PDB-8vc9: Hybrid response regulator LvrB from Leptospira / phosphorylated R...

ID or keywords:

Entry

Database: PDB / ID: 8vc9

Title

Hybrid response regulator LvrB from Leptospira / phosphorylated REC form

Components

Leptospira virulence regulator B (LvrB)

Keywords

SIGNALING PROTEIN / two component systems / hybrid response regulator / seudo-phosphorylated form

Function / homology

PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / BERYLLIUM TRIFLUORIDE ION

Function and homology information

Biological species

Leptospira interrogans serovar Copenhageni (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Mechaly, A. / Buschiazzo, A.

Funding support

Uruguay, 1items

Citation

Journal: To Be Published
Title: Coiled coil formation and symmetry breaking activates the Leptospira virulence regulator LvrB, a hybrid response regulator
Authors: Agustoni, E. / Mechaly, A. / Dalla Rizza, J. / Isaikina, P. / Trajtenberg, F. / Muntener, T. / Wunder, E. / Ko, A.I. / Schirmer, T. / Buschiazzo, A. / Hiller, S.

History

Deposition	Dec 13, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 18, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8vc9.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb8vc9.ent.gz	769.6 KB	Display	PDB format
PDBx/mmJSON format	8vc9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vc/8vc9 ftp://data.pdbj.org/pub/pdb/validation_reports/vc/8vc9	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#168 - Dec 2013 DNA Helicase similarity (2) #150 - Jun 2012 Sliding Clamps similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #118 - Oct 2009 Sodium-Potassium Pump similarity (1) #195 - Mar 2016 RAF Protein Kinases similarity (1)

Deposited unit

A: Leptospira virulence regulator B (LvrB)

B: Leptospira virulence regulator B (LvrB)

C: Leptospira virulence regulator B (LvrB)

D: Leptospira virulence regulator B (LvrB)

E: Leptospira virulence regulator B (LvrB)

F: Leptospira virulence regulator B (LvrB)

hetero molecules

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

1

A: Leptospira virulence regulator B (LvrB)

B: Leptospira virulence regulator B (LvrB)

hetero molecules

defined by author
88.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Leptospira virulence regulator B (LvrB)

D: Leptospira virulence regulator B (LvrB)

hetero molecules

defined by author
88.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Leptospira virulence regulator B (LvrB)

F: Leptospira virulence regulator B (LvrB)

hetero molecules

defined by author
88.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	175.074, 102.327, 184.476
Angle α, β, γ (deg.)	90.000, 92.490, 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	Details
d_1	ens_1	(chain "A" and (resid 3 through 17 or (resid 18...
d_2	ens_1	(chain "B" and (resid 3 through 4 or (resid 5...
d_3	ens_1	(chain "C" and (resid 3 through 4 or (resid 5...
d_4	ens_1	(chain "D" and (resid 3 through 4 or (resid 5...
d_5	ens_1	(chain "E" and (resid 3 through 4 or (resid 5...
d_6	ens_1	(chain "F" and (resid 3 through 4 or (resid 5...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	LYS	LYS	ASP	ASP	A	A	3 - 107	3 - 107
d_1	2	ILE	ILE	ARG	ARG	A	A	109 - 213	109 - 213
d_1	3	GLY	GLY	SER	SER	A	A	217 - 335	217 - 335
d_1	4	GLY	GLY	ASP	ASP	A	A	339 - 378	339 - 378
d_2	1	LYS	LYS	ASP	ASP	B	B	3 - 107	3 - 107
d_2	2	ILE	ILE	SER	SER	B	B	109 - 335	109 - 335
d_2	3	GLY	GLY	ASP	ASP	B	B	339 - 378	339 - 378
d_3	1	LYS	LYS	ASP	ASP	C	C	3 - 107	3 - 107
d_3	2	ILE	ILE	ARG	ARG	C	C	109 - 213	109 - 213
d_3	3	GLY	GLY	SER	SER	C	C	217 - 335	217 - 335
d_3	4	GLY	GLY	ASP	ASP	C	C	339 - 378	339 - 378
d_4	1	LYS	LYS	ASP	ASP	D	D	3 - 107	3 - 107
d_4	2	ILE	ILE	ARG	ARG	D	D	109 - 213	109 - 213
d_4	3	GLY	GLY	ASP	ASP	D	D	217 - 378	217 - 378
d_5	1	LYS	LYS	ASP	ASP	E	E	3 - 107	3 - 107
d_5	2	ILE	ILE	ARG	ARG	E	E	109 - 213	109 - 213
d_5	3	GLY	GLY	SER	SER	E	E	217 - 335	217 - 335
d_5	4	GLY	GLY	ASP	ASP	E	E	339 - 378	339 - 378
d_6	1	LYS	LYS	ASP	ASP	F	F	3 - 107	3 - 107
d_6	2	ILE	ILE	ARG	ARG	F	F	109 - 213	109 - 213
d_6	3	GLY	GLY	SER	SER	F	F	217 - 335	217 - 335
d_6	4	GLY	GLY	ASP	ASP	F	F	339 - 378	339 - 378

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.999810614003, -0.0125120356753, 0.0149058743806), (0.0130037188137, -0.999358840107, 0.0333588368553), (0.0144789303749, 0.0335463509578, 0.99933227853)	93.4358866207, -12.7721868947, 0.291037527902
2	given	(0.300684508981, -0.952587831007, -0.0465322498542), (-0.953632016284, -0.300973920359, -0.000822667717643), (-0.013221330405, 0.0446220066894, -0.99891644943)	28.3117317895, 38.6095815672, 60.1311067128
3	given	(-0.325574032479, 0.941914559092, -0.0824530942167), (0.945166037264, 0.326587781875, -0.00125806733851), (0.0257431812065, -0.0783414583774, -0.996594152361)	70.3948564218, -47.4619438621, 57.2085350972
4	given	(0.654905638829, 0.753424312192, 0.0587401909024), (0.755678415228, -0.653614455475, -0.0416926414701), (0.00698118816807, 0.0716934403677, -0.997402282743)	-33.9294807817, -55.9520450811, 122.072844846
5	given	(-0.634535834491, -0.772887554619, 0.00301706195147), (-0.77280359389, 0.634516755491, 0.0127707584475), (-0.0117847366276, 0.00577190754945, -0.999913898826)	22.8084558472, 18.1116714578, 122.44796899

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein	Leptospira virulence regulator B (LvrB) Mass: 43426.566 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira interrogans serovar Copenhageni (bacteria) Gene: lic11708 / Production host: Escherichia coli (E. coli)

-
Non-polymers , 5 types, 64 molecules

#2: Chemical	ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE Mass: 505.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₁H₁₈N₅O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION Mass: 66.007 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: BeF₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H₂O

-
Details

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: 3.17 Å³/Da / Density % sol: 61.17 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: Tris-HCl, ammonium sulfate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97857 Å / Relative weight: 1
Reflection	Resolution: 2.65→49.3 Å / Num. obs: 94420 / % possible obs: 99.8 % / Redundancy: 4.2 % / B_iso Wilson estimate: 72.78 Å² / R_pim(I) all: 0.028 / Net I/σ(I): 14.4
Reflection shell	Resolution: 2.65→2.7 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4642 / R_pim(I) all: 0.493 / % possible all: 99.7

-
Processing

Software

Name	Version	Classification
Aimless		data scaling
PHENIX	1.20.1_4487	refinement
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.65→49.27 Å / SU ML: 0.4637 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 33.8785
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.254	9089	4.91 %
R_work	0.2103	175875	-
obs	0.2124	94249	99.55 %

Solvent computation

Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 101.49 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→49.27 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17849	0	242	36	18127

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0059	18397
X-RAY DIFFRACTION	f_angle_d	1.1744	24907
X-RAY DIFFRACTION	f_chiral_restr	0.1102	2799
X-RAY DIFFRACTION	f_plane_restr	0.008	3173
X-RAY DIFFRACTION	f_dihedral_angle_d	14.111	6853

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	A	X-RAY DIFFRACTION	Torsion NCS	2.61666360638
ens_1	d_3	A	A	X-RAY DIFFRACTION	Torsion NCS	1.8444545016
ens_1	d_4	A	A	X-RAY DIFFRACTION	Torsion NCS	1.67039894396
ens_1	d_5	A	A	X-RAY DIFFRACTION	Torsion NCS	3.17300762508
ens_1	d_6	A	A	X-RAY DIFFRACTION	Torsion NCS	2.80182183136

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 (%)
2.65-2.68	0.4862	308	0.4436	5885	X-RAY DIFFRACTION	99.42
2.68-2.71	0.3989	264	0.3943	5817	X-RAY DIFFRACTION	99.49
2.71-2.74	0.4277	345	0.371	5907	X-RAY DIFFRACTION	99.54
2.74-2.78	0.4369	289	0.3572	5840	X-RAY DIFFRACTION	99.59
2.78-2.82	0.4188	292	0.341	5925	X-RAY DIFFRACTION	99.42
2.82-2.85	0.3602	272	0.3124	5821	X-RAY DIFFRACTION	99.53
2.85-2.9	0.3684	296	0.3003	5961	X-RAY DIFFRACTION	99.48
2.9-2.94	0.3789	316	0.2912	5759	X-RAY DIFFRACTION	99.59
2.94-2.98	0.3558	322	0.2843	5885	X-RAY DIFFRACTION	99.39
2.98-3.03	0.3519	315	0.3	5789	X-RAY DIFFRACTION	99.71
3.03-3.09	0.324	307	0.2961	5907	X-RAY DIFFRACTION	99.66
3.09-3.14	0.3643	359	0.3069	5786	X-RAY DIFFRACTION	99.5
3.14-3.2	0.3769	354	0.29	5780	X-RAY DIFFRACTION	99.1
3.2-3.27	0.3094	278	0.2787	5942	X-RAY DIFFRACTION	99.66
3.27-3.34	0.3258	318	0.2618	5790	X-RAY DIFFRACTION	99.85
3.34-3.42	0.308	294	0.2447	5942	X-RAY DIFFRACTION	99.7
3.42-3.5	0.3471	279	0.2409	5906	X-RAY DIFFRACTION	99.66
3.5-3.6	0.2709	292	0.2279	5773	X-RAY DIFFRACTION	99.38
3.6-3.7	0.2861	280	0.2252	5913	X-RAY DIFFRACTION	99.41
3.7-3.82	0.2695	337	0.2231	5862	X-RAY DIFFRACTION	99.68
3.82-3.96	0.2622	288	0.2019	5829	X-RAY DIFFRACTION	99.56
3.96-4.12	0.2239	316	0.1816	5916	X-RAY DIFFRACTION	99.81
4.12-4.3	0.219	264	0.1673	5909	X-RAY DIFFRACTION	99.66
4.3-4.53	0.1891	311	0.1633	5826	X-RAY DIFFRACTION	99.82
4.53-4.81	0.1774	323	0.1516	5872	X-RAY DIFFRACTION	99.69
4.81-5.19	0.2347	271	0.1686	5894	X-RAY DIFFRACTION	99.63
5.19-5.71	0.2267	312	0.1972	5904	X-RAY DIFFRACTION	99.73
5.71-6.53	0.2343	275	0.202	5842	X-RAY DIFFRACTION	99.74
6.53-8.22	0.2243	303	0.185	5877	X-RAY DIFFRACTION	99.52
8.22-49.27	0.1797	309	0.1596	5816	X-RAY DIFFRACTION	98.65

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	3.91654324043	-0.415316767737	1.063124296	3.30700277338	-0.501741710118	8.53294743413	-0.00592758098907	-0.262385240982	0.0161163101331	0.649623340613	0.0983120627487	-0.349098370815	-0.158406162795	0.953506433492	-0.0966173109103	0.531896911621	-0.0913994968776	-0.114096516436	0.535013198066	0.0179922091143	0.718232552347	71.1080828867	0.250572258252	21.1096375234
2	0.560166686272	0.168820770696	-0.750345909223	-0.13748117751	-0.479507765004	6.04499351554	0.138247707345	-0.026547354393	0.0477012300728	0.420247020553	0.065195322554	-0.13358712805	-0.716980728187	-0.729572820801	-0.212715100445	1.49449541738	0.000202877920482	-0.0918392454576	0.664891958699	0.0214191871393	0.79099768583	54.2729566539	3.90627475363	58.8729936782
3	7.88090108022	-1.65046915091	-5.26502568155	3.67975405422	0.798703934934	3.57351837734	0.423934535646	-0.159589013233	-0.295386114564	0.600602337923	-0.784056417558	0.168882223106	-0.227188692264	-1.53014675591	0.300289092355	1.34283306519	-0.353608810907	-0.125327698506	1.19376865908	-0.00317414504139	0.843348087143	40.1877252479	-6.43450325994	100.95091763
4	5.51652824986	1.09221437833	-0.966958282309	4.23419314644	1.0089191756	6.18186167332	0.218227244363	-0.619621741732	-0.0287232231918	0.550017242323	0.182333722486	-0.488493466688	0.109395362116	1.01258859938	-0.350574626139	0.774146349018	0.0418312331289	-0.205297817787	0.618115908118	-0.0897446935935	0.567556590573	58.1049359405	-20.8319924537	63.3528225735
5	0.928455213003	0.493656659295	2.74559910152	0.205509164295	0.734587189197	8.40156693343	0.103180080246	-0.47958410096	-0.00892721772029	0.43467478014	-0.019166577141	-0.00274814063272	0.0946007528872	-0.43383604541	-0.113727892636	0.902081111182	0.100393954863	-0.0414838032158	0.775151755502	-0.0526019175828	0.631503943165	33.239455961	-9.87413991745	49.397967576
6	4.97695251523	1.61986999166	-0.129840277997	4.61506287991	-1.57824903258	6.16593136923	0.395987499549	-0.904063679399	-0.173619131875	1.02299653187	0.279485986586	0.463860137709	-0.363062014793	-1.38493745761	-0.621202044425	1.24658146188	0.0579553137075	0.0716022083263	1.12595357125	0.263336005279	0.668234101827	37.169557632	9.07731772909	62.3956378153
7	0.150086369958	-0.177739790862	1.21783910439	0.789095597832	-2.5701509147	8.44362314666	-0.020459172516	0.14765303124	-0.0891373387172	-0.182940322379	0.140623707045	-0.0915259481134	0.194699904857	-0.0490064748659	-0.104150366763	0.683617414004	0.0569274526099	0.0112319701631	0.482310156354	-0.00788838214953	0.669388437454	44.0410589281	-23.3409479578	21.789857249
8	4.22928373522	1.07651020121	2.72559794366	6.34735055023	3.2915932252	2.95954789028	-0.506642607148	0.379759210108	0.891430574219	-0.360419529476	0.109275064969	0.291011166246	-0.0385793000624	-0.238674132955	0.474583245687	1.00351581456	-0.24965881724	0.0261638891575	0.671791908948	0.0488455795323	0.725984947379	40.0631060259	0.840920433901	-42.8225932587
9	5.6499382435	2.07499036916	0.778613337913	5.56080116865	-0.25162427397	7.00019736924	0.120949724637	1.03551550323	-0.591131102328	-0.551079231853	0.146508926434	-0.226093762038	0.73842373788	0.798787830113	-0.241562289711	0.627540709939	0.0945167719685	-0.0578090433953	0.73853618851	-0.145696149508	0.570452655352	62.3889382181	-9.91716886906	-4.62923700058
10	0.00611597671663	0.0498790936837	0.0385067296648	0.473393277869	2.19386742454	8.37392948645	0.0615247238377	0.127799813688	0.0287681688961	-0.101588295491	0.270157139382	-0.1567101667	-0.367596894322	0.0328011967381	-0.278417837175	0.805569540913	-0.0156202706039	-0.0686172165985	0.552010909911	0.0186586339598	0.653479587548	47.8267148818	13.3002619388	20.6144747413
11	6.34723482407	0.751176729454	-2.5314837919	2.81607584349	-2.21131311742	2.35724464505	-0.890313523343	0.0434913277906	-0.576947776396	-0.015128188548	0.28009476695	-0.291576059505	0.98442176985	0.514015030446	0.897760462795	1.21205217586	-0.10074551671	0.0544331817172	0.519073450942	0.0416422803022	0.72536386608	43.1559303997	-10.9378321256	-42.6252759216
12	4.23286300639	1.50402907464	0.422663209338	7.17285014	-0.375811920846	5.23405788234	-0.261863124224	0.338363850878	0.475598060464	-0.491788898927	0.153198553721	0.116135127494	-0.585522750353	-0.0164492386543	0.054940180099	0.570598162345	0.0253640539169	-0.104449179406	0.401917063413	0.082673773937	0.529176835067	26.9455001005	-0.0323729472054	-2.39035371518
13	-0.500422588076	-0.116273713655	0.295867422986	-0.418142063671	-0.35651326738	3.08279512534	0.0463603912914	0.0561478318028	-0.0476644222325	0.191997015606	0.15025978038	-0.00886781088286	-0.182794193272	0.148792456972	-0.286009249763	1.11528461149	0.0177848503521	-0.0478446602035	1.18372866688	-0.0115477189251	0.732111690598	7.44421455603	-12.0248214953	73.7565248961
14	6.95172990547	-0.193712666491	0.65921567363	2.517417134	-0.0844954158249	4.28553091134	-0.327900941653	0.387201215938	0.365721114247	0.0152066352903	0.246549503088	-0.202067172919	-0.915924413323	1.07557643002	0.0563761122531	1.18593866445	-0.352364089137	0.0152233532637	1.08865895569	3.43368342902E-5	0.550428449895	-6.12704778408	-2.3664141542	59.2556898987
15	-0.124621729003	0.402518532326	-1.34761210382	0.0698912374406	-1.50336430296	8.43447511987	0.136390817656	-0.0195584933525	0.0637037628877	0.151810024567	-0.106070771884	0.05909099624	-0.0118605549031	-0.259463110653	-0.00156173880024	1.01674304799	-0.0832716539001	0.042757230682	1.02550059421	-0.022169088014	0.633324721698	-14.5135766634	-27.8409753465	72.6153246819
16	7.1139287077	0.19400034823	0.399576867482	3.08939800609	-0.272173167648	5.93120759945	0.0285817879327	0.463808497062	-0.254783295226	-0.378344676606	0.271588105453	0.208543778791	1.240642676	-0.259613934123	-0.299572135802	1.31816384502	0.0246608051501	-0.0752113605045	1.12386425255	0.123923936667	0.551906124648	1.20144590952	-38.0449717791	59.2979651209

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 2 through 101 )	A	A	2 - 101	1 - 100
2	2	chain 'A' and (resid 102 through 179 )	A	A	102 - 179	101 - 178
3	3	chain 'A' and (resid 180 through 214 )	A	A	180 - 214	179 - 213
4	4	chain 'A' and (resid 215 through 380 )	A	A	215 - 380	214 - 379
5	5	chain 'B' and (resid 1 through 212 )	B	F	1 - 212	1 - 212
6	6	chain 'B' and (resid 213 through 379 )	B	F	213 - 379	213 - 376
7	7	chain 'C' and (resid 1 through 178 )	C	K	1 - 178	1 - 178
8	8	chain 'C' and (resid 179 through 212 )	C	K	179 - 212	179 - 212
9	9	chain 'C' and (resid 213 through 378 )	C	K	213 - 378	213 - 378
10	10	chain 'D' and (resid 1 through 178 )	D	P	1 - 178	1 - 178
11	11	chain 'D' and (resid 179 through 212 )	D	P	179 - 212	179 - 212
12	12	chain 'D' and (resid 213 through 381 )	D	P	213 - 381	213 - 378
13	13	chain 'E' and (resid 3 through 212 )	E	U	3 - 212	1 - 210
14	14	chain 'E' and (resid 213 through 380 )	E	U	213 - 380	211 - 376
15	15	chain 'F' and (resid 3 through 212 )	F	Z	3 - 212	1 - 210
16	16	chain 'F' and (resid 213 through 380 )	F	Z	213 - 380	211 - 378

-
News

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

New format data for meta-information of EMDB entries

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

Related info.:EMDB header

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

-
Aug 12, 2020. Covid-19 info

Covid-19 info

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

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

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

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

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

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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

-
Non-polymers , 5 types, 64 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 6 molecules ABCDEF

-Non-polymers , 5 types, 64 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

-
Non-polymers , 5 types, 64 molecules

-
Details

-
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