PDB-6zzc: MB_CRS6-1 bound to CrSAS-6_6HR

ID or keywords:

Entry

Database: PDB / ID: 6zzc

Title

MB_CRS6-1 bound to CrSAS-6_6HR

Components

Centriole protein
MB_CrS6-1

Keywords

PROTEIN BINDING / Centriole / Cartwheel / Ring-polymer / Monobody

Function / homology

Spindle assembly abnormal protein 6, N-terminal / SAS-6, N-terminal domain superfamily / Centriolar protein SAS N-terminal domain / centriole / cell cycle / identical protein binding / cytoplasm / Centriole protein

Function and homology information

Biological species

Chlamydomonas reinhardtii (plant)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.93 Å

Authors

Hatzopoulos, G.N. / Kukenshoner, T. / Banterle, N. / Favez, T. / Fluckiger, I. / Hantschel, O. / Gonczy, P.

Funding support

Switzerland, 2items

Citation

Journal: Nat Commun / Year: 2021
Title: Tuning SAS-6 architecture with monobodies impairs distinct steps of centriole assembly.
Authors: Hatzopoulos, G.N. / Kukenshoner, T. / Banterle, N. / Favez, T. / Fluckiger, I. / Hamel, V. / Andany, S. / Fantner, G.E. / Hantschel, O. / Gonczy, P.

History

Deposition	Aug 4, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 7, 2021	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6zzc.cif.gz	448.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6zzc.ent.gz		Display	PDB format
PDBx/mmJSON format	6zzc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6zzc_validation.pdf.gz	378.3 KB	Display	wwPDB validaton report
Full document	6zzc_full_validation.pdf.gz	394.4 KB	Display
Data in XML	6zzc_validation.xml.gz	33.6 KB	Display
Data in CIF	6zzc_validation.cif.gz	45 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zz/6zzc ftp://data.pdbj.org/pub/pdb/validation_reports/zz/6zzc	HTTPS FTP

-
Related structure data

Related structure data	6zz8C 6zzdC 6zzgC 3q0xS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3nmu-2 3nmu-1 10609 5mm2-d 1za7-d 3653 3651 7096 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

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Centriole protein

B000: Centriole protein

C: Centriole protein

D: MB_CrS6-1

D0A0: MB_CrS6-1

F: MB_CrS6-1

hetero molecules

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

1

A: Centriole protein

B000: Centriole protein

D: MB_CrS6-1

D0A0: MB_CrS6-1

defined by author
Evidence: isothermal titration calorimetry
71.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Centriole protein

F: MB_CrS6-1

hetero molecules

C: Centriole protein

F: MB_CrS6-1

hetero molecules

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

Unit cell

Length a, b, c (Å)	153.421, 123.171, 73.126
Angle α, β, γ (deg.)	90.000, 107.903, 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

Components on special symmetry positions

ID	Model	Components
1	1	C-423- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
3	1
1	2
2	2
3	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID	Auth seq-ID
1	1	1	(chain 'A' and resid 15 through 204)	A	15 - 204
2	2	1	(chain 'B' and resid 15 through 204)	B	15 - 204
3	3	1	(chain 'C' and resid 15 through 204)	C	15 - 204
1	4	2	chain 'D'	D	2 - 91
2	5	2	chain 'E'	E	2 - 91
3	6	2	chain 'F'	F	2 - 91

NCS ensembles :

ID
1
2

#1: Protein	Centriole protein Mass: 25683.066 Da / Num. of mol.: 3 / Mutation: F145E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CrSAS-6, CHLRE_12g516950v5 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A9CQL4
#2: Protein	MB_CrS6-1 Mass: 9955.156 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Chemical	ChemComp-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 546.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₄H₅₀O₁₃ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 3.07 Å³/Da / Density % sol: 60 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 15% PEG 4000, 0.8M sodium formate, 0.1 M Tris pH 8.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.93→47.08 Å / Num. obs: 53262 / % possible obs: 97.5 % / Redundancy: 2.1 % / B_iso Wilson estimate: 99.15 Å² / R_rim(I) all: 0.0107 / Net I/σ(I): 9.15
Reflection shell	Resolution: 2.93→3.11 Å / Num. unique obs: 8421 / CC_1/2: 0.41

-
Processing

Software

Name	Version	Classification
PHENIX	1.15_3459	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3q0x

3q0x

Resolution: 2.93→47.07 Å / SU ML: 0.6212 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 37.6674
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2901	2652	4.99 %
R_work	0.2444	50485	-
obs	0.2468	53137	97.41 %

Solvent computation

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

Displacement parameters

B_iso mean: 124.85 Å²

Refinement step

Cycle: LAST / Resolution: 2.93→47.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6937	0	37	59	7033

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0047	7118
X-RAY DIFFRACTION	f_angle_d	0.9017	9652
X-RAY DIFFRACTION	f_chiral_restr	0.0514	1111
X-RAY DIFFRACTION	f_plane_restr	0.0063	1235
X-RAY DIFFRACTION	f_dihedral_angle_d	16.9956	4280

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 (%)
2.93-2.99	0.4536	135	0.4761	2515	X-RAY DIFFRACTION	90.94
2.99-3.04	0.5551	134	0.4645	2626	X-RAY DIFFRACTION	98.08
3.04-3.11	0.4608	140	0.4355	2637	X-RAY DIFFRACTION	97.3
3.11-3.17	0.413	145	0.3556	2747	X-RAY DIFFRACTION	97.97
3.17-3.25	0.3405	136	0.3446	2629	X-RAY DIFFRACTION	98.68
3.25-3.33	0.375	141	0.3225	2700	X-RAY DIFFRACTION	98.34
3.33-3.42	0.3467	139	0.3259	2646	X-RAY DIFFRACTION	97.86
3.42-3.52	0.4063	137	0.317	2666	X-RAY DIFFRACTION	96.32
3.52-3.63	0.372	143	0.313	2665	X-RAY DIFFRACTION	98.42
3.63-3.76	0.3438	138	0.2936	2634	X-RAY DIFFRACTION	97.23
3.76-3.91	0.3035	137	0.2856	2646	X-RAY DIFFRACTION	97.24
3.91-4.09	0.2752	145	0.2443	2745	X-RAY DIFFRACTION	98.7
4.09-4.31	0.2445	139	0.2096	2639	X-RAY DIFFRACTION	98.27
4.31-4.58	0.2179	135	0.1991	2650	X-RAY DIFFRACTION	96.94
4.58-4.93	0.2792	141	0.1919	2709	X-RAY DIFFRACTION	98.17
4.93-5.42	0.2576	138	0.2017	2637	X-RAY DIFFRACTION	97.47
5.42-6.21	0.3167	141	0.241	2702	X-RAY DIFFRACTION	98.24
6.21-7.82	0.2822	142	0.2469	2621	X-RAY DIFFRACTION	97.19
7.82-47.07	0.2274	146	0.1825	2671	X-RAY DIFFRACTION	97.54

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	6.11899853121	-0.756658013163	0.532354846513	4.71809907656	-2.83675238432	5.02075485136	0.619886922428	0.784882326803	-0.483351149973	-0.84740918194	-0.269070049754	-0.0534594955296	1.23843095796	0.281069536247	-0.284866904519	1.37375062041	0.322328074949	-0.220589373567	0.96011048668	0.00811031883326	0.588903407017	17.796111089	-100.999258207	45.4746641819
2	2.55594481987	1.41190980037	-1.93600387351	8.11484755923	0.247823688952	2.66373913613	0.0482049044671	0.630795036269	0.271392998277	-1.18573795222	-0.696705935566	0.444106340392	-1.40031113355	0.197815014974	0.97578712901	1.15822672831	0.470082955945	-0.17540128728	1.01879893787	0.169330915041	0.779376199236	19.2133091341	-86.1959374574	43.7941731028
3	0.928662164482	-1.03307389214	1.56985659352	2.59986832458	-0.577713419999	5.4469651036	0.630330571003	0.17228014454	-0.026708049937	-0.253258695709	-0.21005329851	0.265491155895	0.803659931215	0.0868582454374	-0.51528855051	0.644361524221	-0.141047135842	0.126047575918	0.775864567174	0.129857052349	0.45065055259	26.7475028402	-98.2668633538	67.4733628923
4	8.68388359128	0.0437837925476	-4.61700869329	7.95339454841	1.23066669057	6.01245917852	-0.611990592782	0.0147802378536	-0.0317588245831	-0.184304468875	0.82854617797	0.54736622188	0.301505872875	0.452110209151	-0.311756673749	1.07012953394	0.088580149668	-0.00738907721866	0.790966461626	0.312057510429	0.902801080334	17.2660427729	-129.452639143	62.5612838703
5	7.62710863599	-2.40435963197	-5.68333823935	1.94950330875	3.19394199925	5.74716914002	0.274949118797	-0.758106481437	1.55582188221	-0.468328287065	0.101875205628	0.18392543042	0.340423590059	-0.630198055849	-0.211052336525	1.20751156669	0.174914899291	-0.274686650454	1.04705335683	-0.0547277301984	0.939130470004	2.79086091387	-125.3805456	69.3923960892
6	3.09889280017	-2.6541737848	0.771958545446	4.33209307967	-3.09886062692	3.53452114153	1.57514821583	0.0460355772206	-0.0688426583808	-3.64384389653	-0.156632297758	-1.5777462032	0.396220923674	0.253578216635	-1.50839686754	2.00894636974	0.219330541886	-0.138861239753	0.843723561178	-0.135855991467	1.07358312898	21.1263327621	-123.070322723	55.442489245
7	6.69518828266	-0.473300665814	1.14735622092	2.85100229389	3.69014372204	5.99952301591	0.965546219334	-0.994002208994	-1.40877804788	0.185480525706	-0.529902793748	0.974866161688	0.545336111856	-0.882286771512	-0.817113083219	1.35501261665	-0.110226281357	-0.149905751955	0.901077117094	0.244791721716	1.17704431117	8.21449773134	-137.56971593	69.5509063188
8	7.49233265449	-0.22716714112	-8.48944598097	1.6876074737	0.0411567480431	9.62769145658	-0.395829828853	0.389250870004	-1.82426106242	-0.608351595583	0.156040980253	0.227156306926	1.48857273813	-0.156237296081	-0.902440970376	1.82852605453	1.09596182228	-0.705642445952	2.79033787042	0.575706646085	1.39863419677	29.8082661703	-145.042131014	67.9019762535
9	3.50007652029	-3.71250650929	-2.39166216116	4.95715229422	4.19687013944	7.17730390075	1.09347395816	-0.31193239279	-0.408545897161	-1.37482824341	1.13849447062	0.93123862581	1.63911620237	0.300099946736	-1.77440071661	1.63125178198	-0.343674685708	-0.365079468141	0.903323283338	-0.0716056307481	1.57250671349	17.2875561848	-139.170492299	55.9011584865
10	2.66762926074	1.76109811592	-1.85978118831	2.12820898198	0.232719351897	3.63898852148	0.00227100251825	-0.718187744753	-0.243418328652	0.0311768277805	-0.528393333064	0.135822288982	0.0457912966481	0.878486856325	0.311252682509	1.59970887086	-0.0394681082396	-0.319223789711	1.15210350578	-0.0697939527201	1.00860488033	15.3225691442	-142.59718419	60.6468062861
11	6.00357962784	5.65371664995	3.56224991854	6.16659516907	2.30472449222	5.94555769139	0.289605764554	-0.315953491126	0.206898419937	0.385798662946	-0.250460738631	0.142765871208	-0.171494365778	0.0564178223556	0.316609627074	0.89469814614	0.273946817813	0.0597672746283	0.537273513168	-0.0535188064381	0.723625543607	32.435031099	-99.8678643882	81.107703652
12	7.6416518695	-1.49266146378	-0.495574447134	5.13837268337	-0.906652346886	7.3574892777	0.156631808882	0.376482264663	0.116400430996	-0.413989504781	-0.0769111899577	-0.390763735082	0.336799605479	-0.00939993414616	-0.153791052173	0.424850611544	0.00197937465533	0.0940263166066	0.450832867234	-0.0162250240893	0.432237567888	3.73535149988	-77.0831622751	15.7057957442
13	6.85037857019	-0.966094890036	-0.782549225958	6.90881287177	-1.49409959036	8.60686796064	0.290842561696	-0.359844315609	-1.08592711106	0.497120216476	-0.322612243003	0.301975889508	0.520691483139	-0.176720018294	-0.0450404108462	0.589883499909	0.0022860312295	0.0667868307508	0.421362750474	-0.0113146537565	0.455696045941	-4.58407324752	-81.1352176053	18.9724775854
14	5.41490509016	-3.16061419465	1.28241092517	5.9241258358	4.61094341237	7.52902050056	-1.24139248789	-1.70780977615	-0.850080888931	1.37893308969	-0.0825044956669	0.407627585408	0.918110149212	0.678376170154	-0.0287398414542	2.64005370363	0.861784525217	-0.278400789862	0.730796699468	0.776601841604	0.582788085149	1.01436341072	-81.5175923801	34.4042901724
15	6.38872594134	-0.310607926972	-0.903526883617	7.74959489038	-1.25693539087	8.73201915728	-0.332633700949	-1.20027213696	-0.0617836460478	0.839020672579	0.238508782063	-0.914125714496	0.346660642636	1.53393769993	0.0494671647784	0.64919005353	0.240986103815	-0.0377740082366	0.751797441507	0.128364494099	0.537118348985	10.0017209895	-77.9646697644	26.208491493
16	4.95752020142	-1.30200910567	-1.71194113311	2.11944859097	0.188598651588	2.14389589554	-0.00336205515447	0.46574651756	1.70160935008	-0.152802092093	-0.317902969141	0.762904740389	-1.62730980017	0.1841733693	-0.23244212302	1.91025826942	-0.0498016282476	-0.383853583725	0.965736056702	0.0319950960801	1.14413904372	-4.8642206594	-55.9700374987	1.44240747947
17	8.33058284881	-1.11362683599	-3.85569296751	1.92476338373	-0.82690895537	2.786964144	0.533091878818	1.87130179836	0.204835627215	0.87767213072	0.67632669118	-0.0987280952845	-1.12161753441	-2.97904061503	-0.238790437761	1.18639616886	-0.322051616773	-0.364560213661	1.72958886993	0.0669682558848	0.992590101186	23.7732117772	-123.307168649	91.4669280752
18	7.33706926064	-2.67317325937	-4.46860999269	3.54038574788	3.00526489991	3.44414190138	-0.488988278205	1.16741318575	1.36649404699	1.47249539376	1.13014308681	0.126484645308	-0.135466315831	-1.51591861455	-0.426155153253	1.14435246473	0.253416879152	0.0784882907484	1.57789871002	0.263465553514	0.748144465966	23.8253907329	-118.210999606	87.5666439576
19	3.7190970631	2.06193974426	2.73941429605	2.18006113008	3.48490689273	7.09155257241	-0.105545565922	0.74240531784	-2.44007923836	0.876877806766	0.313131683623	0.278409325439	1.00890895872	-1.41146282537	-0.762804283658	1.59938405532	0.0311951779373	-0.250904066617	0.96425969676	0.100844864538	1.23286323121	10.2053988587	-122.518575385	84.7438337768
20	3.00417680929	1.81242659561	-0.857405536018	3.19033839589	-2.13377147312	7.4624605835	0.169990769174	-0.0582730619395	0.0869563332454	-0.928391703515	0.569779636792	0.582617921701	0.730736022363	-0.115918468936	-0.576597429571	1.33390902921	0.0549235896963	-0.138443006479	1.05848904487	0.14672893207	0.88925277161	17.361951757	-119.155671055	84.1514457434
21	4.16725986149	3.34096171601	-0.525759168595	2.73609392464	-0.399067785812	0.056792672559	2.98993136915	-0.80656988727	-0.176768561322	-0.343680084507	0.095048520699	2.10746407776	1.92883379888	-1.00222470108	-1.9901079412	1.88018520862	0.180003723445	0.0478806336706	1.18031447773	0.152870151761	1.10146766896	15.0793325816	-126.464029034	94.2429082986
22	1.99350721944	-2.77650649093	1.76813507475	1.95147112186	2.05609239716	4.55222293096	2.17461926037	-2.17319266153	3.07145995016	-0.320432797281	-2.12488673971	-1.38095315368	0.384824910385	0.641144790565	-0.927482753484	1.44502331194	-0.407561755576	-0.168067216628	1.94979261853	0.876980010183	1.56987837897	39.9913893153	-88.3817808427	60.183533723
23	1.58232378674	1.05460783534	-1.48903466097	2.68927641994	2.07009795707	5.7085803141	0.877361091846	3.50346905306	1.6466444725	0.875160665733	0.281385442107	-0.608442669185	2.08221007671	-2.23577441152	-1.74372516441	1.20083918612	0.305886915032	-0.201067558854	2.00316701201	0.390299093899	1.50127731898	47.7977594091	-96.0409448334	56.4986201398
24	8.0940761691	0.867718600386	-3.74281818302	8.94323728858	2.58509505995	2.7710288709	0.567018043228	-0.145088664419	0.962391417642	-0.137727854463	-1.22165473612	-1.31964056721	-0.183974591669	1.89634992846	0.867360784283	1.14846014993	0.371672430147	-0.260391932314	1.3256534599	0.409955510006	0.917253772887	34.030065465	-96.3505369178	59.8487038721
25	2.96975704565	-1.61633949499	0.851160641692	9.09904344586	-2.73731293849	1.28022106684	0.171610960423	1.73110584652	-0.521645775831	0.792687383938	1.9701511757	2.13033303556	1.28234162646	-0.833827601083	-1.32827722719	1.31305655219	0.170919353074	0.162527197457	2.02352945352	0.822287742225	1.41568979148	36.0219616132	-98.9237421666	43.3370586443
26	1.99291095116	0.344372641122	-1.61777968854	4.19811922879	3.53144957158	3.30172104864	2.16751458961	2.3346202459	-0.949839543858	-2.34693949119	-2.83116425212	-1.61965136098	0.341280010637	-0.641620131899	0.612561709522	1.39663270649	0.238481089349	-0.49587338446	0.99899507412	0.0742433158526	1.78341177633	35.9224666794	-103.080318067	58.662472363
27	2.54131187651	-3.66663493319	-1.79414735493	9.12268826896	6.10870673418	4.40073617887	-0.793617825086	0.185249717546	0.819894997259	0.42876297607	0.347668303884	-2.04125566639	0.370923359466	1.21713630697	-0.257289758427	1.48474875199	-0.16783726393	-0.192084741122	1.80175300938	0.567786924831	1.40376944927	44.9580077332	-99.2199681463	55.321611627
28	2.3029874443	-2.41742190136	0.645099356041	6.86669082328	2.77327813541	3.05756141557	-0.0149271449256	1.63844960988	-0.767446427657	-1.6944822974	-1.57812665271	-0.98762305668	-0.403660247047	1.96550054667	0.401206284018	0.904361794287	0.474012831277	-0.0727047612802	1.76501147982	0.147677900378	1.56638756762	36.7694580957	-95.1149875029	52.3571172001
29	2.54602051567	-2.38389113863	-4.06265965249	7.49276994846	-0.171510630688	9.53477779445	0.10337100243	0.145112622894	0.890107477406	0.0227372679161	1.24512578024	1.0081620065	0.755456899846	-1.9292936208	-1.70978343845	1.29674116848	0.267454620665	-0.0608120317721	1.19204294122	0.221989176552	0.616228237956	24.0708895007	-96.2349078153	60.6065479404
30	5.10808430041	-2.20012200681	-6.90297929482	1.48958157773	2.63001299709	9.59986529552	-0.862334157195	1.41259512275	1.055023698	-0.0100101112989	0.918291187801	1.06524850863	0.824159550385	-0.0652733020044	-0.620873529582	0.902084782732	-0.035461774218	-0.0256167812967	1.63613512721	0.399426403498	1.38786359255	44.3693989558	-89.7229232917	49.9336693355
31	3.04872482432	-0.528214360106	5.15033117577	8.21883709894	-1.36779325104	8.83466190503	-2.42355228163	0.94864793412	0.14418462401	-0.877643100801	-1.17818152559	-0.897713650399	-1.54866705146	-1.85690345108	0.814657350484	0.739983102613	-0.101407717347	0.189799928158	0.631889531004	0.178357355698	0.464579201084	-5.26760472669	-50.6808080046	23.4046240162
32	6.72377089222	3.13169094082	-2.18715062624	3.54921504231	-2.02171324189	2.7600335498	0.0120620623772	0.0364233282099	0.998391497168	0.929622426103	-0.43115658144	0.0438777260893	-0.651866512993	-0.60971450813	-0.294796323702	0.181116541289	0.843498499407	0.261014050712	1.54615123693	-0.258442377467	0.250193168413	-18.4110090567	-50.9779786159	23.5978220192
33	7.70437867055	-7.08549210469	-1.64063996375	6.55408107168	1.80786542245	2.78481163455	-0.992903335302	0.410949344616	0.641120359017	0.704879892928	1.40118183502	-1.36904051215	0.00963758535821	2.08268987451	-0.295298331334	0.768185540437	-0.425120624977	-0.0109839603899	0.897810125293	0.132788369811	0.818945376764	-0.183966652627	-52.2006414809	14.132733106
34	4.83890247351	0.0335973615266	-4.81140466979	8.50354794168	-1.23173616853	5.00683564809	-0.49901373889	1.02997928254	-1.08134312727	-0.596916013701	0.24098052315	0.197028253378	-0.17586578744	0.0357113634005	0.137149818828	0.342407833901	0.0783284386618	0.00485796975535	0.803972144203	0.0974260271182	0.417906895678	-11.0659760449	-60.7514804501	18.9339953818
35	9.3173018115	2.69350771869	-4.52624156238	3.12685438169	-5.14362745188	8.38581411996	-0.870342793603	-0.835029787303	-1.66269910657	-0.695407763713	0.425491575627	-1.49129697187	3.09463940869	0.463980410966	0.493392204961	1.58634712649	0.0689338159523	0.0620420209115	0.800420565842	0.125147454624	0.674910209308	-13.3654256843	-68.4988352591	25.5024989397
36	6.02623594322	3.58196261974	-2.60772866957	4.24455061755	-4.02778525741	3.87801579616	0.909693675278	0.408896825687	-0.675561534081	1.30789350115	-1.02171612355	0.0995384174872	-0.219725069789	-1.37074169987	-0.0454597020089	1.19247763985	0.230425253427	-0.00517938094842	0.739154628519	0.0017054477808	0.354010911123	-11.6817625622	-59.8261667328	13.1700719959
37	5.22284938831	-5.77586618465	-6.25807328557	7.13702800551	5.91417339076	8.64804738893	0.755430857362	0.6603788599	1.09990568054	-0.186026187847	-0.421670401729	-0.886555113399	-0.678785003183	-1.42943982577	-0.221592360076	0.955603543605	0.0800317485782	0.0187598236103	0.791906190236	0.148241840215	0.513571173017	-11.2759933464	-51.4285826155	14.8261244085
38	6.64109289074	-0.309237583279	-0.191163385225	4.39345543932	-1.46974172815	7.64804861321	-0.604199206811	-1.90465770432	0.0600328348017	0.25259460562	0.632087915876	0.464952721387	0.475805998749	-0.0716670287489	-0.242113945969	0.653668582074	0.101581323283	-0.0726112156224	0.520409926047	-0.0155376987165	0.285831041071	-14.3157643638	-59.6988582017	24.7359225622
39	7.7449466223	-3.25706821801	-9.93328470652	5.15682379009	5.68774522897	2.00446792202	2.20450095169	-0.133267033229	1.26749348545	-0.558029732308	-0.132234897192	0.086701798814	-1.96006732005	2.5953685892	-0.918097506621	0.959363392093	0.126773070995	0.0190388906736	1.05756312371	0.195363623059	0.406259394113	2.15587008869	-62.8841648703	12.950524506
40	4.19916690483	-0.902464971253	1.21654437275	6.89559784509	4.88295833299	4.63897562059	0.652299162303	-0.555179122107	0.134720503764	-0.127579782638	-1.50825411782	1.6635604841	1.78834561865	-1.77820250547	0.876698256862	0.949332136011	0.247952380053	0.0529145550549	1.76833632229	0.0495082733816	0.0369683389116	-12.5543645326	-55.6144660594	30.0182984085

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 90 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 91 through 122 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 123 through 221 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 15 through 53 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 54 through 68 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 69 through 75 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 76 through 114 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 115 through 123 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 124 through 133 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 134 through 159 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 160 through 218 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 12 through 53 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 54 through 90 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 91 through 98 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 99 through 159 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 160 through 204 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 3 through 14 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 15 through 30 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 31 through 46 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 47 through 84 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 85 through 91 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 3 through 12 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 13 through 22 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 23 through 38 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 39 through 47 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 48 through 52 )
27	X-RAY DIFFRACTION	27	chain 'E' and (resid 53 through 67 )
28	X-RAY DIFFRACTION	28	chain 'E' and (resid 68 through 76 )
29	X-RAY DIFFRACTION	29	chain 'E' and (resid 77 through 84 )
30	X-RAY DIFFRACTION	30	chain 'E' and (resid 85 through 91 )
31	X-RAY DIFFRACTION	31	chain 'F' and (resid 2 through 13 )
32	X-RAY DIFFRACTION	32	chain 'F' and (resid 14 through 21 )
33	X-RAY DIFFRACTION	33	chain 'F' and (resid 22 through 30 )
34	X-RAY DIFFRACTION	34	chain 'F' and (resid 31 through 38 )
35	X-RAY DIFFRACTION	35	chain 'F' and (resid 39 through 47 )
36	X-RAY DIFFRACTION	36	chain 'F' and (resid 48 through 52 )
37	X-RAY DIFFRACTION	37	chain 'F' and (resid 53 through 60 )
38	X-RAY DIFFRACTION	38	chain 'F' and (resid 61 through 76 )
39	X-RAY DIFFRACTION	39	chain 'F' and (resid 77 through 84 )
40	X-RAY DIFFRACTION	40	chain 'F' and (resid 85 through 91 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi