PDB-7nx0: LTK:ALKAL1 complex stabilized by a Nanobody

ID or keywords:

Entry

Database: PDB / ID: 7nx0

Title

LTK:ALKAL1 complex stabilized by a Nanobody

Components

ALK and LTK ligand 1
Leukocyte tyrosine kinase receptor
Nb3.16

Keywords

PROTEIN BINDING / Cell Surface Receptor Cytokine binding Cytokine receptor complex

Function / homology

Function and homology information

positive regulation of ERK5 cascade / receptor signaling protein tyrosine kinase activator activity / Signaling by LTK / regulation of neuron differentiation / Signaling by ALK / positive regulation of cardiac muscle cell apoptotic process / transmembrane receptor protein tyrosine kinase activator activity / peptidyl-tyrosine autophosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / cellular response to retinoic acid ...
Similarity search - Function

Biological species

Homo sapiens (human)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

De Munck, S. / Savvides, S.N.

Funding support

Belgium, 1items

Citation

Journal: Nature / Year: 2021
Title: Structural basis of cytokine-mediated activation of ALK family receptors.
Authors: De Munck, S. / Provost, M. / Kurikawa, M. / Omori, I. / Mukohyama, J. / Felix, J. / Bloch, Y. / Abdel-Wahab, O. / Bazan, J.F. / Yoshimi, A. / Savvides, S.N.

History

Deposition	Mar 17, 2021	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 27, 2021	Provider: repository / Type: Initial release
Revision 1.1	Dec 15, 2021	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	May 25, 2022	Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7nx0.cif.gz	592.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7nx0.ent.gz	407.7 KB	Display	PDB format
PDBx/mmJSON format	7nx0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7nx0_validation.pdf.gz	467.8 KB	Display	wwPDB validaton report
Full document	7nx0_full_validation.pdf.gz	478.1 KB	Display
Data in XML	7nx0_validation.xml.gz	39.7 KB	Display
Data in CIF	7nx0_validation.cif.gz	58.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nx/7nx0 ftp://data.pdbj.org/pub/pdb/validation_reports/nx/7nx0	HTTPS FTP

-
Related structure data

Related structure data	7nwzC 7nx1SC 7nx2C 7nx3C 7nx4C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4qt8-2 4cem-d 4jo8-1 4ezm-3 6n0v-d 3afg-d 1wu2-d 3w6p-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
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #182 - Feb 2015 Insulin receptor similarity (2) #68 - Aug 2005 Neurotrophins similarity (2) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #60 - Dec 2004 Ubiquitin similarity (1)

Deposited unit

C: Leukocyte tyrosine kinase receptor

D: Nb3.16

B: Leukocyte tyrosine kinase receptor

E: Nb3.16

A: ALK and LTK ligand 1

hetero molecules

101 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: isothermal titration calorimetry

Unit cell

Length a, b, c (Å)	129.110, 129.110, 109.750
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	169
Space group name H-M	P6₁
Space group name Hall	P6₁
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/6 #3: y,-x+y,z+5/6 #4: -y,x-y,z+1/3 #5: -x+y,-x,z+2/3 #6: -x,-y,z+1/2

#1: Protein	Leukocyte tyrosine kinase receptor / Protein tyrosine kinase 1 Mass: 32069.816 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LTK, TYK1 / Production host: Homo sapiens (human) References: UniProt: P29376, receptor protein-tyrosine kinase
#2: Antibody	Nb3.16 Mass: 13690.101 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Komagataella phaffii (fungus)
#3: Protein	ALK and LTK ligand 1 / Augmentor beta / AUG-beta / Protein FAM150A Mass: 9045.223 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ALKAL1, FAM150A, UNQ9433/PRO34745 / Production host: Homo sapiens (human) / References: UniProt: Q6UXT8
#4: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 678 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.63 Å³/Da / Density % sol: 53.16 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop Details: MOPSO/BIS-TRIS pH 6.5 20% PEG 8000 40% w/v 1,5-pentanediol 5mM Na2CrO4 . 4H2O 5mM Na2MoO4 . 4H2O 5mM Na2WO4 . 4H2O 5mM Na2VO4 . 4H2O

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
Detector	Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 1, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.95→42.3 Å / Num. obs: 75541 / % possible obs: 99.9 % / Redundancy: 20.8 % / B_iso Wilson estimate: 38.41 Å² / CC_1/2: 0.99 / R_rim(I) all: 0.076 / Net I/σ(I): 26.6
Reflection shell	Resolution: 1.95→2 Å / Num. unique obs: 5362 / CC_1/2: 0.88 / R_rim(I) all: 1.47

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7NX1

7nx1

Resolution: 1.95→42.26 Å / SU ML: 0.1898 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.5692
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1958	3778	5 %
R_work	0.1689	71763	-
obs	0.1703	75541	99.69 %

Solvent computation

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

Displacement parameters

B_iso mean: 53.43 Å²

Refinement step

Cycle: LAST / Resolution: 1.95→42.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6502	0	4	678	7184

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0055	6648
X-RAY DIFFRACTION	f_angle_d	0.8989	8980
X-RAY DIFFRACTION	f_chiral_restr	0.0474	906
X-RAY DIFFRACTION	f_plane_restr	0.0054	1210
X-RAY DIFFRACTION	f_dihedral_angle_d	14.7455	2312

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 (%)
1.95-1.97	0.2513	128	0.2432	2445	X-RAY DIFFRACTION	92.39
1.97-2	0.236	140	0.2352	2649	X-RAY DIFFRACTION	99.93
2-2.03	0.2626	140	0.2272	2653	X-RAY DIFFRACTION	99.96
2.03-2.06	0.2523	139	0.2244	2643	X-RAY DIFFRACTION	99.86
2.06-2.09	0.2607	140	0.2201	2666	X-RAY DIFFRACTION	99.93
2.09-2.12	0.2535	142	0.2049	2690	X-RAY DIFFRACTION	99.96
2.12-2.15	0.213	138	0.1922	2633	X-RAY DIFFRACTION	100
2.15-2.19	0.2224	141	0.1898	2668	X-RAY DIFFRACTION	99.96
2.19-2.23	0.2174	139	0.1876	2649	X-RAY DIFFRACTION	100
2.23-2.27	0.2337	139	0.1869	2641	X-RAY DIFFRACTION	100
2.27-2.32	0.2273	141	0.1893	2669	X-RAY DIFFRACTION	99.96
2.32-2.37	0.2155	139	0.1877	2649	X-RAY DIFFRACTION	100
2.37-2.42	0.2299	141	0.1805	2677	X-RAY DIFFRACTION	100
2.43-2.49	0.241	140	0.1753	2661	X-RAY DIFFRACTION	100
2.49-2.55	0.2331	139	0.1758	2636	X-RAY DIFFRACTION	99.96
2.55-2.63	0.2166	141	0.1779	2677	X-RAY DIFFRACTION	100
2.63-2.71	0.2231	139	0.1821	2645	X-RAY DIFFRACTION	99.96
2.71-2.81	0.2499	142	0.182	2700	X-RAY DIFFRACTION	100
2.81-2.92	0.2156	141	0.1798	2669	X-RAY DIFFRACTION	100
2.92-3.05	0.2113	138	0.1681	2633	X-RAY DIFFRACTION	100
3.06-3.22	0.1645	141	0.1704	2680	X-RAY DIFFRACTION	100
3.22-3.42	0.2167	141	0.1667	2676	X-RAY DIFFRACTION	100
3.42-3.68	0.2076	141	0.1661	2681	X-RAY DIFFRACTION	100
3.68-4.05	0.1426	141	0.1484	2675	X-RAY DIFFRACTION	100
4.05-4.64	0.1678	141	0.1252	2674	X-RAY DIFFRACTION	100
4.64-5.84	0.1569	142	0.1459	2694	X-RAY DIFFRACTION	100
5.84-42.26	0.1841	144	0.1885	2730	X-RAY DIFFRACTION	99.83

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	4.47463703457	-0.704436133575	-0.195541127048	5.77138939004	0.490296368662	2.63275344382	-0.0623518662687	-0.0965495316601	0.189311215144	0.225728675422	0.17415519218	0.0184790665122	-0.308067730922	0.00428203298873	-0.11597844225	0.265663566212	-0.00359996726172	-0.00307690353689	0.201804843422	-0.00840469159892	0.233944599713	-45.2037444289	24.6296441288	8.91445763048
2	9.35758208806	-1.87003305311	2.57159158586	2.05040821123	-0.870599172413	2.4614968114	-0.092066838526	-0.431913505514	-0.0198500917754	0.048745031654	0.0346165344093	-0.129124747226	-0.0193629374031	0.017401658544	0.0450265719404	0.325047302008	0.0528945404137	0.0409508364323	0.241666979629	-0.0468679848696	0.157646453359	-46.2374661534	14.6741102523	9.81765491782
3	6.59982617256	-1.94674189075	1.24366127827	1.98969186563	-0.193085807456	1.55958688528	-0.198246276506	-0.330719758905	-0.259259441813	0.0370599602884	0.133201092004	0.167450704352	-0.0311056777651	-0.0187475562204	0.0241532516491	0.352418943817	0.0107303050573	0.00908688964976	0.259623112109	-0.00349114384043	0.218838998001	-51.3774004229	13.5221422916	7.60842575444
4	1.71873813648	-1.95769008752	-1.15111754464	9.01843544446	2.77351231805	9.52244096731	-0.0984566771021	-0.160091744622	-0.524267452886	0.337902951432	-0.0523291374982	0.870353079509	0.0519090631112	-1.24635013495	0.17510957507	0.391110744789	0.125649641437	-0.0832504306699	0.663469846747	0.0154199428787	0.562506299119	-79.0440348103	18.966718243	-5.1780675906
5	5.88695043786	-0.251577743295	0.828312763548	1.88030048578	-0.13933382852	1.035282864	-0.0725285026265	0.15435999535	-0.267277122892	-0.236537754186	-0.00105477951717	-0.0535754722125	0.00861184742099	0.0624040722947	0.0221992884681	0.394842863985	0.0168283634509	0.0211938730009	0.252240326934	-0.0180016180879	0.256525605414	-48.6581090317	11.9575924178	-1.40447857753
6	2.71006438682	-0.944819564227	0.942033180329	1.60561823999	-0.0469897929081	2.46722129715	-0.190886263042	-0.355188194525	-0.89675433168	0.258228767793	0.179993706537	0.697105924351	0.214048054964	-0.416938386421	-0.110716747748	0.395700784131	-0.0607050788233	0.0274241636115	0.340598978843	0.0615110897797	0.541054939194	-63.2377524575	3.50209258958	1.972656197
7	3.11538977235	-3.20127973799	2.06182531411	3.57875956376	-1.56570407671	2.51326133257	0.440156202608	0.0889537031519	-0.778697206902	-0.408306230878	-0.180755230521	0.243795610761	0.355616791321	0.149855707743	-0.0998864907985	0.469647413129	0.0230698148311	-0.0179747626694	0.375067086114	-0.0142635352401	0.397445347986	-48.7831098796	5.12308930194	-6.5543221
8	2.97750605857	-1.99208768395	2.83951406911	3.2371340357	-0.886063393615	3.17320420627	-0.0606127873145	0.538903094146	0.262305103262	-0.323164326163	-0.102357073769	0.0781210798935	-0.0516616660723	0.107795217455	0.136933212945	0.441897434055	0.0151008029867	-0.032031456545	0.409883094261	0.0211726329418	0.333754034186	-51.4967257465	15.5839938527	-9.28438104346
9	7.02076302915	-3.57930828563	2.50761050669	2.38025477253	-1.35741901933	1.70516566132	0.145331653194	0.243567432853	-0.448129778357	-0.193601143262	-0.114175029825	0.292038860127	0.147610899838	-0.062292995697	-0.0455360791921	0.372916593433	0.00154320997897	-0.0211537216964	0.304200853487	-0.0235251289365	0.315496438722	-58.9961239291	10.2700599455	-4.29299338232
10	3.91258656561	-0.389542029621	2.79659707168	5.87868222037	-2.88839163631	4.97912049217	-0.324688043233	-0.556096462475	-0.295629217927	0.541257125574	0.212604215567	0.300854374983	0.170504046924	0.0852886442243	0.120350129628	0.405482162401	0.0619066843012	0.0937456353327	0.39801368978	-0.00245445300287	0.258696949657	-47.608120923	8.08330396937	15.4072755984
11	9.18344011278	0.370647946329	7.70384295721	3.3103233019	-0.429847562411	7.52872392569	0.183028045827	0.0680027175665	-0.560630071366	-0.743819146496	-0.167397054488	-0.278063052316	0.708215089696	-0.273530537031	0.0197562711662	0.604478240944	-0.0428092949306	0.177488062864	0.435302763419	-0.0321313739521	0.415160908	-16.130762573	14.3307826542	-18.4624482416
12	5.06003519379	-3.54368590527	-1.13127641002	9.75203410368	-3.35168675645	6.65275565016	0.0519689303905	0.00290344127851	-0.982332271246	-0.425685373451	0.108449725996	0.581944591765	0.571339082879	-0.144219939708	-0.212083730833	0.367881025548	-0.0734253862386	0.0417606101489	0.310384362528	0.0412546091506	0.429844849643	-25.0357734356	14.0435965272	-10.1141448413
13	3.43497415828	0.318928839	-1.18932667399	2.93274327692	0.173027341398	0.743960122636	-0.0783313931857	0.00115454371505	-0.0366636602606	-0.258917335311	0.0517736159068	-0.106196118965	0.0878534572567	0.0430842245681	0.0437453779211	0.431209407894	-0.025423536955	0.0423077526581	0.33897800159	0.0136805475348	0.325446326208	-22.1313889556	21.3384925558	-10.4814249223
14	9.26168543023	-0.750655584828	-4.70207690058	3.26298939865	0.498728196509	4.61708527005	-0.52459924313	0.193554520461	-0.806370435043	-0.259132849589	0.053960353938	0.0271654191057	0.577430427374	-0.106039000671	0.445665508792	0.509176839712	-0.0384377440796	0.100715627276	0.248889322276	0.0211671830736	0.413033744887	-23.4844959405	10.2922735131	-11.943587694
15	2.53774665933	0.000238650783479	-0.455810654357	1.19725233786	-0.126170960644	1.81844663189	-0.0392172925074	-0.158766464123	0.026160145652	0.0676205302926	-0.0307489834432	0.308951864064	-0.0051835188754	-0.247526951653	0.053028940433	0.376519136966	0.0575472393161	0.0175003963114	0.360686209081	-0.0418700284946	0.434804442165	-74.2203056129	19.1984257655	16.2047737295
16	4.29417601216	1.23872487305	-0.585148155186	1.53310794636	-0.755839735629	1.7060196795	0.0421831959857	-0.242152751396	0.147957245525	0.316326759623	0.00795311155288	0.229055798304	-0.234806624172	-0.232408411548	-0.120301073139	0.492347838139	0.086852128445	0.0858244518322	0.376127207591	-0.0952605538361	0.460429388173	-70.5577032701	27.1550025872	26.2870960862
17	3.41409554242	1.01712601652	-0.0916792762694	3.84247379814	-1.2025807538	1.51126358791	0.148806393933	-0.764325784858	0.819674086618	0.461168690996	-0.139389404385	0.306866083323	-0.0603927804837	-0.181632571549	-0.110590904965	0.504582534296	0.060088709929	0.126516325766	0.458932316992	-0.139482473382	0.651476758295	-78.3935966696	33.6234195961	24.3935248989
18	2.38755363389	0.550547259136	-0.45313825279	1.98016238297	-0.521597987916	1.90905794392	-0.0612369082006	-0.279938265783	0.195069868381	0.219976900439	0.035432670224	0.165043746317	-0.0603307545087	-0.109641214609	0.0102405397313	0.394146893292	0.0545309629459	0.0464763690379	0.397999215869	-0.0697578676069	0.439178199914	-70.5219490386	25.5191234186	22.9019182161
19	1.51038255227	-0.180585165863	1.3468949459	3.18151174402	1.63895793381	2.23338229142	-0.912949444267	-0.295424608349	-0.912325079952	0.545696047878	0.408279952985	0.686215217649	-0.0223286024461	-1.09746250548	0.247275055019	0.668195993135	0.167462335362	0.207366136768	1.30472717793	0.115048478199	0.925238461636	-112.217919795	27.6896373204	37.1859669507
20	4.1766338553	-2.53477697681	-0.381436431154	7.12901698848	0.091548890692	4.43548901891	-0.0962463377735	-0.904282804957	0.735615173526	0.194904372909	0.457483232099	0.190770553569	-0.583418005537	-0.556887338712	-0.319893083685	0.557179944094	0.165900046046	0.0775687088327	1.01327066567	-0.116593585176	0.675013537248	-105.3609129	29.5165959728	28.1774989557
21	3.69564064132	-2.22885637835	0.173945025204	6.17615364578	-1.05103256158	5.9565228571	-0.580950722171	-1.25083031617	-0.167462730326	0.891157206653	0.655098319601	0.151312123107	-0.0889810450524	-0.353270147	-0.226210344812	0.537105471516	0.167914618878	0.0934901847215	0.997714763638	0.0575639479179	0.559439453417	-103.138888234	18.7995468267	32.8255390783
22	3.58192929511	-2.10814248176	0.311633075756	4.26359877469	1.77382948106	5.71916254861	-0.147472877551	-0.699749264355	0.00527143526447	0.250919758581	0.162833999464	0.529323135877	0.0974264550867	-0.94862104585	0.0349049312367	0.388341814113	0.0286721521081	0.0669115796384	0.823224154863	-0.0609981839879	0.637881533546	-108.59299756	22.6808209754	26.5513402192
23	5.05381458002	-1.38102845672	-0.748502667609	4.89724923463	2.30832952012	6.00184226055	-0.307004304437	-1.31596987012	0.0985306112385	1.0414105062	0.625389677705	-0.380014345944	-0.0877838687497	-0.0346959461224	-0.263704115726	0.547028807745	0.1874531678	0.0211447002431	0.928213185602	-0.00350601155278	0.638622645865	-100.460717689	26.4713625865	33.9642324737
24	4.8835775924	-1.57063867709	-4.49914821684	1.50557269355	3.09580980232	6.83892677315	-0.547158578975	-0.920841004188	-0.911343370736	1.29137909718	0.406311044906	0.0244682964619	0.907122610801	0.227876792229	0.284417088719	0.819774047545	0.14499721257	0.156576677348	0.710455016303	0.164882933004	0.508343371491	-52.0684155563	3.83417170584	26.8472877218
25	5.43144338015	-1.21996137516	-1.23748518425	5.18514989458	0.937675693294	2.04241451933	-0.694763877056	-0.952320140196	-0.598640398207	0.999588629195	0.0433680470673	0.888878219297	0.809215362682	-0.459798207269	0.497082972284	0.879104286151	0.13372782356	0.322265141343	0.660381956485	0.182514744968	0.846043952034	-63.436047274	3.0205006877	31.6016110655
26	5.55853999265	0.464054152447	-0.376593547096	9.20284314168	6.73479026862	4.97886102255	-0.416395533377	-0.308635536528	-0.30933444391	0.134941319983	0.473141889422	0.104733134325	0.099465534561	0.446635993491	0.15906001407	0.515389267275	0.0202282730449	0.0668594959147	0.613281232206	0.0798149528612	0.617921884932	-59.7445297097	9.03265443826	24.0764940309
27	4.0067751872	4.84412055629	-4.95763393486	5.86331775119	-6.01631510377	6.1692449799	0.27949048058	0.809376286624	-0.0734609660649	-0.277129653583	0.0207185978556	-0.458178245888	0.383497071559	-0.579896035241	-0.394408613282	1.08521911464	0.0325540569416	0.168019084025	0.906477574564	0.0633659983864	0.584640629871	-58.5056558836	13.7621032967	40.365470166

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 66 through 105 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 106 through 134 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 135 through 172 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 173 through 189 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 190 through 231 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 232 through 257 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 258 through 277 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 278 through 300 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 301 through 357 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 358 through 379 )
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 3 through 23 )
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 24 through 45 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 46 through 109 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 110 through 126 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 66 through 189 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 190 through 264 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 265 through 292 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 293 through 378 )
19	X-RAY DIFFRACTION	19	chain 'E' and (resid 2 through 17 )
20	X-RAY DIFFRACTION	20	chain 'E' and (resid 18 through 39 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 40 through 52 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 53 through 108 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 109 through 124 )
24	X-RAY DIFFRACTION	24	chain 'A' and (resid 71 through 87 )
25	X-RAY DIFFRACTION	25	chain 'A' and (resid 88 through 106 )
26	X-RAY DIFFRACTION	26	chain 'A' and (resid 107 through 121 )
27	X-RAY DIFFRACTION	27	chain 'A' and (resid 122 through 128 )

-
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