[English] 日本語
Yorodumi
- PDB-8vc9: Crystal structure of Rec-controlled histidine kinase LvrB, BeF3-a... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vc9
TitleCrystal structure of Rec-controlled histidine kinase LvrB, BeF3-activated
ComponentsLeptospira virulence regulator B (LvrB)
KeywordsSIGNALING PROTEIN / two component systems / hybrid response regulator / seudo-phosphorylated form
Function / homologyPHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / BERYLLIUM TRIFLUORIDE ION
Function and homology information
Biological speciesLeptospira interrogans serovar Copenhageni (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsMechaly, A. / Buschiazzo, A.
Funding supportUruguay, 1items
OrganizationGrant numberCountry
Agencia Nacional de Investigacion e Innovacion (ANII)Uruguay
CitationJournal: Nat Commun / Year: 2026
Title: Activation mechanism of the full-length histidine kinase LvrB from pathogenic Leptospira.
Authors: Elia Agustoni / Ariel Mechaly / Joaquín Dalla Rizza / David Beriashvili / Kristyna Pluhackova / Polina Isaikina / Felipe Trajtenberg / Thomas Müntener / Elsio A Wunder / Albert I Ko / ...Authors: Elia Agustoni / Ariel Mechaly / Joaquín Dalla Rizza / David Beriashvili / Kristyna Pluhackova / Polina Isaikina / Felipe Trajtenberg / Thomas Müntener / Elsio A Wunder / Albert I Ko / Tilman Schirmer / Alejandro Buschiazzo / Sebastian Hiller /
Abstract: Pathogenic Leptospira modulate their virulence via the Lvr signaling system, with the histidine kinase LvrB being a central element. LvrB is a prototype of Rec-controlled histidine kinases, which are ...Pathogenic Leptospira modulate their virulence via the Lvr signaling system, with the histidine kinase LvrB being a central element. LvrB is a prototype of Rec-controlled histidine kinases, which are frequently found in bacterial two-component systems, and yet whose regulatory mechanisms remain largely unknown. Here, we report full-length structures of LvrB in different states uncovering its mechanism of activation. Kinase-inactive LvrB is a symmetric homodimer, with its catalytic domains rigidly clasped onto the central helical domain. Phosphorylation of the N-terminal Rec domains induces coiled-coil formation of the central αS helices thereby breaking symmetry through liberation of the catalytic domains into a dynamic, auto-phosphorylation competent state. We further identified LvrB's downstream effector partner LvrC, an anti-σ factor that reprograms the transcription of hundreds of virulence genes. Our findings set a mechanistic paradigm for Rec-controlled histidine kinases enabling the design of virulence inhibitors.
History
DepositionDec 13, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2026Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Jul 1, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Aug 12, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _pdbx_entry_details.has_protein_modification / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)264,66334
Polymers260,5596
Non-polymers4,10328
Water64936
1
A: Leptospira virulence regulator B (LvrB)
B: Leptospira virulence regulator B (LvrB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,18911
Polymers86,8532
Non-polymers1,3369
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Leptospira virulence regulator B (LvrB)
D: Leptospira virulence regulator B (LvrB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,09310
Polymers86,8532
Non-polymers1,2408
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Leptospira virulence regulator B (LvrB)
F: Leptospira virulence regulator B (LvrB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,38113
Polymers86,8532
Non-polymers1,52811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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 number5
Space group name H-MC121
Space group name HallC2y
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:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 3 through 17 or (resid 18...
d_2ens_1(chain "B" and (resid 3 through 4 or (resid 5...
d_3ens_1(chain "C" and (resid 3 through 4 or (resid 5...
d_4ens_1(chain "D" and (resid 3 through 4 or (resid 5...
d_5ens_1(chain "E" and (resid 3 through 4 or (resid 5...
d_6ens_1(chain "F" and (resid 3 through 4 or (resid 5...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11LYSLYSASPASPAA3 - 1073 - 107
d_12ILEILEARGARGAA109 - 213109 - 213
d_13GLYGLYSERSERAA217 - 335217 - 335
d_14GLYGLYASPASPAA339 - 378339 - 378
d_21LYSLYSASPASPBB3 - 1073 - 107
d_22ILEILESERSERBB109 - 335109 - 335
d_23GLYGLYASPASPBB339 - 378339 - 378
d_31LYSLYSASPASPCC3 - 1073 - 107
d_32ILEILEARGARGCC109 - 213109 - 213
d_33GLYGLYSERSERCC217 - 335217 - 335
d_34GLYGLYASPASPCC339 - 378339 - 378
d_41LYSLYSASPASPDD3 - 1073 - 107
d_42ILEILEARGARGDD109 - 213109 - 213
d_43GLYGLYASPASPDD217 - 378217 - 378
d_51LYSLYSASPASPEE3 - 1073 - 107
d_52ILEILEARGARGEE109 - 213109 - 213
d_53GLYGLYSERSEREE217 - 335217 - 335
d_54GLYGLYASPASPEE339 - 378339 - 378
d_61LYSLYSASPASPFF3 - 1073 - 107
d_62ILEILEARGARGFF109 - 213109 - 213
d_63GLYGLYSERSERFF217 - 335217 - 335
d_64GLYGLYASPASPFF339 - 378339 - 378

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

-
Components

-
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 interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

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

-
Data collection

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

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.20.1_4487refinement
XDSdata reduction
PHASERphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.254 9089 4.91 %
Rwork0.2103 175875 -
obs0.2124 94249 99.55 %
Solvent computationShrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 101.49 Å2
Refinement stepCycle: LAST / Resolution: 2.65→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17849 0 242 36 18127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005918397
X-RAY DIFFRACTIONf_angle_d1.174424907
X-RAY DIFFRACTIONf_chiral_restr0.11022799
X-RAY DIFFRACTIONf_plane_restr0.0083173
X-RAY DIFFRACTIONf_dihedral_angle_d14.1116853
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS2.61666360638
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.8444545016
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS1.67039894396
ens_1d_5AAX-RAY DIFFRACTIONTorsion NCS3.17300762508
ens_1d_6AAX-RAY DIFFRACTIONTorsion NCS2.80182183136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.680.48623080.44365885X-RAY DIFFRACTION99.42
2.68-2.710.39892640.39435817X-RAY DIFFRACTION99.49
2.71-2.740.42773450.3715907X-RAY DIFFRACTION99.54
2.74-2.780.43692890.35725840X-RAY DIFFRACTION99.59
2.78-2.820.41882920.3415925X-RAY DIFFRACTION99.42
2.82-2.850.36022720.31245821X-RAY DIFFRACTION99.53
2.85-2.90.36842960.30035961X-RAY DIFFRACTION99.48
2.9-2.940.37893160.29125759X-RAY DIFFRACTION99.59
2.94-2.980.35583220.28435885X-RAY DIFFRACTION99.39
2.98-3.030.35193150.35789X-RAY DIFFRACTION99.71
3.03-3.090.3243070.29615907X-RAY DIFFRACTION99.66
3.09-3.140.36433590.30695786X-RAY DIFFRACTION99.5
3.14-3.20.37693540.295780X-RAY DIFFRACTION99.1
3.2-3.270.30942780.27875942X-RAY DIFFRACTION99.66
3.27-3.340.32583180.26185790X-RAY DIFFRACTION99.85
3.34-3.420.3082940.24475942X-RAY DIFFRACTION99.7
3.42-3.50.34712790.24095906X-RAY DIFFRACTION99.66
3.5-3.60.27092920.22795773X-RAY DIFFRACTION99.38
3.6-3.70.28612800.22525913X-RAY DIFFRACTION99.41
3.7-3.820.26953370.22315862X-RAY DIFFRACTION99.68
3.82-3.960.26222880.20195829X-RAY DIFFRACTION99.56
3.96-4.120.22393160.18165916X-RAY DIFFRACTION99.81
4.12-4.30.2192640.16735909X-RAY DIFFRACTION99.66
4.3-4.530.18913110.16335826X-RAY DIFFRACTION99.82
4.53-4.810.17743230.15165872X-RAY DIFFRACTION99.69
4.81-5.190.23472710.16865894X-RAY DIFFRACTION99.63
5.19-5.710.22673120.19725904X-RAY DIFFRACTION99.73
5.71-6.530.23432750.2025842X-RAY DIFFRACTION99.74
6.53-8.220.22433030.1855877X-RAY DIFFRACTION99.52
8.22-49.270.17973090.15965816X-RAY DIFFRACTION98.65
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
13.91654324043-0.4153167677371.0631242963.30700277338-0.5017417101188.53294743413-0.00592758098907-0.2623852409820.01611631013310.6496233406130.0983120627487-0.349098370815-0.1584061627950.953506433492-0.09661731091030.531896911621-0.0913994968776-0.1140965164360.5350131980660.01799220911430.71823255234771.10808288670.25057225825221.1096375234
20.5601666862720.168820770696-0.750345909223-0.13748117751-0.4795077650046.044993515540.138247707345-0.0265473543930.04770123007280.4202470205530.065195322554-0.13358712805-0.716980728187-0.729572820801-0.2127151004451.494495417380.000202877920482-0.09183924545760.6648919586990.02141918713930.7909976858354.27295665393.9062747536358.8729936782
37.88090108022-1.65046915091-5.265025681553.679754054220.7987039349343.573518377340.423934535646-0.159589013233-0.2953861145640.600602337923-0.7840564175580.168882223106-0.227188692264-1.530146755910.3002890923551.34283306519-0.353608810907-0.1253276985061.19376865908-0.003174145041390.84334808714340.1877252479-6.43450325994100.95091763
45.516528249861.09221437833-0.9669582823094.234193146441.00891917566.181861673320.218227244363-0.619621741732-0.02872322319180.5500172423230.182333722486-0.4884934666880.1093953621161.01258859938-0.3505746261390.7741463490180.0418312331289-0.2052978177870.618115908118-0.08974469359350.56755659057358.1049359405-20.831992453763.3528225735
50.9284552130030.4936566592952.745599101520.2055091642950.7345871891978.401566933430.103180080246-0.47958410096-0.008927217720290.43467478014-0.019166577141-0.002748140632720.0946007528872-0.43383604541-0.1137278926360.9020811111820.100393954863-0.04148380321580.775151755502-0.05260191758280.63150394316533.239455961-9.8741399174549.397967576
64.976952515231.61986999166-0.1298402779974.61506287991-1.578249032586.165931369230.395987499549-0.904063679399-0.1736191318751.022996531870.2794859865860.463860137709-0.363062014793-1.38493745761-0.6212020444251.246581461880.05795531370750.07160220832631.125953571250.2633360052790.66823410182737.1695576329.0773177290962.3956378153
70.150086369958-0.1777397908621.217839104390.789095597832-2.57015091478.44362314666-0.0204591725160.14765303124-0.0891373387172-0.1829403223790.140623707045-0.09152594811340.194699904857-0.0490064748659-0.1041503667630.6836174140040.05692745260990.01123197016310.482310156354-0.007888382149530.66938843745444.0410589281-23.340947957821.789857249
84.229283735221.076510201212.725597943666.347350550233.29159322522.95954789028-0.5066426071480.3797592101080.891430574219-0.3604195294760.1092750649690.291011166246-0.0385793000624-0.2386741329550.4745832456871.00351581456-0.249658817240.02616388915750.6717919089480.04884557953230.72598494737940.06310602590.840920433901-42.8225932587
95.64993824352.074990369160.7786133379135.56080116865-0.251624273977.000197369240.1209497246371.03551550323-0.591131102328-0.5510792318530.146508926434-0.2260937620380.738423737880.798787830113-0.2415622897110.6275407099390.0945167719685-0.05780904339530.73853618851-0.1456961495080.57045265535262.3889382181-9.91716886906-4.62923700058
100.006115976716630.04987909368370.03850672966480.4733932778692.193867424548.373929486450.06152472383770.1277998136880.0287681688961-0.1015882954910.270157139382-0.1567101667-0.3675968943220.0328011967381-0.2784178371750.805569540913-0.0156202706039-0.06861721659850.5520109099110.01865863395980.65347958754847.826714881813.300261938820.6144747413
116.347234824070.751176729454-2.53148379192.81607584349-2.211313117422.35724464505-0.8903135233430.0434913277906-0.576947776396-0.0151281885480.28009476695-0.2915760595050.984421769850.5140150304460.8977604627951.21205217586-0.100745516710.05443318171720.5190734509420.04164228030220.7253638660843.1559303997-10.9378321256-42.6252759216
124.232863006391.504029074640.4226632093387.17285014-0.3758119208465.23405788234-0.2618631242240.3383638508780.475598060464-0.4917888989270.1531985537210.116135127494-0.585522750353-0.01644923865430.0549401800990.5705981623450.0253640539169-0.1044491794060.4019170634130.0826737739370.52917683506726.9455001005-0.0323729472054-2.39035371518
13-0.500422588076-0.1162737136550.295867422986-0.418142063671-0.356513267383.082795125340.04636039129140.0561478318028-0.04766442223250.1919970156060.15025978038-0.00886781088286-0.1827941932720.148792456972-0.2860092497631.115284611490.0177848503521-0.04784466020351.18372866688-0.01154771892510.7321116905987.44421455603-12.024821495373.7565248961
146.95172990547-0.1937126664910.659215673632.517417134-0.08449541582494.28553091134-0.3279009416530.3872012159380.3657211142470.01520663529030.246549503088-0.202067172919-0.9159244133231.075576430020.05637611225311.18593866445-0.3523640891370.01522335326371.088658955693.43368342902E-50.550428449895-6.12704778408-2.366414154259.2556898987
15-0.1246217290030.402518532326-1.347612103820.0698912374406-1.503364302968.434475119870.136390817656-0.01955849335250.06370376288770.151810024567-0.1060707718840.05909099624-0.0118605549031-0.259463110653-0.001561738800241.01674304799-0.08327165390010.0427572306821.02550059421-0.0221690880140.633324721698-14.5135766634-27.840975346572.6153246819
167.11392870770.194000348230.3995768674823.08939800609-0.2721731676485.931207599450.02858178793270.463808497062-0.254783295226-0.3783446766060.2715881054530.2085437787911.240642676-0.259613934123-0.2995721358021.318163845020.0246608051501-0.07521136050451.123864252550.1239239366670.5519061246481.20144590952-38.044971779159.2979651209
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 101 )AA2 - 1011 - 100
22chain 'A' and (resid 102 through 179 )AA102 - 179101 - 178
33chain 'A' and (resid 180 through 214 )AA180 - 214179 - 213
44chain 'A' and (resid 215 through 380 )AA215 - 380214 - 379
55chain 'B' and (resid 1 through 212 )BF1 - 2121 - 212
66chain 'B' and (resid 213 through 379 )BF213 - 379213 - 376
77chain 'C' and (resid 1 through 178 )CK1 - 1781 - 178
88chain 'C' and (resid 179 through 212 )CK179 - 212179 - 212
99chain 'C' and (resid 213 through 378 )CK213 - 378213 - 378
1010chain 'D' and (resid 1 through 178 )DP1 - 1781 - 178
1111chain 'D' and (resid 179 through 212 )DP179 - 212179 - 212
1212chain 'D' and (resid 213 through 381 )DP213 - 381213 - 378
1313chain 'E' and (resid 3 through 212 )EU3 - 2121 - 210
1414chain 'E' and (resid 213 through 380 )EU213 - 380211 - 376
1515chain 'F' and (resid 3 through 212 )FZ3 - 2121 - 210
1616chain 'F' and (resid 213 through 380 )FZ213 - 380211 - 378

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more