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- PDB-3ug6: Crystal Structure of Get3 from Methanocaldococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 3ug6
TitleCrystal Structure of Get3 from Methanocaldococcus jannaschii
Componentsarsenical pump-driving ATPase
KeywordsHYDROLASE / tail-anchored / membrane protein / targeting factor / ATP-binding / GET3 / TRC40 / ATPase / ARSA / nucleotide-binding / protein targeting / protein transport
Function / homology
Function and homology information


arsenite-transporting ATPase / ATPase-coupled arsenite transmembrane transporter activity / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
Arsenical pump ATPase, ArsA/GET3 / Anion-transporting ATPase-like domain / Anion-transporting ATPase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Putative arsenical pump-driving ATPase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSuloway, C.J.M. / Rome, M.E. / Clemons Jr., W.M.
CitationJournal: Embo J. / Year: 2012
Title: Tail-anchor targeting by a Get3 tetramer: the structure of an archaeal homologue.
Authors: Suloway, C.J. / Rome, M.E. / Clemons, W.M.
History
DepositionNov 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Feb 15, 2012Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: arsenical pump-driving ATPase
B: arsenical pump-driving ATPase
C: arsenical pump-driving ATPase
D: arsenical pump-driving ATPase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,84714
Polymers159,9104
Non-polymers1,93710
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24250 Å2
ΔGint-276 kcal/mol
Surface area49260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.736, 76.874, 127.810
Angle α, β, γ (deg.)90.00, 108.828, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 24:192 or resseq 210:333 )
211chain 'B' and (resseq 24:192 or resseq 210:333 )
311chain 'C' and (resseq 24:192 or resseq 210:333 )
411chain 'D' and (resseq 24:192 or resseq 210:333 )

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Components

#1: Protein
arsenical pump-driving ATPase / ATPase Get3 / Arsenical resistance ATPase / Arsenite-translocating ATPase / Arsenite-transporting ATPase


Mass: 39977.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ1142 / Plasmid: pET33b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q58542, EC: 3.6.3.16
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 9% PEG3350, 0.1 M sodium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.292→120.971 Å / Num. all: 24112 / Num. obs: 23100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.2_869)refinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→42.864 Å / SU ML: 0.98 / σ(F): 0 / Phase error: 29.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2875 1190 5.19 %
Rwork0.2486 --
obs0.2506 22945 95.76 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.442 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-21.1021 Å2-0 Å214.7112 Å2
2---8.5416 Å20 Å2
3----8.5922 Å2
Refinement stepCycle: LAST / Resolution: 3.3→42.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9708 0 114 0 9822
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0229996
X-RAY DIFFRACTIONf_angle_d1.66413416
X-RAY DIFFRACTIONf_dihedral_angle_d14.3323932
X-RAY DIFFRACTIONf_chiral_restr0.0891492
X-RAY DIFFRACTIONf_plane_restr0.0061688
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2342X-RAY DIFFRACTIONPOSITIONAL
12B2342X-RAY DIFFRACTIONPOSITIONAL0.063
13C2342X-RAY DIFFRACTIONPOSITIONAL0.054
14D2342X-RAY DIFFRACTIONPOSITIONAL0.061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.43210.36171270.34922325X-RAY DIFFRACTION94
3.4321-3.58820.35481390.32142468X-RAY DIFFRACTION98
3.5882-3.77730.34731170.29492430X-RAY DIFFRACTION97
3.7773-4.01380.31911210.28832402X-RAY DIFFRACTION95
4.0138-4.32340.2811240.25392360X-RAY DIFFRACTION94
4.3234-4.7580.26561370.21882464X-RAY DIFFRACTION97
4.758-5.44530.23911410.21572405X-RAY DIFFRACTION96
5.4453-6.8560.34031580.24482430X-RAY DIFFRACTION96
6.856-42.86780.22411260.20392471X-RAY DIFFRACTION94
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
15.0854-1.7345-0.27093.47820.11063.16371.25280.18880.983-0.60660.2878-1.7151-0.42381.3513-0.44380.34790.1827-0.85671.0978-0.27890.7254-34.89112.09177.5751
29.086-1.1635-6.67941.6581-0.52279.67760.88541.42780.1781-0.9492-0.3227-0.25971.02542.2441-0.82961.40480.1372-0.03571.623-0.17310.891-21.5238111.627254.0176
36.612-3.5163-3.73593.23862.15084.92560.52160.9048-0.3602-1.09290.4385-0.84680.82121.0173-0.57380.51650.52670.04511.7555-0.6260.6707-26.0797113.09944.9568
42.53481.5794-0.09851.5591.68253.9910.1724-0.01470.0322-0.14010.3865-1.0917-0.45550.9225-0.248-0.98160.4797-1.01970.86760.02160.2892-40.5059104.830966.441
53.4088-1.0893-3.4413.70143.68036.27080.03740.3405-0.0957-0.5634-0.0945-0.86631.17720.34670.29050.92170.22120.02050.71960.11820.6397-43.069887.501938.3545
64.9331-0.6701-4.63224.10823.66147.4394-0.3513-0.0712-0.66660.22550.0893-0.98360.37531.50240.1460.63720.2275-0.16830.88270.05060.6957-41.637893.546657.9005
72.3467-0.03030.7961.46580.41092.5681-0.2663-0.18890.0272-0.45340.45440.36120.0154-0.3782-0.15650.5922-0.0823-0.29980.65610.02090.5614-54.3082111.163575.9785
81.4037-1.51020.91444.9564-0.08743.01140.2193-0.7455-0.32240.9859-0.0290.13390.12230.0522-0.27830.9555-0.1975-0.31441.1842-0.130.5902-57.2708132.833392.0943
97.2284-0.14970.47784.9468-0.96852.97380.36420.14420.11360.588-0.20780.15020.60910.1061-0.18130.4988-0.0078-0.24530.8092-0.18350.6583-51.9342118.986986.2887
103.5889-0.4172-1.60415.95130.19953.91280.27150.1377-0.4733-0.5209-0.1720.60220.3601-0.415-0.05180.29750.0588-0.0710.5613-0.05480.5744-58.3255129.803458.4975
111.31292.4411.30345.72814.56725.77991.27871.3809-1.3321-0.5845-0.7741.24830.4482-0.1937-0.23431.08140.3625-0.8241.6987-0.67821.3747-59.056106.449544.7916
124.06241.32012.87524.52445.52968.64590.10410.7662-1.0359-0.2519-0.69450.95420.2237-0.927-0.046-0.56290.05-1.91241.1422-0.195-0.5896-51.465399.59544.9758
130.8754-0.1329-1.07183.50392.06112.07230.20270.2221-0.7754-0.31380.04140.5506-0.0233-0.225-0.12420.4890.0895-0.120.7716-0.08810.6278-46.6699125.627651.0795
141.5639-1.1488-1.32544.01895.71958.09780.00660.457-0.6333-1.877-0.1499-0.2858-0.06430.23470.52391.37630.08980.2280.719-0.28260.9602-27.5159111.134728.4076
155.3085-4.2567-2.31652.1538.77262.28980.37370.6103-0.4314-1.5077-0.6980.6326-0.5196-0.05070.44280.88430.0979-0.05150.5776-0.00360.4519-39.0167124.136139.2301
162.3731-1.2658-0.09143.11730.22883.3676-0.0049-0.45980.24620.0208-0.1382-0.9625-0.48840.94080.18440.4525-0.1276-0.1430.5142-0.12630.7751-40.7054134.711465.3059
172.6539-0.91971.03912.8262-0.63324.1201-0.04670.16530.69220.15750.02520.1173-0.9198-0.42130.23241.0234-0.0325-0.59191.8266-0.69340.3714-50.82138.887690.1859
182.60380.28340.18212.6999-0.09575.90660.1967-0.81420.51880.41780.0947-0.0469-0.92210.246-0.0710.37970.136-0.14450.7749-0.180.7344-49.3315138.922374.3086
194.70060.06842.10073.701-0.80532.8256-0.0495-0.22890.63390.47360.2693-1.3214-0.87790.6995-0.12620.8743-0.16950.01340.894-0.14730.6928-21.822595.0376-6.3197
202.80172.67850.57643.20072.50736.54750.1734-0.45960.54370.92850.8426-0.2805-1.66320.4052-0.74881.5065-0.14970.00621.2811-0.18061.1238-15.7852103.741818.6115
212.21062.98050.83477.2955.39086.50270.906-0.03320.45060.61340.0429-0.1744-0.91320.5952-0.52571.14940.0766-0.15010.9286-0.36750.741-18.832298.91927.1159
221.7702-0.00820.52531.76961.93412.5112-0.0984-0.40840.0557-0.66380.0046-0.5894-0.51830.46850.1121.03410.0093-0.08740.6644-0.03180.5561-32.17495.27623.7305
230.87830.42960.37940.78791.21374.15450.9673-0.59930.30960.8110.2830.2277-1.2638-0.4719-0.8150.68060.349-0.22450.78940.17950.4725-49.5085103.776630.5158
243.81160.7074-2.39415.61683.58028.825-0.4608-0.09730.19410.1386-0.46820.0088-1.22980.55930.40160.51670.1626-0.19830.4645-0.04230.4924-42.1004101.683811.5753
252.69810.480.40451.87540.21941.5750.1496-0.1613-0.2239-0.031-0.3236-0.0133-0.32140.29250.15640.51880.0722-0.06920.6484-0.03650.3696-35.826781.4651-7.0788
261.1148-0.5526-0.243.8098-0.76321.292-0.22770.75580.1448-0.8238-0.0610.1509-0.0317-0.06780.10340.8037-0.1797-0.0371.3536-0.34780.9283-20.224265.3807-22.4459
277.4582.011-0.39045.7681-0.16381.35130.2697-0.03560.4754-0.60160.1099-0.7179-0.62430.7861-0.12570.7324-0.16560.08490.6275-0.19090.4122-27.344678.4204-16.6802
284.7387-1.60970.96945.2888-0.85443.3675-0.4498-0.5379-0.43170.84670.33060.03330.3025-0.30930.00760.96780.1153-0.26580.6772-0.08080.6556-26.867364.63910.6652
293.9968-0.90340.67533.45380.11180.1402-0.56120.1688-0.04550.69250.91060.5625-0.2369-0.3681-0.04251.38040.22510.09990.94440.08871.6716-46.230679.04222.996
302.1236-0.3681-6.70773.61231.53369.0831-0.25570.118-1.22740.5465-0.1561-0.08080.2483-0.17350.35470.42030.1030.02050.62270.13390.7467-46.238889.264623.3476
312.596-1.160.39121.07791.12682.84520.0805-0.4420.21940.27340.53450.55530.3932-0.4178-0.40940.83410.1787-0.04490.7234-0.13880.6444-23.095675.68519.1556
320.59030.1499-0.62372.65251.891.77-0.0526-0.78260.33822.56930.26080.541-1.1158-0.1433-0.49540.2521.7468-0.16041.2001-0.33110.8963-23.647698.433843.1613
335.6005-4.4052-4.36599.62422.60745.47980.1939-0.4906-0.44331.1960.03750.76640.42390.20450.16890.6420.1725-0.3821.1989-0.21070.3968-20.494481.745931.7139
340.46890.27980.72112.5106-0.29881.6947-0.2255-0.22860.57960.33390.3818-0.90670.1091.1131-0.01970.59280.2505-0.20270.9047-0.29740.9569-10.790674.76386.1747
351.90750.31851.16052.8236-1.13932.94130.4823-0.1204-0.4270.0867-0.013-0.75870.70970.3248-0.05051.1193-0.34760.0921.4362-0.3180.802-11.579465.7462-19.4561
364.18910.8899-0.82683.3174-2.02354.3675-0.6081-0.0231-0.098-0.49710.6844-0.86020.87081.1458-0.08340.92990.004-0.09561.0254-0.46680.6058-12.368866.0108-3.5388
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 24:95)
2X-RAY DIFFRACTION2(chain A and resid 96:112)
3X-RAY DIFFRACTION3(chain A and resid 113:133)
4X-RAY DIFFRACTION4(chain A and resid 134:172)
5X-RAY DIFFRACTION5(chain A and resid 173:201)
6X-RAY DIFFRACTION6(chain A and resid 210:235)
7X-RAY DIFFRACTION7(chain A and resid 236:277)
8X-RAY DIFFRACTION8(chain A and resid 278:288)
9X-RAY DIFFRACTION9(chain A and resid 289:333)
10X-RAY DIFFRACTION10(chain B and resid 24:95)
11X-RAY DIFFRACTION11(chain B and resid 96:112)
12X-RAY DIFFRACTION12(chain B and resid 113:133)
13X-RAY DIFFRACTION13(chain B and resid 134:172)
14X-RAY DIFFRACTION14(chain B and resid 173:201)
15X-RAY DIFFRACTION15(chain B and resid 210:235)
16X-RAY DIFFRACTION16(chain B and resid 236:277)
17X-RAY DIFFRACTION17(chain B and resid 278:288)
18X-RAY DIFFRACTION18(chain B and resid 289:333)
19X-RAY DIFFRACTION19(chain C and resid 24:95)
20X-RAY DIFFRACTION20(chain C and resid 96:112)
21X-RAY DIFFRACTION21(chain C and resid 113:133)
22X-RAY DIFFRACTION22(chain C and resid 134:172)
23X-RAY DIFFRACTION23(chain C and resid 173:201)
24X-RAY DIFFRACTION24(chain C and resid 210:235)
25X-RAY DIFFRACTION25(chain C and resid 236:277)
26X-RAY DIFFRACTION26(chain C and resid 278:288)
27X-RAY DIFFRACTION27(chain C and resid 289:333)
28X-RAY DIFFRACTION28(chain D and resid 24:95)
29X-RAY DIFFRACTION29(chain D and resid 96:112)
30X-RAY DIFFRACTION30(chain D and resid 113:133)
31X-RAY DIFFRACTION31(chain D and resid 134:172)
32X-RAY DIFFRACTION32(chain D and resid 173:201)
33X-RAY DIFFRACTION33(chain D and resid 210:235)
34X-RAY DIFFRACTION34(chain D and resid 236:277)
35X-RAY DIFFRACTION35(chain D and resid 278:288)
36X-RAY DIFFRACTION36(chain D and resid 289:333)

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

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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

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