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- PDB-4lte: Structure of Cysteine-free Human Insulin Degrading Enzyme in Comp... -

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Basic information

Entry
Database: PDB / ID: 4lte
TitleStructure of Cysteine-free Human Insulin Degrading Enzyme in Complex with Macrocyclic Inhibitor
Components
  • Insulin-degrading enzyme
  • Macrocyclic Inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / METAL-BINDING / METALLOPROTEASE / PROTEASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / insulin binding / regulation of aerobic respiration / peptide catabolic process ...insulysin / ubiquitin recycling / insulin catabolic process / insulin metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / insulin binding / regulation of aerobic respiration / peptide catabolic process / amyloid-beta clearance / peroxisomal matrix / amyloid-beta metabolic process / Insulin receptor recycling / peptide binding / proteolysis involved in protein catabolic process / Peroxisomal protein import / protein catabolic process / antigen processing and presentation of endogenous peptide antigen via MHC class I / metalloendopeptidase activity / positive regulation of protein catabolic process / positive regulation of protein binding / peroxisome / insulin receptor signaling pathway / virus receptor activity / basolateral plasma membrane / endopeptidase activity / Ub-specific processing proteases / external side of plasma membrane / cell surface / protein homodimerization activity / mitochondrion / proteolysis / extracellular space / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / : / PQQ synthase PqqF-like, C-terminal lobe domain 4 / : / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal ...Peptidase M16, middle/third domain / Middle or third domain of peptidase_M16 / : / PQQ synthase PqqF-like, C-terminal lobe domain 4 / : / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FUMARIC ACID / 2,6-DIAMINO-HEXANOIC ACID AMIDE / Insulin-degrading enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.705 Å
AuthorsFoda, Z.H. / Seeliger, M.A. / Saghatelian, A. / Liu, D.R.
CitationJournal: Nature / Year: 2014
Title: Anti-diabetic activity of insulin-degrading enzyme inhibitors mediated by multiple hormones.
Authors: Maianti, J.P. / McFedries, A. / Foda, Z.H. / Kleiner, R.E. / Du, X.Q. / Leissring, M.A. / Tang, W.J. / Charron, M.J. / Seeliger, M.A. / Saghatelian, A. / Liu, D.R.
History
DepositionJul 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Jul 23, 2014Group: Database references
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / software / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _software.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr2_label_atom_id
Revision 3.0Apr 24, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _pdbx_struct_mod_residue.label_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Insulin-degrading enzyme
B: Insulin-degrading enzyme
M: Macrocyclic Inhibitor
N: Macrocyclic Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)228,60312
Polymers227,4714
Non-polymers1,1328
Water10,142563
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A: Insulin-degrading enzyme
M: Macrocyclic Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3026
Polymers113,7362
Non-polymers5664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-31 kcal/mol
Surface area37600 Å2
MethodPISA
2
B: Insulin-degrading enzyme
N: Macrocyclic Inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,3026
Polymers113,7362
Non-polymers5664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-30 kcal/mol
Surface area37700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)261.973, 261.973, 90.775
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABMN

#1: Protein Insulin-degrading enzyme / Abeta-degrading protease / Insulin protease / Insulinase / Insulysin


Mass: 113191.031 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 42-1019
Mutation: C110L, E111Q, C171S, C178A, C257V, C414L, C573N, C590S, C789S, C812A, C819A, C904S, C966N, C974A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IDE / Plasmid: PPROEX-H6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14735, insulysin
#2: Protein/peptide Macrocyclic Inhibitor


Mass: 544.598 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 571 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-LYN / 2,6-DIAMINO-HEXANOIC ACID AMIDE


Type: L-peptide linking / Mass: 146.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H16N3O
#6: Chemical ChemComp-FUM / FUMARIC ACID


Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 563 / Source method: isolated from a natural source / Formula: H2O

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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: 4.01 Å3/Da / Density % sol: 69.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 20 % PEGMME-5000, 12 % tacsimate, 10 % dioxane, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.7 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2012
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7 Å / Relative weight: 1
ReflectionResolution: 2.705→130.99 Å / Num. all: 97302 / Num. obs: 97263 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.7047-2.7635199
2.7635-2.82781100
2.8278-2.89861100
2.8986-2.97691100
2.9769-3.06451100
3.0645-3.16351100
3.1635-3.27651100
3.2765-3.40771100
3.4077-3.56281100
3.5628-3.75071100
3.7507-3.98571100
3.9857-4.29351100
4.2935-4.72551100
4.7255-5.40941100
5.4094-6.81521100
6.8152-227.681100

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
autoPROCdata scaling
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YPU

2ypu


Resolution: 2.705→130.986 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 19.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 2214 2.28 %
Rwork0.1575 --
obs0.1584 97263 99.92 %
all-97302 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.1429 Å2
Refinement stepCycle: LAST / Resolution: 2.705→130.986 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15621 0 32 563 16216
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01116052
X-RAY DIFFRACTIONf_angle_d1.27321723
X-RAY DIFFRACTIONf_dihedral_angle_d15.786048
X-RAY DIFFRACTIONf_chiral_restr0.0592331
X-RAY DIFFRACTIONf_plane_restr0.0082812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7047-2.76350.30451380.25375886X-RAY DIFFRACTION99
2.7635-2.82780.25681390.22685903X-RAY DIFFRACTION100
2.8278-2.89860.24751360.20955894X-RAY DIFFRACTION100
2.8986-2.97690.28891360.20175935X-RAY DIFFRACTION100
2.9769-3.06450.22161360.19765896X-RAY DIFFRACTION100
3.0645-3.16350.23151370.18965900X-RAY DIFFRACTION100
3.1635-3.27650.27871410.18655917X-RAY DIFFRACTION100
3.2765-3.40770.24911380.17845909X-RAY DIFFRACTION100
3.4077-3.56280.20361410.15745939X-RAY DIFFRACTION100
3.5628-3.75070.17691350.14465956X-RAY DIFFRACTION100
3.7507-3.98570.18811380.13435921X-RAY DIFFRACTION100
3.9857-4.29350.15811370.12525963X-RAY DIFFRACTION100
4.2935-4.72550.13161340.11185945X-RAY DIFFRACTION100
4.7255-5.40940.16241390.12645962X-RAY DIFFRACTION100
5.4094-6.81520.19321430.15586001X-RAY DIFFRACTION100
6.8152-131.14030.16791460.14286122X-RAY DIFFRACTION100
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)
12.9913-0.46880.24711.5032-0.17382.13130.06470.0352-0.3945-0.11530.020.24270.374-0.0641-0.0670.19420.04040.00520.2012-0.00050.2372-98.4461-90.8042.0626
20.79860.17860.06010.76030.04450.77350.010.0019-0.10020.0386-0.047-0.13720.01510.10650.02560.20780.07950.00380.24220.05620.2019-80.093-79.803211.7247
30.58080.14570.01210.9571-0.12660.57020.0308-0.1949-0.04640.2847-0.06030.08910.0054-0.00080.03110.2710.00930.02480.24860.02310.1435-101.9321-70.779230.8803
41.2295-0.8579-0.65050.63750.5260.55260.01070.0568-0.0637-0.0128-0.03570.13330.029-0.0855-0.02630.23030.01240.01730.24530.02430.2957-108.609-82.077513.2227
50.83940.52310.21791.54670.29530.53510.1453-0.3143-0.05090.5708-0.0758-0.1215-0.03510.132-0.03330.34060.0013-0.00070.33210.00530.1631-96.1881-66.9839.1382
60.70910.14860.13150.5916-0.03490.7977-0.05680.03040.09030.0120.06480.1384-0.0601-0.0323-0.00770.20470.0486-0.00010.17660.01710.2341-112.5635-55.40758.9596
70.91370.3670.03050.25730.13780.4353-0.008-0.02660.2043-0.0153-0.04820.1552-0.14220.08670.03820.29010.0495-0.00510.15310.0480.2978-100.7046-44.30718.0078
81.3604-0.19820.02320.70640.05840.38630.08390.07510.134-0.0847-0.0368-0.1151-0.03120.0874-0.02160.23840.02760.01270.20850.06370.1773-86.6205-53.3466-2.0216
91.4910.44730.16881.59820.15230.9912-0.02810.13380.0542-0.20570.0067-0.0761-0.07410.08770.01990.22740.02750.01190.22950.09370.1545-85.1785-55.5337-9.0068
101.91960.08820.32022.5311-0.64392.7462-0.0036-0.00090.33370.2542-0.0055-0.0993-0.41140.25120.02120.3369-0.11130.00410.24860.03440.2502-89.374820.3837-17.251
110.98650.1512-0.0140.69340.17980.5444-0.0180.0602-0.0202-0.09690.0003-0.059-0.02640.11190.02720.3003-0.01430.02830.22180.07560.2027-100.79057.1129-33.0876
120.9215-0.06530.22680.7340.01110.5255-0.016-0.1058-0.04810.27730.0031-0.11950.0845-0.0150.01080.4271-0.01760.00420.18550.03380.2046-104.7376-7.58774.7873
130.4557-0.0931-0.08490.844-0.04150.63350.0245-0.0156-0.13560.0722-0.0507-0.0070.1639-0.04440.0410.4340.00430.02410.18810.04870.2552-106.0622-21.3841-3.687
140.47680.09210.05331.0926-0.01521.3645-0.02580.0027-0.0491-0.0764-0.004-0.14030.16950.16040.03980.29360.05170.01410.21670.04850.2251-93.6626-18.884-18.6539
150.99860.27390.08231.81810.040.9761-0.03670.05190.0023-0.046-0.0796-0.31750.13840.25660.10970.29350.0659-0.00260.25150.05740.2723-86.2817-18.5131-19.9437
160.640.111-0.45140.7292-0.1771.35280.04710.0230.07660.0876-0.03080.0717-0.1705-0.08060.00670.256-0.00370.0280.16520.00770.2484-122.33858.5201-11.7144
170.31250.0505-0.18630.07360.07090.2234-0.00820.0560.07530.0041-0.0233-0.0042-0.0927-0.00370.02550.3962-0.0627-0.00790.2350.03360.2531-102.821517.2299-6.3305
181.64020.21740.05761.3477-0.06061.6269-0.07690.1245-0.0057-0.1186-0.04430.2801-0.0421-0.31460.10160.2423-0.00370.01440.20220.0380.2269-130.91035.1113-17.16
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 43:92)A43 - 92
2X-RAY DIFFRACTION2chain 'A' and (resseq 93:275)A93 - 275
3X-RAY DIFFRACTION3chain 'A' and (resseq 276:404)A276 - 404
4X-RAY DIFFRACTION4chain 'A' and (resseq 405:460)A405 - 460
5X-RAY DIFFRACTION5chain 'A' and (resseq 461:514)A461 - 514
6X-RAY DIFFRACTION6chain 'A' and (resseq 515:675)A515 - 675
7X-RAY DIFFRACTION7chain 'A' and (resseq 676:734)A676 - 734
8X-RAY DIFFRACTION8chain 'A' and (resseq 735:876)A735 - 876
9X-RAY DIFFRACTION9chain 'A' and (resseq 877:1011)A877 - 1011
10X-RAY DIFFRACTION10chain 'B' and (resseq 43:92)B43 - 92
11X-RAY DIFFRACTION11chain 'B' and (resseq 93:275)B93 - 275
12X-RAY DIFFRACTION12chain 'B' and (resseq 515:675)B515 - 675
13X-RAY DIFFRACTION13chain 'B' and (resseq 676:734)B676 - 734
14X-RAY DIFFRACTION14chain 'B' and (resseq 735:876)B735 - 876
15X-RAY DIFFRACTION15chain 'B' and (resseq 877:1011)B877 - 1011
16X-RAY DIFFRACTION16chain 'B' and (resseq 276:404)B276 - 404
17X-RAY DIFFRACTION17chain 'B' and (resseq 405:460)B405 - 460
18X-RAY DIFFRACTION18chain 'B' and (resseq 461:514)B461 - 514

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Major update of PDB

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  • 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

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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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