Keywords

DNA BINDING PROTEIN / pseudo-dimeric architecture / CCCH-type zinc finger /

RNase /

DNA binding

Function / homology

Function and homology information

cell differentiation /

ATP binding /

nucleus
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.29477066393 Å

Authors

Yang, J.Y. / Luo, M. / Ou, J.Y. / Wang, Z.W. / Gao, S.

Funding support

China, 3items

Organization	Grant number	Country
National Natural Science Foundation of China (NSFC)	81772977	China
National Natural Science Foundation of China (NSFC)	81902841	China
Chinese Academy of Sciences	2018M640852	China

Citation

Journal: To Be Published
Title: Crystal structure of human Schlafen 5 N'-terminal domain (SLFN5-N) involved in ssRNA cleaving and DNA binding
Authors: Yang, J.Y. / Luo, M. / Ou, J.Y. / Wang, Z.W. / Gao, S.

History

Deposition	Aug 25, 2020	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 25, 2021	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7cux.cif.gz	874.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7cux.ent.gz	617.8 KB	Display	PDB format
PDBx/mmJSON format	7cux.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cu/7cux ftp://data.pdbj.org/pub/pdb/validation_reports/cu/7cux	HTTPS FTP

-
Related structure data

Related structure data	5yd0S S: Starting model for refinement
Similar structure data	2gww-2 5xvv-d 7992 12994 7l8u-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Schlafen family member 5

B: Schlafen family member 5

C: Schlafen family member 5

D: Schlafen family member 5

E: Schlafen family member 5

F: Schlafen family member 5

hetero molecules

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	211.860, 156.442, 131.459
Angle α, β, γ (deg.)	90.000, 110.382, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
4	1
5	1
6	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	GLU	GLU	ARG	ARG	(chain 'A' and (resid 13 through 71 or (resid 76...	A	A	13 - 71	2 - 60
1	2	LEU	LEU	GLN	GLN	(chain 'A' and (resid 13 through 71 or (resid 76...	A	A	76 - 142	65 - 131
1	3	ASN	ASN	MET	MET	(chain 'A' and (resid 13 through 71 or (resid 76...	A	A	169 - 333	158 - 322
2	4	GLU	GLU	ARG	ARG	(chain 'B' and (resid 13 through 71 or resid 76...	B	B	13 - 71	2 - 60
2	5	LEU	LEU	GLN	GLN	(chain 'B' and (resid 13 through 71 or resid 76...	B	B	76 - 142	65 - 131
2	6	ASN	ASN	MET	MET	(chain 'B' and (resid 13 through 71 or resid 76...	B	B	169 - 333	158 - 322
3	7	GLU	GLU	ARG	ARG	(chain 'C' and (resid 13 through 22 or (resid 23...	C	C	13 - 71	2 - 60
3	8	LEU	LEU	GLN	GLN	(chain 'C' and (resid 13 through 22 or (resid 23...	C	C	76 - 142	65 - 131
3	9	ASN	ASN	MET	MET	(chain 'C' and (resid 13 through 22 or (resid 23...	C	C	169 - 333	158 - 322
4	10	GLU	GLU	ARG	ARG	(chain 'D' and (resid 13 through 22 or (resid 23...	D	D	13 - 71	2 - 60
4	11	LEU	LEU	GLN	GLN	(chain 'D' and (resid 13 through 22 or (resid 23...	D	D	76 - 142	65 - 131
4	12	ASN	ASN	MET	MET	(chain 'D' and (resid 13 through 22 or (resid 23...	D	D	169 - 333	158 - 322
5	13	GLU	GLU	ARG	ARG	(chain 'E' and (resid 13 through 22 or (resid 23...	E	E	13 - 71	2 - 60
5	14	LEU	LEU	GLN	GLN	(chain 'E' and (resid 13 through 22 or (resid 23...	E	E	76 - 142	65 - 131
5	15	ASN	ASN	MET	MET	(chain 'E' and (resid 13 through 22 or (resid 23...	E	E	169 - 333	158 - 322
6	16	GLU	GLU	ARG	ARG	(chain 'F' and (resid 13 through 22 or (resid 23...	F	F	13 - 71	2 - 60
6	17	LEU	LEU	GLN	GLN	(chain 'F' and (resid 13 through 22 or (resid 23...	F	F	76 - 142	65 - 131
6	18	ASN	ASN	MET	MET	(chain 'F' and (resid 13 through 22 or (resid 23...	F	F	169 - 333	158 - 322

#1: Protein	Schlafen family member 5 Mass: 36803.141 Da / Num. of mol.: 6 / Fragment: N'-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SLFN5 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q08AF3
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / 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: 4.55 Å³/Da / Density % sol: 72.95 %
Crystal grow	Temperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 100 mM Tris, pH 7.5, 80 mM magnesium chloride, 1.6 M ammonium sulfate PH range: 6.5-8.5

-
Data collection

Diffraction	Mean temperature: 87.15 K / Serial crystal experiment: Y
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 27, 2019
Radiation	Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9785 Å / Relative weight: 1
Reflection	Resolution: 3.294→50 Å / Num. obs: 43847 / % possible obs: 90.2 % / Redundancy: 6.8 % / B_iso Wilson estimate: 80 Å² / CC_1/2: 1 / Net I/σ(I): 13.5
Reflection shell	Resolution: 3.3→3.61 Å / Num. unique obs: 2193 / CC_1/2: 0.731
Serial crystallography sample delivery	Method: fixed target

-
Processing

Software

Name	Version	Classification
PHENIX	1.11.1-2575	refinement
REFMAC	7.0.077	refinement
XDS		data reduction
STARANISO		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5YD0

5yd0

Resolution: 3.29477066393→41.0761808916 Å / SU ML: 0.357439767352 / Cross valid method: FREE R-VALUE / σ(F): 1.34999900373 / Phase error: 34.7159202908
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.247153773675	2162	4.95439754343 %
R_work	0.201355733206	41476	-
obs	0.203555713424	43638	71.9161489148 %

Solvent computation

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

Displacement parameters

B_iso mean: 70 Å²

Refinement step

Cycle: LAST / Resolution: 3.29477066393→41.0761808916 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14069	0	6	0	14075

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0028929713363	14347
X-RAY DIFFRACTION	f_angle_d	0.758545511386	19339
X-RAY DIFFRACTION	f_chiral_restr	0.0462753104805	2137
X-RAY DIFFRACTION	f_plane_restr	0.00398805901482	2487
X-RAY DIFFRACTION	f_dihedral_angle_d	3.23155903385	8713

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 (%)
3.2948-3.3714	0.349562531198	7	0.34122778378	110	X-RAY DIFFRACTION	20
3.3714-3.4556	0.315485469713	8	0.308762183914	208	X-RAY DIFFRACTION	20
3.4556-3.549	0.332664790032	59	0.323707485602	878	X-RAY DIFFRACTION	23.2448523939
3.549-3.6534	0.399056442846	79	0.34395555145	1431	X-RAY DIFFRACTION	40.9880564604
3.6534-3.7712	0.363556775146	119	0.321119914351	1962	X-RAY DIFFRACTION	66.4856230032
3.7712-3.9059	0.334678916616	138	0.290214674125	2580	X-RAY DIFFRACTION	78.8054508553
3.9059-4.0622	0.304626827868	180	0.26604360151	3584	X-RAY DIFFRACTION	94.335839599
4.0622-4.2469	0.26003126441	201	0.220360731486	3878	X-RAY DIFFRACTION	99.902032819
4.2469-4.4705	0.21981555362	211	0.188927950438	3784	X-RAY DIFFRACTION	99.8250874563
4.4705-4.7502	0.239497955707	153	0.180855103107	3886	X-RAY DIFFRACTION	99.8269896194
4.7502-5.1164	0.207430865985	223	0.179735550549	3806	X-RAY DIFFRACTION	99.8265609514
5.1164-5.6301	0.235819671938	205	0.182903071563	3852	X-RAY DIFFRACTION	99.9015020931
5.6301-6.4421	0.238675994457	200	0.197893819367	3848	X-RAY DIFFRACTION	99.9753025438
6.4421-8.1061	0.230726990499	193	0.210902328731	3902	X-RAY DIFFRACTION	99.951183793
8-10	0.244803625905	186	0.177298113386	3767	X-RAY DIFFRACTION	95.5523326082

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	5.21836089503	-1.8761298124	1.32523115645	3.59486560135	-0.38260210645	3.70457890688	0.550176247098	0.949896839876	0.299216518367	-0.805386735807	0.399341839735	0.0361621835043	1.49857785582	-0.248256607558	-0.621770364188	1.4300799316	-0.286073957266	-0.0839635315141	1.50087193973	-0.0352639789708	2.27593667333	-88.2489037957	-0.944345336013	27.2796870855
2	3.30608192816	-1.25387427606	2.0639995565	3.07807969319	-1.48848665388	3.72833317013	-0.0346137588588	-0.398047127266	-1.6792593304	0.870756675961	0.576743738748	0.317023728239	0.523468653306	0.139693115608	-0.830174742334	1.4584852027	-0.490259183358	-0.113444956213	1.88652689193	0.0268366154703	2.5101822882	-91.4338274863	-5.3086317336	34.4513898122
3	5.71036629886	1.53973795053	1.04183972593	2.30827426228	-1.99036700086	1.81830918456	0.444179952334	-1.9084877739	-0.446137527093	0.16443081267	-0.350596534039	0.855874962787	-0.270043392442	-1.18668852419	-0.139743887844	1.05328660965	-0.277873358314	-0.0212193882669	1.69543262671	0.161867038026	2.09252698101	-88.2259158828	20.5915380395	32.4882782811
4	7.85282511139	1.25441663837	-0.1723079669	5.11232711596	0.455502771744	5.1055726393	0.0175429514344	0.836580759249	-0.21330729549	-0.63936067838	0.0937803661306	0.991183335147	0.221868016024	-0.631326738139	-0.0776615364156	0.922266661163	-0.0241450293648	-0.242463564076	1.07337456675	0.125369805875	1.07987880426	-70.0519096156	28.2858391725	19.4696757688
5	3.16336020696	2.79234889764	-2.88710488611	2.47481616289	-2.62842241487	2.79747584795	-0.216263805491	1.06822246524	2.28727105747	-0.329984122662	0.897913562572	2.86520545251	-1.09708355483	-0.641135985898	-0.338184733301	1.0039656918	0.260587541415	-0.28152260606	1.94484171376	0.221770515722	2.86745267456	-93.3963144302	33.2670378143	20.2636606509
6	6.9153596888	1.75033619699	-0.357984371825	2.46546090304	-0.0489033123465	4.19201169482	0.562613874904	0.229920694221	-0.164622964968	-0.0154786531405	-0.150398375402	1.09467600007	0.314254052729	-1.09054770062	-0.16857857698	0.924263200666	-0.108066351535	-0.378304041767	1.45062830119	0.101157992699	1.57599400858	-84.6599246761	24.3989397831	20.0090718723
7	7.33165504807	-0.123530423972	4.03072548192	3.57415552959	-3.21092662503	6.17186535033	0.754752399794	-1.17425018658	-2.57874467681	0.817743920758	1.30458494014	0.204220632102	3.54323502439	-1.37458129925	-0.491760849825	1.2060927656	1.04349368532	-0.227943263705	0.956912592589	-0.200486820327	2.637043439	-12.6589687204	-0.888780197385	37.4953651225
8	2.83571980216	2.76170060709	-0.944209524743	3.19298603569	0.375118586646	4.08310181673	-0.478423227614	-0.98201805522	-0.569852448687	0.727753710962	0.510975149104	0.735744950225	1.28580120415	0.16065406205	-0.251125482421	1.25828458613	0.204397182212	-0.438487702148	1.32664651378	-0.408941478112	2.89792920208	-10.9977074915	-10.4452499745	33.0936798245
9	4.78267630137	-3.27488009353	0.0780073799072	3.25646201712	0.680558302404	3.85498616313	0.906750284192	0.982504361935	-1.67072088183	-1.49801528693	-0.480567153836	0.340707380522	0.282199706789	1.40702423579	-0.230941290371	1.20743414105	0.713048118833	-0.059927825194	1.93633323974	-0.34330260281	1.34180958441	-9.27112439597	11.6622664709	29.6838952549
10	5.290654573	2.00171081999	0.369964051099	0.858378954861	1.13657162308	8.42679786838	0.0670390958302	0.43342107731	0.00268667816517	-0.255369149852	-0.21771005708	-0.253580932349	0.345362664452	0.00733943341243	0.147775663515	0.75182557865	0.142223522709	-0.0402911338989	0.392288772302	0.1510153181	0.699380482474	-31.3886852018	30.2110946281	41.9186576539
11	9.86060173284	-3.42116478566	-4.19379451006	1.98155171382	3.04376753291	6.52144824772	0.0702124897475	-1.39728722727	1.0711110383	0.111014710602	0.315628575209	-0.644727648541	-0.745136438817	0.462871715311	-0.392745110442	0.829261020215	0.0642715893484	-0.20178785184	0.747776604388	0.0916556758326	0.709094139837	-24.9636857904	31.4260225638	50.8082540828
12	7.53025653189	-1.98701761371	-2.41229618671	6.3489045778	0.53705015259	6.27936086073	0.414723236639	0.748434695877	-0.261157949962	0.12048735326	-0.11153641961	-0.682258021358	1.24527296558	1.7949255466	-0.355967903172	0.787266210913	0.402505814176	-0.172525379308	1.39145184697	-0.109473629894	1.23076935799	-4.59532877749	19.0380529924	41.0178577085
13	7.33632226403	1.53757411862	-1.11812891893	6.99532719237	-4.5778079368	6.68684797741	0.848894407597	0.407367604731	0.314622741498	3.00334346783	-0.693208479925	-0.0301232746566	-1.20013183357	1.06490327112	-0.170906313993	2.40006243989	-0.498573400743	0.0674921593522	1.54568826623	-0.197160850725	2.40769391278	-12.6147845231	66.7336431848	39.46172145
14	0.137792551635	-0.352117716517	0.577444251798	3.8434964959	-4.17957199337	5.16360302592	-1.15301000288	0.911932802958	1.02762541028	0.643144433014	0.230947378148	-0.820142372573	-1.11368791228	-1.00793399201	-0.0748445601254	1.71361513797	-0.887005082011	-0.416434424125	1.22916601881	0.040860634407	2.18434302515	-15.6205376682	64.3786405417	31.0020067517
15	2.36916566422	-3.01186046665	-0.808622104478	3.6236072436	0.135663266534	4.89754254638	-1.78848147908	-0.68305717462	-0.922774445419	1.0293639538	0.129650687942	0.494790735365	-0.217755117765	1.63600908533	1.44708095964	2.10395652908	-1.04718165535	-0.074720043338	2.47391090545	0.499910892052	2.16246592015	-7.30174514262	65.724732966	39.8928060488
16	5.63145545952	-0.200367343602	3.15320692526	3.04231399318	0.214415912424	3.09553100702	-0.157192744783	0.215368010687	0.998871236907	0.461716915159	-0.124356450517	-0.686689122516	-0.267414010342	1.24088975913	0.0992689431197	1.3919216821	-0.38849615579	0.0261317343427	1.94790712569	0.49382598317	2.31099112161	-11.7044121751	54.0281814277	23.6776484999
17	8.64528105315	-0.457454178221	-2.68458243701	5.73452730214	-1.59171808976	4.39038291485	-0.621447053403	0.606082695558	0.501616162906	-0.145872126075	0.523820280716	-0.00877761809216	-0.338082037598	0.109559636324	0.108417775444	0.88320020775	-0.0494043976638	-0.177988258908	0.637637897128	0.150970284894	0.809053756242	-41.608186333	46.6051129936	20.0775527958
18	9.06320607311	1.26806708771	2.47461189229	3.93964363401	-1.27187415275	1.58069405557	-0.167109814414	1.80197308042	1.57182885255	-0.527451306015	0.333075144278	-0.0894654951589	-1.02455966347	0.99967795131	-0.00526056544053	1.65553190229	-0.42466876629	-0.0684287998528	1.47994582423	0.47525010276	1.44017710361	-32.5129515343	57.626229389	13.4198541653
19	5.59546729802	-1.86319609905	0.630517236958	4.71187867339	-0.14158082046	3.80119294011	0.0256864500379	1.0313146877	1.32171450571	-0.94343969508	-0.307589738728	-1.02314932486	-0.392912707609	-1.85079702869	0.174087487996	1.56267741039	0.827587957938	-0.110694104992	1.52573619067	-0.080057047079	1.75095016228	-86.8159142135	65.7287668757	29.514802025
20	2.81685331201	-0.851036121784	1.6017549905	5.56309910274	-0.965606049337	1.52070706734	-0.58736030172	0.384421088084	0.916647316076	-1.33439815588	1.8070721398	-0.411920723337	-0.90259465088	-0.605070331628	0.487239892859	1.09052516065	1.2069100242	-0.149856566427	1.61161338513	-0.625348802594	1.9519252126	-93.9444905045	64.9084587378	24.8257323599
21	4.87697946727	-2.98488670374	0.872934315261	1.63640536903	-0.943616104347	0.66178060065	0.102637827555	-0.265644202897	-0.509956415433	0.360423619067	-0.199750207438	1.01538360013	0.174173929201	-0.623535896051	0.11672632772	1.09589005672	0.416453751083	-0.121667816798	1.4056504671	-0.321091024518	1.87799069899	-82.5351851454	51.8648180253	43.1549730521
22	7.28565573566	-2.23606143873	1.87532269985	2.82033860384	0.147125262487	3.10804576722	-0.494812374306	-1.14409908121	0.59579601006	0.360736524948	0.375330538256	0.0283592932171	-0.844921927317	-0.966572225265	-0.0391420849067	1.25989725447	0.594480328146	-0.0720730510305	0.973357775849	-0.161077740993	1.14425996526	-65.3979276428	53.8299653798	47.8705214659
23	5.51580709544	-0.279205027164	0.232639461696	4.64981388535	0.0412399035094	4.35342632199	-1.79388266702	-0.155308106269	0.399946234932	-2.03623114457	-0.624574176506	2.37350962992	1.05088761343	-2.28640502022	0.973462089379	2.12183698097	0.666006319823	0.422909895791	2.71289413865	0.108396773221	0.242119465054	-38.8402484686	29.8242489994	-16.2595861657
24	2.22762150203	0.744548428227	3.17416429248	3.5922571211	-3.04477313168	7.1199817273	0.244136018582	0.945343551792	0.222320594193	-0.0831867182444	-0.336519923217	-0.0970999457203	-0.689698382301	1.07259263916	0.297373666376	1.72506313939	0.240762470886	0.538691868961	1.74747334197	-0.0868849142826	1.14601517966	-29.5377390646	30.5004894315	-10.4412139437
25	7.86037690927	-1.30784577312	-0.589463850987	5.34359585335	1.30768924082	4.16622547619	0.0124394893812	0.496522272711	-0.0142931236241	-0.493299942147	-0.105892767704	0.10812778534	0.211016628072	0.395528836685	-0.0304002060286	1.2006716187	0.108289131917	-0.0176181165779	0.870949562147	-0.009049426273	0.657113469078	-43.6878330666	17.0503372982	17.6853001587
26	2.38026113708	0.868519394273	-4.13481846418	3.13423914092	-1.09172408841	6.41329318595	-0.278201811679	0.534771254641	-0.757939163352	-0.932885052027	-0.364471611834	-0.504415333776	1.43983102846	0.147808703643	0.571046865047	1.78911576806	0.312862622147	0.0912094226416	1.26439185535	-0.221429986554	0.95495068444	-35.0110569248	10.3657180642	4.92562582352
27	6.17329934892	3.93814856195	-2.67459621118	4.73773854693	-1.16810046899	5.90816570199	0.410879539003	-0.435773095063	0.54236254237	1.13627856369	-0.385098376645	0.0678270732934	0.405100406774	0.274436040824	0.100807397196	1.44448411308	0.207392563062	0.219417674391	1.77363798549	-0.104123474065	0.82455713642	-61.9179883349	32.1691839597	83.2805938953
28	2.02857696724	-0.600862808594	-2.27824586554	1.8043082496	1.21703135349	2.66125901238	1.58887171727	-0.229788612543	1.49943916022	1.65094558612	0.832234260225	0.990217840254	-1.09114224624	-1.12322232207	-0.543216414283	2.15499233131	0.828178518014	0.751956845933	2.22789438415	0.220924553421	1.00372344591	-69.533532532	35.5466057223	83.67187455
29	3.17971047275	-1.14438426446	-0.902709221268	3.22493497308	0.379834609774	4.76888211278	0.41899413317	-0.399331274205	0.17368296859	-0.0107316146859	-0.106919354436	0.902111604501	-1.14305177317	-1.2046702581	-0.717180954453	1.16458028508	0.0734258055943	0.153245717578	1.88127643417	0.0713242153496	1.26206188775	-76.6169193392	23.7731315818	63.1697805436
30	7.64523670025	-0.565944641703	-2.48110199312	6.44240674863	0.543930123842	5.62913897	0.00984544820842	-0.101632597931	-0.2666017855	-0.097982275217	-0.423613109978	0.0419316431707	1.39857114529	-0.696105676749	0.340033328364	1.15470044256	-0.162295646563	-0.0575960304823	0.686330092119	0.0520875136752	0.593985020349	-58.4057543686	13.3321420927	48.6314798586
31	3.6202696632	-1.76976585201	-0.787006619956	4.99705828325	0.870900570207	6.55938187968	-0.0427461462638	-0.692571699195	-0.737655394109	1.89784041806	0.419044414507	0.369056768447	-0.347168205738	-2.5857911416	0.299404560671	1.98871525327	-0.392563490498	0.321471798249	1.98594082823	0.310985706545	1.08161611149	-74.0587904217	14.3163159781	70.8682388111

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 53 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 54 through 91 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 92 through 178 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 179 through 260 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 261 through 275 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 276 through 333 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 13 through 53 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 54 through 72 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 73 through 140 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 141 through 242 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 243 through 298 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 299 through 333 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 13 through 32 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 33 through 52 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 53 through 79 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 80 through 140 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 141 through 242 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 243 through 333 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 13 through 52 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 53 through 79 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 80 through 182 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 183 through 333 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 13 through 53 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 54 through 140 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 141 through 247 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 248 through 333 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 13 through 72 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 73 through 99 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 100 through 140 )
30	X-RAY DIFFRACTION	30	chain 'F' and (resid 141 through 298 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 299 through 334 )

-
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