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- PDB-9e2b: Structure of a solute binding protein from Desulfonauticus sp. bo... -

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Basic information

Entry
Database: PDB / ID: 9e2b
TitleStructure of a solute binding protein from Desulfonauticus sp. bound to L-tryptophan
ComponentsABC-type transporter, periplasmic subunit family 3
KeywordsPEPTIDE BINDING PROTEIN / Solute binding protein / tryptophan / amino acid binding protein
Function / homology
Function and homology information


ligand-gated monoatomic ion channel activity / membrane
Similarity search - Function
Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins.
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / TRYPTOPHAN / ABC-type transporter, periplasmic subunit family 3
Similarity search - Component
Biological speciesDesulfonauticus sp. 38_4375 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRahman, M. / Frkic, R.L. / Smith, O.B. / Jackson, C.J.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
Australian Research Council (ARC)CE200100029 Australia
CitationJournal: To Be Published
Title: Structure of a solute binding protein from Desulfonauticus sp. bound to L-tryptophan
Authors: Rahman, M. / Frkic, R.L. / Smith, O.B. / Jackson, C.J.
History
DepositionOct 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC-type transporter, periplasmic subunit family 3
B: ABC-type transporter, periplasmic subunit family 3
C: ABC-type transporter, periplasmic subunit family 3
D: ABC-type transporter, periplasmic subunit family 3
E: ABC-type transporter, periplasmic subunit family 3
F: ABC-type transporter, periplasmic subunit family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,19741
Polymers183,9146
Non-polymers3,28435
Water16,015889
1
A: ABC-type transporter, periplasmic subunit family 3
B: ABC-type transporter, periplasmic subunit family 3
D: ABC-type transporter, periplasmic subunit family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,58621
Polymers91,9573
Non-polymers1,62918
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint11 kcal/mol
Surface area31220 Å2
MethodPISA
2
C: ABC-type transporter, periplasmic subunit family 3
E: ABC-type transporter, periplasmic subunit family 3
F: ABC-type transporter, periplasmic subunit family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,61220
Polymers91,9573
Non-polymers1,65517
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9230 Å2
ΔGint10 kcal/mol
Surface area31720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.507, 74.593, 92.348
Angle α, β, γ (deg.)98.21, 91.24, 119.84
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
ABC-type transporter, periplasmic subunit family 3


Mass: 30652.303 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfonauticus sp. 38_4375 (bacteria) / Gene: XD41_0486 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A101DJ27

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Non-polymers , 6 types, 924 molecules

#2: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 889 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 27% PEG 3350, 0.1M sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.8→39.14 Å / Num. obs: 153832 / % possible obs: 97.8 % / Redundancy: 3.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.054 / Rrim(I) all: 0.104 / Χ2: 0.99 / Net I/σ(I): 7.6 / Num. measured all: 568516
Reflection shellResolution: 1.8→1.83 Å / % possible obs: 96.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 1.254 / Num. measured all: 28491 / Num. unique obs: 7559 / CC1/2: 0.484 / Rpim(I) all: 0.746 / Rrim(I) all: 1.461 / Χ2: 0.99 / Net I/σ(I) obs: 0.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.14 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2161 7969 5.18 %
Rwork0.185 --
obs0.1866 153748 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→39.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12138 0 224 889 13251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.886
X-RAY DIFFRACTIONf_dihedral_angle_d16.0424723
X-RAY DIFFRACTIONf_chiral_restr0.0571843
X-RAY DIFFRACTIONf_plane_restr0.0092158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.46082190.43654914X-RAY DIFFRACTION96
1.82-1.840.4442620.39794748X-RAY DIFFRACTION96
1.84-1.860.41132290.35264888X-RAY DIFFRACTION97
1.86-1.890.38082810.31814661X-RAY DIFFRACTION96
1.89-1.910.31833210.29044824X-RAY DIFFRACTION97
1.91-1.940.31192630.26894742X-RAY DIFFRACTION97
1.94-1.970.30992590.24264895X-RAY DIFFRACTION97
1.97-20.26382500.22884764X-RAY DIFFRACTION97
2-2.030.26832470.22254836X-RAY DIFFRACTION97
2.03-2.060.25522600.2154848X-RAY DIFFRACTION97
2.06-2.10.2552930.2124808X-RAY DIFFRACTION97
2.1-2.130.25072840.2144879X-RAY DIFFRACTION97
2.13-2.180.25162760.2144736X-RAY DIFFRACTION97
2.18-2.220.23473020.20644837X-RAY DIFFRACTION98
2.22-2.270.24382630.20464908X-RAY DIFFRACTION98
2.27-2.320.21542500.18054841X-RAY DIFFRACTION98
2.32-2.380.24082510.17874845X-RAY DIFFRACTION98
2.38-2.440.22062360.18054925X-RAY DIFFRACTION98
2.44-2.510.22782210.19364881X-RAY DIFFRACTION98
2.51-2.60.2422760.18984893X-RAY DIFFRACTION98
2.6-2.690.24342600.18484887X-RAY DIFFRACTION98
2.69-2.80.21842800.18174877X-RAY DIFFRACTION98
2.8-2.920.22532620.18834874X-RAY DIFFRACTION98
2.92-3.080.23682540.19264962X-RAY DIFFRACTION99
3.08-3.270.21852480.19154905X-RAY DIFFRACTION99
3.27-3.520.222880.1834917X-RAY DIFFRACTION99
3.52-3.880.18243000.16224889X-RAY DIFFRACTION99
3.88-4.440.15823500.13874847X-RAY DIFFRACTION99
4.44-5.590.15412690.13844921X-RAY DIFFRACTION99
5.59-39.140.16092150.14575027X-RAY DIFFRACTION100
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)
12.47291.83291.07836.8264-0.13481.75970.00790.5258-0.0782-0.88250.0046-0.3529-0.0260.258-0.02040.25330.05320.06010.41210.0760.181616.9211-13.9518-20.1353
20.84310.09320.05641.52340.20790.56110.05240.10930.2862-0.0484-0.0759-0.0214-0.08620.01320.0270.17710.0309-0.00940.22040.07920.23367.70712.0077-5.2043
32.2171-1.6376-1.2042.73261.51721.656-0.01530.02590.13730.0906-0.01870.2180.0026-0.20020.0520.17630.0399-0.00070.20290.04770.2531-8.2919-2.25463.7903
42.7625-0.82150.46942.62250.56332.1403-0.0163-0.0191-0.04950.0171-0.04430.6147-0.0513-0.27490.05060.21760.0521-0.03270.25740.0310.3794-16.07494.88182.588
50.9469-0.40810.0111.09730.23760.3681-0.0514-0.03250.15040.08090.02030.0975-0.0562-0.0170.02340.1920.02630.0110.18010.03880.23661.8794-0.25976.1805
63.418-0.51041.49592.14351.47462.5254-0.09760.78010.3544-0.51630.04620.0203-0.05890.10720.03670.29170.0594-0.03250.30860.05370.1424-0.0038-17.3826-22.8791
71.0123-0.13840.16611.6442-0.36180.9650.03980.1742-0.1772-0.08260.02060.23520.0579-0.1199-0.05730.20150.0176-0.04750.2779-0.03160.2542-10.564-31.3098-8.3808
83.23881.87370.21196.0166-0.96761.90970.144-0.4513-0.48990.463-0.0835-0.14460.08140.008-0.04110.24890.01430.00060.25950.01160.2631-8.2181-48.21513.3455
92.30920.1015-0.3672.5685-0.75812.38680.00410.0449-0.39760.0096-0.0205-0.11690.20620.10850.01240.21260.0247-0.01370.2146-0.03640.3226-5.8581-51.82124.4367
100.76540.5515-0.12131.5877-0.42970.10980.06450.006-0.07960.1616-0.05950.0924-0.0275-0.02690.00080.19690.0081-0.01880.2158-0.01670.2231-7.7733-35.69023.0986
114.76060.4175-2.0162.8428-1.11693.32440.0448-0.0674-0.36240.2988-0.03780.34760.083-0.20670.02990.19320.02780.01690.22760.01750.2754-18.212-28.29296.6584
121.57250.3209-0.09961.91460.49691.2203-0.0670.07050.1135-0.32770.0436-0.1463-0.03050.065-0.01550.3043-0.04380.04160.17670.04760.219812.04654.6538-54.3949
131.2357-0.30330.01341.63180.69671.3283-0.0656-0.11320.0873-0.0148-0.0630.1003-0.0227-0.17060.12760.251-0.0376-0.0140.2279-0.01160.18870.10944.3331-42.0989
144.151-1.1393-2.33523.57370.40985.0853-0.07470.06050.2263-0.3263-0.1380.3525-0.1054-0.71570.21510.3011-0.0138-0.08030.3634-0.06990.2632-11.47835.0795-38.0914
155.23791.4066-0.30014.8039-0.07372.89480.04790.05520.6328-0.2306-0.30010.2592-0.4717-0.54970.22750.40260.0706-0.0520.4248-0.10140.3466-12.247813.9379-35.303
161.8392-0.4942-0.8031.57910.53753.2874-0.1161-0.35960.2760.21480.0730.1058-0.0825-0.16560.0540.2386-0.0124-0.01510.2836-0.06850.2717-3.14087.4025-32.8455
172.4669-0.03512.2791.4730.61484.29170.06340.1088-0.0698-0.1524-0.0069-0.13890.1062-0.0898-0.0530.3115-0.03910.06530.1864-0.00770.187714.025-7.4683-49.1457
183.3975-0.14930.14111.7385-0.22213.4784-0.022-0.45270.2140.54060.035-0.0895-0.1037-0.0144-0.0370.2696-0.063-0.00260.2802-0.05020.233313.61646.7225-32.0703
192.9556-2.2903-0.74655.3462-0.66631.05830.40130.7337-0.2351-0.7397-0.28840.11880.33760.355-0.14550.27440.0370.01310.3281-0.09210.183511.4872-30.6812-20.8176
201.2485-0.63730.17852.2377-0.2210.51250.02760.1091-0.12040.0296-0.0381-0.31190.05060.10890.02190.16090.03070.00580.1998-0.00790.220124.7804-30.3769-2.5721
212.5339-0.31530.18850.721-0.72112.49290.06580.03850.29010.6309-0.0947-0.488-0.52790.56330.06020.4254-0.0604-0.16650.33480.02090.400733.9496-13.958914.9196
222.2064-1.5446-0.19098.72011.29372.5259-0.20520.00290.05120.04160.185-1.1784-0.25960.7177-0.01610.4284-0.0625-0.06590.5510.08150.54441.1913-17.4310.2356
233.9833-1.62841.72750.6844-0.51292.83770.31520.0008-0.32710.6677-0.0912-1.00030.40470.8778-0.08360.4930.0491-0.24410.4474-0.01660.560336.7068-23.055216.3135
240.83610.21220.16221.74450.00711.32370.0775-0.0232-0.07330.3364-0.0688-0.15420.16240.0907-0.0070.2090.0487-0.03220.19960.01150.181619.9785-24.94234.5315
251.31420.25040.43692.5714-0.07483.086-0.0782-0.3818-0.25610.40950.0868-0.29440.10360.06950.01270.2620.0176-0.06580.21960.0310.23622.1682-36.257113.3446
268.91971.3021-1.21552.00780.49192.5587-0.20950.89060.3057-0.62910.22570.0572-0.1715-0.31890.010.4823-0.0574-0.05010.2922-0.01550.21-3.7147-9.1724-65.3507
271.2227-0.2666-0.2291.8671-0.32660.9859-0.026-0.0113-0.1332-0.18710.03180.33570.0874-0.105-0.00440.2813-0.0891-0.02840.2719-0.06010.2732-13.6977-24.4885-50.8076
281.05360.8422-1.04331.8718-1.32911.23770.00960.0106-0.11-0.0589-0.08-0.0770.2227-0.07310.03670.3043-0.09260.01170.2668-0.05450.21540.8774-29.4171-47.5717
293.6747-0.7255-5.26692.8242-0.16518.2931-0.0691-0.9947-0.66090.1119-0.0883-0.70760.42880.79520.1680.4112-0.0738-0.10180.43110.0710.5178-0.1101-52.762-33.2176
301.97270.7091-0.40891.64-0.67721.21390.00120.0473-0.2623-0.1551-0.0211-0.14170.0889-0.03470.02610.3459-0.08240.00710.2952-0.07930.3616-6.3428-44.8521-41.7787
310.76350.5653-0.33691.5926-0.20730.14920.0571-0.0932-0.04450.0885-0.0979-0.0620.0047-0.02010.04780.3224-0.08690.00050.2676-0.03450.2104-3.1649-26.2745-43.2604
322.5729-1.3085-0.09362.0898-0.34645.41390.0971-0.4446-0.23710.2769-0.08450.15060.1805-0.21930.00760.2849-0.09860.03150.3316-0.0160.222-13.742-24.5577-34.2834
331.4458-0.44540.18111.8607-0.13020.7272-0.01250.111-0.0812-0.0621-0.0656-0.14110.06240.0450.06440.3339-0.04620.08590.2208-0.02670.206422.1166-23.7353-57.1367
341.9391-0.24810.64220.7550.00230.6404-0.1261-0.18190.22650.07360.0042-0.5435-0.02650.25690.17130.4166-0.05130.01870.4097-0.03640.549433.9566-15.2105-40.576
352.0301-0.24350.90541.60970.06711.5095-0.2699-0.4505-0.02720.30510.2329-0.19520.0836-0.0084-0.07260.40590.03140.02020.29390.01470.289626.1531-31.9448-38.7025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 111 )
3X-RAY DIFFRACTION3chain 'A' and (resid 112 through 143 )
4X-RAY DIFFRACTION4chain 'A' and (resid 144 through 189 )
5X-RAY DIFFRACTION5chain 'A' and (resid 190 through 301 )
6X-RAY DIFFRACTION6chain 'B' and (resid 22 through 41 )
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 124 )
8X-RAY DIFFRACTION8chain 'B' and (resid 125 through 143 )
9X-RAY DIFFRACTION9chain 'B' and (resid 144 through 189 )
10X-RAY DIFFRACTION10chain 'B' and (resid 190 through 251 )
11X-RAY DIFFRACTION11chain 'B' and (resid 252 through 301 )
12X-RAY DIFFRACTION12chain 'C' and (resid 22 through 65 )
13X-RAY DIFFRACTION13chain 'C' and (resid 66 through 152 )
14X-RAY DIFFRACTION14chain 'C' and (resid 153 through 169 )
15X-RAY DIFFRACTION15chain 'C' and (resid 170 through 189 )
16X-RAY DIFFRACTION16chain 'C' and (resid 190 through 235 )
17X-RAY DIFFRACTION17chain 'C' and (resid 236 through 251 )
18X-RAY DIFFRACTION18chain 'C' and (resid 252 through 301 )
19X-RAY DIFFRACTION19chain 'D' and (resid 22 through 41 )
20X-RAY DIFFRACTION20chain 'D' and (resid 42 through 124 )
21X-RAY DIFFRACTION21chain 'D' and (resid 125 through 169 )
22X-RAY DIFFRACTION22chain 'D' and (resid 170 through 189 )
23X-RAY DIFFRACTION23chain 'D' and (resid 190 through 209 )
24X-RAY DIFFRACTION24chain 'D' and (resid 210 through 251 )
25X-RAY DIFFRACTION25chain 'D' and (resid 252 through 301 )
26X-RAY DIFFRACTION26chain 'E' and (resid 23 through 41 )
27X-RAY DIFFRACTION27chain 'E' and (resid 42 through 107 )
28X-RAY DIFFRACTION28chain 'E' and (resid 108 through 133 )
29X-RAY DIFFRACTION29chain 'E' and (resid 134 through 152 )
30X-RAY DIFFRACTION30chain 'E' and (resid 153 through 209 )
31X-RAY DIFFRACTION31chain 'E' and (resid 210 through 251 )
32X-RAY DIFFRACTION32chain 'E' and (resid 252 through 301 )
33X-RAY DIFFRACTION33chain 'F' and (resid 22 through 122 )
34X-RAY DIFFRACTION34chain 'F' and (resid 123 through 251 )
35X-RAY DIFFRACTION35chain 'F' and (resid 252 through 301 )

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  • 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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