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- PDB-5v0d: Crystal structure of human exonuclease 1 Exo1 (WT) in complex wit... -

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Basic information

Entry
Database: PDB / ID: 5v0d
TitleCrystal structure of human exonuclease 1 Exo1 (WT) in complex with 5' flap DNA (f2II)
Components
  • (DNA (5'-D(P*GP*TP*AP*CP*TP*AP*GP*CP*G)- ...) x 2
  • DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*AP*CP*TP*CP*A)-3')
  • Exonuclease 1
KeywordsHYDROLASE/DNA / exonuclease / endonuclease / HYDROLASE-DNA complex
Function / homology
Function and homology information


double-stranded DNA 5'-3' DNA exonuclease activity / single-stranded DNA 5'-3' DNA exonuclease activity / flap endonuclease activity / t-circle formation / DNA strand resection involved in replication fork processing / 5'-flap endonuclease activity / humoral immune response mediated by circulating immunoglobulin / Impaired BRCA2 binding to PALB2 / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) ...double-stranded DNA 5'-3' DNA exonuclease activity / single-stranded DNA 5'-3' DNA exonuclease activity / flap endonuclease activity / t-circle formation / DNA strand resection involved in replication fork processing / 5'-flap endonuclease activity / humoral immune response mediated by circulating immunoglobulin / Impaired BRCA2 binding to PALB2 / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / 5'-3' exonuclease activity / 5'-3' DNA exonuclease activity / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / exonuclease activity / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / somatic hypermutation of immunoglobulin genes / mismatch repair / meiotic cell cycle / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / RNA-DNA hybrid ribonuclease activity / Processing of DNA double-strand break ends / DNA recombination / Regulation of TP53 Activity through Phosphorylation / Hydrolases; Acting on ester bonds / nuclear body / DNA repair / chromatin binding / DNA binding / nucleoplasm / metal ion binding / nucleus / plasma membrane
Similarity search - Function
Exonuclease-1, H3TH domain / Exonuclease 1-like, PIN-like domain / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region ...Exonuclease-1, H3TH domain / Exonuclease 1-like, PIN-like domain / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / 5'-nuclease / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Exonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsShi, Y. / Beese, L.S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM091487 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA092584 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Interplay of catalysis, fidelity, threading, and processivity in the exo- and endonucleolytic reactions of human exonuclease I.
Authors: Shi, Y. / Hellinga, H.W. / Beese, L.S.
History
DepositionFeb 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...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 / struct_conn
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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Z: Exonuclease 1
A: DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*AP*CP*TP*CP*A)-3')
B: DNA (5'-D(P*GP*TP*AP*CP*TP*AP*GP*CP*G)-3')
E: DNA (5'-D(P*GP*TP*AP*CP*TP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9707
Polymers47,8994
Non-polymers723
Water1,26170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-56 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.976, 72.976, 180.612
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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DNA (5'-D(P*GP*TP*AP*CP*TP*AP*GP*CP*G)- ... , 2 types, 2 molecules BE

#3: DNA chain DNA (5'-D(P*GP*TP*AP*CP*TP*AP*GP*CP*G)-3')


Mass: 2755.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*TP*AP*CP*TP*AP*GP*CP*G)-3')


Mass: 861.624 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / DNA chain , 2 types, 2 molecules ZA

#1: Protein Exonuclease 1 / hExo1 / Exonuclease I / hExoI


Mass: 40354.762 Da / Num. of mol.: 1 / Fragment: UNP residues 1-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EXO1, EXOI, HEX1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UQ84, Hydrolases; Acting on ester bonds
#2: DNA chain DNA (5'-D(*CP*GP*CP*TP*AP*GP*TP*AP*CP*TP*CP*A)-3')


Mass: 3926.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 73 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM sodium acetate, pH 7.0, 10 mM potassium chloride, 2-4% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 18, 2016
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: 2.63→50 Å / Num. obs: 27368 / % possible obs: 98.9 % / Redundancy: 4.73 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.06 / Net I/σ(I): 16.08
Reflection shellResolution: 2.63→2.79 Å / Redundancy: 4.72 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.17 / Num. unique obs: 4490 / CC1/2: 0.82 / Rrim(I) all: 0.661 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3QEA

3qea


Resolution: 2.63→33.98 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.67
RfactorNum. reflection% reflection
Rfree0.237 2227 8.14 %
Rwork0.205 --
obs0.208 27346 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.63→33.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 468 3 70 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023306
X-RAY DIFFRACTIONf_angle_d0.5094550
X-RAY DIFFRACTIONf_dihedral_angle_d15.4611275
X-RAY DIFFRACTIONf_chiral_restr0.02513
X-RAY DIFFRACTIONf_plane_restr0.002505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6313-2.68850.32781260.33121602X-RAY DIFFRACTION99
2.6885-2.7510.39461410.32161569X-RAY DIFFRACTION100
2.751-2.81970.31391560.30761587X-RAY DIFFRACTION100
2.8197-2.89590.32681330.28731593X-RAY DIFFRACTION100
2.8959-2.98110.31921360.2891572X-RAY DIFFRACTION100
2.9811-3.07730.32391410.2831577X-RAY DIFFRACTION100
3.0773-3.18720.32341510.25791598X-RAY DIFFRACTION100
3.1872-3.31470.2911390.23961594X-RAY DIFFRACTION100
3.3147-3.46540.22931400.23331593X-RAY DIFFRACTION100
3.4654-3.64790.29161440.22561561X-RAY DIFFRACTION100
3.6479-3.87620.23341390.22111565X-RAY DIFFRACTION99
3.8762-4.17490.1971390.20351567X-RAY DIFFRACTION98
4.1749-4.59420.25121400.17771544X-RAY DIFFRACTION98
4.5942-5.25690.22031390.17381545X-RAY DIFFRACTION97
5.2569-6.61510.24331350.19641535X-RAY DIFFRACTION97
6.6151-33.98350.1571280.14861517X-RAY DIFFRACTION95
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)
13.9242-1.1118-0.10943.79932.8453.42121.12040.4173-0.2336-1.37970.49070.33681.1872-0.3886-1.40371.36940.2144-0.11721.10060.39721.4907-23.653346.5814-20.8202
22.6569-2.8272-0.45537.33516.92469.61770.6499-2.8699-2.4228-0.8653-1.81171.21081.13010.52640.80931.76890.02460.18541.26870.59491.6058-29.188338.0832-9.053
36.2221-2.90120.53862.9033-2.86764.43550.22160.4964-1.98630.40810.8951.70741.7027-0.8236-1.1091.8263-0.2904-0.50210.98480.34431.808-22.96121.5555-5.9699
46.8269-0.7965-2.48088.6544-1.16449.23390.48120.30730.211-0.62991.021.9342-0.6504-0.3942-1.45970.87380.0531-0.09320.70770.08381.3089-19.777433.2322-11.5766
55.53370.3844-4.70240.1413-0.90947.33592.39040.8557-0.4321.2785-2.17021.3438-1.4351-0.9594-0.69191.3841-0.0219-0.36071.01570.52991.9071-31.659544.3788-19.3458
62.17572.80550.41175.19640.99555.9204-0.2255-3.41780.64661.8068-0.05450.0002-0.22092.33580.92051.8659-0.1338-0.03431.48560.12210.944710.459225.19971.9929
70.85271.95330.58156.4132-1.63217.00620.17870.5769-0.6524-0.83330.17180.48010.86580.0788-0.32670.7670.0677-0.00980.6837-0.22060.7173-6.194627.8267-16.8444
82.8718-2.0225-2.85874.67164.24827.9957-0.52350.1906-0.8320.4073-0.18030.8720.23620.41720.98081.1552-0.01470.0140.51860.12620.9992-12.384625.2421-1.8196
95.0227-1.3813-2.3533.1348-0.24743.6687-0.0365-1.1335-0.16560.67670.71192.06752.3544-1.9772-0.5351.2871-0.43360.03211.0750.29281.084-22.365219.94437.8541
106.1755-1.45520.383.37090.42864.4845-0.20030.4008-1.55570.3991-0.17580.45562.4895-0.01840.5091.71670.0730.00430.5547-0.08321.0636-7.948215.2675-3.2037
114.64692.23381.68637.4619-2.12667.20380.1093-0.799-0.19450.78690.00130.5723-0.02960.4268-0.08940.587-0.02520.01750.6214-0.08230.591-4.20832.51291.0854
123.55111.6016-0.01054.99390.85424.3039-0.3746-1.0424-0.09360.85150.0975-0.0052-0.4364-0.30430.13621.36730.08280.2371.0324-0.04861.2539-22.27737.67975.6434
137.53712.64522.45653.47513.4523.43830.81230.98331.05960.98270.56491.85411.4945-2.3367-1.79821.7328-0.48790.27262.2931-0.08281.613-36.909426.548210.2821
148.49440.5276-5.13452.2104-3.09599.68162.05651.7462.56711.5023-0.74091.9372-0.0807-2.6438-1.15951.5019-0.17140.34251.53930.24431.6769-28.611325.92093.236
155.71932.62940.25615.2115-0.76195.54450.9812-0.1458-0.55151.1996-0.331-0.57591.54970.4733-0.6551.44710.1436-0.14970.6327-0.05910.7254-4.084220.53786.0342
163.31282.3007-0.93394.6524-2.39036.38510.159-0.04040.0950.2494-0.1201-0.1187-0.17960.9069-0.03930.72870.0758-0.04180.7449-0.10820.6778-0.683632.5223-5.6951
175.8588-2.442-0.8138.8480.17066.50780.22050.008-0.66120.5953-0.2884-0.10181.07820.06020.04890.73210.0291-0.10570.5464-0.08870.5536-6.481627.2657-14.5337
187.8762-3.3856-4.2473.8905-0.78676.1130.99380.8893-0.0125-1.047-1.2406-0.1425-0.27110.30390.18110.78740.04390.05180.9799-0.1570.7332-3.565840.8377-23.9974
192.1358-2.4004-0.98442.49261.14535.75880.1911-0.55820.03820.1977-0.00090.5716-1.26410.3453-0.28240.8216-0.06240.06180.5136-0.08320.7328-8.346946.7522-12.0616
203.3608-0.84352.65345.8206-0.48423.52630.35910.8246-0.1092-0.2255-0.05011.201-1.0827-0.5638-0.39911.11040.09830.10520.566-0.02460.8567-14.241651.2672-18.9414
217.5615-2.48811.65755.58690.2567.510.92310.44662.1466-0.6358-0.4814-0.0105-1.60120.173-0.31831.23310.00820.10120.58840.12561.0396-9.931760.1604-18.7257
225.36171.90894.24155.183.47824.283-0.966-0.50740.62052.27660.98861.3961-3.05860.4620.06491.739-0.07480.26580.726-0.25571.0319-9.425257.2448-5.6165
232.98852.26861.62515.6036-2.21499.2080.0866-0.02840.67260.4571-0.4923-0.9627-1.05682.04240.2850.6027-0.15580.00150.9606-0.1160.63634.872740.3909-1.2135
247.3539-1.3436-1.93861.8233-0.99311.6010.3512-0.35731.19680.60340.0553-0.2716-2.22951.8281-0.4461.3894-0.5094-0.12291.1225-0.2140.96326.175752.7441-1.1518
250.9705-1.2861.59795.5078-1.53029.96180.6833-0.08850.18820.8186-0.6616-0.294-0.50341.4001-0.08640.9178-0.18-0.01670.969-0.08380.75183.248838.04848.9014
263.09463.6848-1.40458.92670.91252.72620.3527-1.0915-1.17182.36030.44190.13721.93190.5402-0.86511.1377-0.0444-0.08460.97170.04540.7735-3.184429.872115.6501
275.09314.4338-6.19826.9121-5.02267.59450.7653-2.3757-5.3740.0133-1.7104-1.54560.47782.6530.81521.40510.4896-0.16521.57850.19431.2648.911520.725711.8805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:4)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 5:8)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 9:12)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 1:4)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 5:9)
6X-RAY DIFFRACTION6(CHAIN Z AND RESID 355:357)
7X-RAY DIFFRACTION7(CHAIN Z AND RESID 2:31)
8X-RAY DIFFRACTION8(CHAIN Z AND RESID 32:37)
9X-RAY DIFFRACTION9(CHAIN Z AND RESID 38:51)
10X-RAY DIFFRACTION10(CHAIN Z AND RESID 52:71)
11X-RAY DIFFRACTION11(CHAIN Z AND RESID 72:85)
12X-RAY DIFFRACTION12(CHAIN Z AND RESID 86:103)
13X-RAY DIFFRACTION13(CHAIN Z AND RESID 104:111)
14X-RAY DIFFRACTION14(CHAIN Z AND RESID 112:124)
15X-RAY DIFFRACTION15(CHAIN Z AND RESID 125:144)
16X-RAY DIFFRACTION16(CHAIN Z AND RESID 145:173)
17X-RAY DIFFRACTION17(CHAIN Z AND RESID 174:195)
18X-RAY DIFFRACTION18(CHAIN Z AND RESID 196:213)
19X-RAY DIFFRACTION19(CHAIN Z AND RESID 214:227)
20X-RAY DIFFRACTION20(CHAIN Z AND RESID 228:244)
21X-RAY DIFFRACTION21(CHAIN Z AND RESID 245:267)
22X-RAY DIFFRACTION22(CHAIN Z AND RESID 268:277)
23X-RAY DIFFRACTION23(CHAIN Z AND RESID 278:300)
24X-RAY DIFFRACTION24(CHAIN Z AND RESID 301:310)
25X-RAY DIFFRACTION25(CHAIN Z AND RESID 311:328)
26X-RAY DIFFRACTION26(CHAIN Z AND RESID 329:339)
27X-RAY DIFFRACTION27(CHAIN Z AND RESID 340:346)

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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

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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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