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- PDB-1s1u: Crystal structure of L100I mutant HIV-1 reverse transcriptase in ... -

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Entry
Database: PDB / ID: 1s1u
TitleCrystal structure of L100I mutant HIV-1 reverse transcriptase in complex with nevirapine
Components(Reverse transcriptase) x 2
KeywordsTRANSFERASE / HIV-1 REVERSE TRANSCRIPTASE / AIDS / NNRTI / NEVIRAPINE / DRUG RESISTANCE MUTATIONS
Function / homology
Function and homology information


integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus ...integrase activity / Integration of viral DNA into host genomic DNA / Autointegration results in viral DNA circles / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / 2-LTR circle formation / Vpr-mediated nuclear import of PICs / Early Phase of HIV Life Cycle / Integration of provirus / APOBEC3G mediated resistance to HIV-1 infection / Binding and entry of HIV virion / viral life cycle / Assembly Of The HIV Virion / HIV-1 retropepsin / : / Budding and maturation of HIV virion / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / protein processing / host multivesicular body / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / peptidase activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding
Similarity search - Function
HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NVP / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsRen, J. / Nichols, C.E. / Chamberlain, P.P. / Stammers, D.K.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structures of HIV-1 reverse transcriptases mutated at codons 100, 106 and 108 and mechanisms of resistance to non-nucleoside inhibitors
Authors: Ren, J. / Nichols, C.E. / Chamberlain, P.P. / Weaver, K.L. / Short, S.A. / Stammers, D.K.
#1: Journal: J.VIROL. / Year: 2002
Title: Crystal structures of Zidovudine- or Lamivudine-resistant human immunodeficiency virus type 1 reverse transcriptases containing mutations at codons 41, 184, and 215
Authors: Chamberlain, P.P. / Ren, J. / Nichols, C.E. / Douglas, L. / Lennerstrand, J. / Larder, B.A. / Stuart, D.I. / Stammers, D.K.
#2: Journal: J.Mol.Biol. / Year: 2001
Title: Structural Mechanisms of Drug Resistance for Mutations at Codons 181 and 188 in HIV-1 Reverse Transcriptase and the Improved Resilience of Second Generation Non-Nucleoside Inhibitors
Authors: Ren, J. / Nichols, C. / Bird, L. / Chamberlain, P. / Weaver, K.L. / Short, S.A. / Stuart, D.I. / Stammers, D.K.
#3: Journal: J.Med.Chem. / Year: 2001
Title: 2-Amino-6-Arylsulfonylbenzonitriles as Non-Nucleoside reverse Transcriptase Inhibitors of HIV-1
Authors: Chan, J.H. / Hong, J.S. / Hunter III, R.N. / Orr, G.F. / Cowan, J.R. / Sherman, D.B. / Sparks, S.M. / Reitter, B.E. / Andrews III, C.W. / Hazen, R.J. / St Clair, M. / Boone, L.R. / Ferris, R. ...Authors: Chan, J.H. / Hong, J.S. / Hunter III, R.N. / Orr, G.F. / Cowan, J.R. / Sherman, D.B. / Sparks, S.M. / Reitter, B.E. / Andrews III, C.W. / Hazen, R.J. / St Clair, M. / Boone, L.R. / Ferris, R.G. / Creech, K.L. / Roberts, G.B. / Short, S.A. / Weaver, K. / Ott, R.J. / Ren, J. / Hopkins, A. / Stuart, D.I. / Stammers, D.K.
#4: Journal: Structure / Year: 2000
Title: Structural Basis for the Resilience of Efavirenz (Dmp-266) to Drug Resistance Mutations in HIV-1 Reverse Transcriptase
Authors: Ren, J. / Milton, J. / Weaver, K.L. / Short, S.A. / Stuart, D.I. / Stammers, D.K.
#5: Journal: J.Biol.Chem. / Year: 2000
Title: Binding of the Second Generation Non-Nucleoside Inhibitor S-1153 to HIV-1 Reverse Transcriptase Involves Extensive Main Chain Hydrogen Bonding
Authors: Ren, J. / Nichols, C. / Bird, L.E. / Fujiwara, T. / Suginoto, H. / Stuart, D.I. / Stammers, D.K.
#6: Journal: J.Biol.Chem. / Year: 2000
Title: Phenethylthiazolylthiourea (Pett) Non-Nucleoside Inhibitors of HIV-1 and HIV-2 Reverse Transcriptases. Structural and Biochemical Analyses
Authors: Ren, J. / Diprose, J. / Warren, J. / Esnouf, R.M. / Bird, L.E. / Ikemizu, S. / Slater, M. / Milton, J. / Balzarini, J. / Stuart, D.I. / Stammers, D.K.
#7: Journal: J.Med.Chem. / Year: 1999
Title: Crystallographic Analysis of the Binding Modes of Thiazoloisoindolinone Non-Nucleoside Inhibitors to HIV-1 Reverse Transcriptase and Comparison with Modeling Studies
Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Stuart, D.I. / Stammers, D.K.
#8: Journal: J.Med.Chem. / Year: 1999
Title: Design of Mkc-442 (Emivirine) Analogues with Improved Activity Against Drug-Resistant HIV Mutants
Authors: Hopkins, A.L. / Ren, J. / Tanaka, H. / Baba, M. / Okamato, M. / Stuart, D.I. / Stammers, D.K.
#9: Journal: Biochemistry / Year: 1998
Title: Crystal Structures of HIV-1 Reverse Transcriptase in Complex with Carboxanilide Derivatives
Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Warren, J. / Balzarini, J. / Stuart, D.I. / Stammers, D.K.
#10: Journal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: 3'-Azido-3'-Deoxythymidine Drug Resistance Mutations in HIV-1 Reverse Transcriptase Can Induce Long Range Conformational Changes
Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Jones, E.Y. / Kirby, I. / Keeling, J. / Ross, C.K. / Larder, B.A. / Stuart, D.I. / Stammers, D.K.
#11: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Continuous and Discontinuous Changes in the Unit Cell of HIV-1 Reverse Transcriptase Crystals on Dehydration
Authors: Esnouf, R.M. / Ren, J. / Garman, E. / Somers, D.O. / Ross, C.K. / Jones, E.Y. / Stammers, D.K. / Stuart, D.I.
#12: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Unique Features in the Structure of the Complex between HIV-1 Reverse Transcriptase and the Bis(Heteroaryl)Piperazine (Bhap) U-90152 Explain Resistance Mutations for This Non-Nucleoside Inhibitor
Authors: Esnouf, R.M. / Ren, J. / Hopkins, A.L. / Ross, C.K. / Jones, E.Y. / Stammers, D.K. / Stuart, D.I.
#13: Journal: J.Med.Chem. / Year: 1996
Title: Complexes of HIV-1 Reverse Transcriptase with Inhibitors of the HEPT Series Reveal Conformational Changes Relevant to the Design of Potent Non-Nucleoside Inhibitors
Authors: L Hopkins, A. / Ren, J. / Esnouf, R.M. / Willcox, B.E. / Jones, E.Y. / Ross, C.K. / Miyasaka, T. / Walker, R.T. / Tanaka, H. / Stammers, D.K. / Stuart, D.I.
#14: Journal: Structure / Year: 1995
Title: The Structure of HIV-1 Reverse Transcriptase Complexed with 9-Chloro-TIBO: Lessons for Inhibitor Design
Authors: Ren, J. / Esnouf, R.M. / Hopkins, A.L. / Ross, C.K. / Jones, E.Y. / Stammers, D.K. / Stuart, D.I.
#15: Journal: Nat.Struct.Biol. / Year: 1995
Title: High Resolution Structures of HIV-1 RT from Four RT-Inhibitor Complexes
Authors: Ren, J. / Esnouf, R.M. / Garman, E. / Somers, D.O. / Ross, C.K. / Kirby, I. / Keeling, J. / Darby, G. / Jones, E.Y. / Stuart, D.I. / Stammers, D.K.
#16: Journal: Nat.Struct.Biol. / Year: 1995
Title: Mechanism of Inhibition of HIV-1 Reverse Transcriptase by Non-Nucleoside Inhibitors
Authors: Esnouf, R.M. / Ren, J. / Ross, C.K. / Jones, E.Y. / Stammers, D.K. / Stuart, D.I.
#17: Journal: J.Mol.Biol. / Year: 1994
Title: Crystals of HIV-1 Reverse Transcriptase Diffracting to 2.2 A Resolution
Authors: Stammers, D.K. / Somers, D.O. / Ross, C.K. / Kirby, I. / Ray, P.H. / Wilson, J.E. / Norman, M. / Ren, J. / Esnouf, R.M. / Garman, E. / Jones, E.Y. / Stuart, D.I.
History
DepositionJan 7, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Reverse transcriptase
B: Reverse transcriptase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2603
Polymers115,9942
Non-polymers2661
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-29 kcal/mol
Surface area44930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.800, 115.500, 66.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Reverse transcriptase / / HIV-1 RT


Mass: 64594.949 Da / Num. of mol.: 1 / Fragment: P66 / Mutation: L100I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Plasmid: PKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): HXB2 / References: UniProt: P04585, RNA-directed DNA polymerase
#2: Protein Reverse transcriptase / / HIV-1 RT


Mass: 51399.047 Da / Num. of mol.: 1 / Fragment: P51 / Mutation: L100I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Gene: POL / Plasmid: PKK233-2 / Production host: Escherichia coli (E. coli) / Strain (production host): HXB2 / References: UniProt: P04585, RNA-directed DNA polymerase
#3: Chemical ChemComp-NVP / 11-CYCLOPROPYL-5,11-DIHYDRO-4-METHYL-6H-DIPYRIDO[3,2-B:2',3'-E][1,4]DIAZEPIN-6-ONE / NON-NUCLEOSIDE RT INHIBITOR NEVIRAPINE / Nevirapine


Mass: 266.298 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H14N4O / Comment: medication, antiretroviral*YM

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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: 2.48 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jun 4, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 21774 / % possible obs: 98.6 % / Observed criterion σ(I): -0.5 / Redundancy: 4.09 % / Biso Wilson estimate: 84.6 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.59 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1 / Num. unique all: 2119 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→29.9 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2599523.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: THE STANDARD CRYSTALLOGRAPHIC RESIDUAL WAS USED AS TARGET FUNCTION IN THE FINAL ROUND OF REFINEMENT INCLUDING ALL THE REFLECTIONS INSTEAD OF THE MLF IN THE PREVIOUS ROUNDS OF REFINEMENT WITH ...Details: THE STANDARD CRYSTALLOGRAPHIC RESIDUAL WAS USED AS TARGET FUNCTION IN THE FINAL ROUND OF REFINEMENT INCLUDING ALL THE REFLECTIONS INSTEAD OF THE MLF IN THE PREVIOUS ROUNDS OF REFINEMENT WITH CROSS-VALIDATION, WHICH RESULTED IN THE R-FACTOR FOR ALL DATA BEING SMALLER THAN R-WORKING. DUE TO THE LOW RATIO BETWEEN THE NUMBER OF REFLECTIONS AND THE NUMBER OF PARAMETERS TO BE REFINED, POSITIONAL RESTRAINTS WERE APPLIED TO ALL ATOMS DISTANT FROM THE NNRTI-BINDING SITE(DEFINED AS ATOMS MORE THAN 25 ANGSTROM FROM THE CA ATOM OF TYR188) THROUGHOUT THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1060 4.9 %RANDOM
Rwork0.227 ---
obs0.219 21738 98.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9817 Å2 / ksol: 0.303661 e/Å3
Displacement parametersBiso mean: 91 Å2
Baniso -1Baniso -2Baniso -3
1--8.5 Å20 Å20 Å2
2---6.07 Å20 Å2
3---14.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.4 Å
Luzzati d res low-30 Å
Luzzati sigma a0.55 Å0.52 Å
Refinement stepCycle: LAST / Resolution: 3→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7640 0 20 0 7660
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.623
X-RAY DIFFRACTIONc_mcangle_it6.266
X-RAY DIFFRACTIONc_scbond_it5.264
X-RAY DIFFRACTIONc_scangle_it8.78
LS refinement shellResolution: 3→3.11 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.378 96 4.5 %
Rwork0.361 2016 -
obs--97.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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