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- PDB-4kvo: The NatA (Naa10p/Naa15p) amino-terminal acetyltrasferase complex ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4kvo
TitleThe NatA (Naa10p/Naa15p) amino-terminal acetyltrasferase complex bound to AcCoA
Components(N-terminal acetyltransferase A complex ...) x 2
KeywordsTRANSFERASE / acetyltransferase / tetratricopeptide repeats (TPR motif) / amino-terminal acetyltransferase
Function / homology
Function and homology information


peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / acetyltransferase activator activity / protein maturation / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1010 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1040 / N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / TPR repeat region circular profile. ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1010 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #1040 / N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / N-acetyltransferase Ard1-like / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / TPR repeat region circular profile. / Acyl-CoA N-acyltransferase / Tetratricopeptide repeats / Aminopeptidase / Tetratricopeptide repeat / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / N-terminal acetyltransferase A complex subunit nat1 / N-terminal acetyltransferase A complex catalytic subunit ard1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.15 Å
AuthorsLiszczak, G.P. / Marmorstein, R.Q.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: Molecular basis for N-terminal acetylation by the heterodimeric NatA complex.
Authors: Liszczak, G. / Goldberg, J.M. / Foyn, H. / Petersson, E.J. / Arnesen, T. / Marmorstein, R.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Oct 9, 2013Group: 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_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 / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _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

Downloads & links

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Assembly

Deposited unit
A: N-terminal acetyltransferase A complex subunit nat1
B: N-terminal acetyltransferase A complex subunit nat1
C: N-terminal acetyltransferase A complex subunit nat1
D: N-terminal acetyltransferase A complex subunit nat1
E: N-terminal acetyltransferase A complex catalytic subunit ard1
F: N-terminal acetyltransferase A complex catalytic subunit ard1
G: N-terminal acetyltransferase A complex catalytic subunit ard1
H: N-terminal acetyltransferase A complex catalytic subunit ard1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)413,66882
Polymers407,8898
Non-polymers5,77974
Water1,892105
1
A: N-terminal acetyltransferase A complex subunit nat1
E: N-terminal acetyltransferase A complex catalytic subunit ard1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,55024
Polymers101,9722
Non-polymers1,57722
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-terminal acetyltransferase A complex subunit nat1
F: N-terminal acetyltransferase A complex catalytic subunit ard1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,34919
Polymers101,9722
Non-polymers1,37717
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: N-terminal acetyltransferase A complex subunit nat1
G: N-terminal acetyltransferase A complex catalytic subunit ard1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,40821
Polymers101,9722
Non-polymers1,43519
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: N-terminal acetyltransferase A complex subunit nat1
H: N-terminal acetyltransferase A complex catalytic subunit ard1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,36218
Polymers101,9722
Non-polymers1,39016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.739, 119.692, 132.024
Angle α, β, γ (deg.)80.28, 76.85, 70.65
Int Tables number1
Space group name H-MP1

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Components

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N-terminal acetyltransferase A complex ... , 2 types, 8 molecules ABCDEFGH

#1: Protein
N-terminal acetyltransferase A complex subunit nat1 / NatA complex subunit nat1


Mass: 83941.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: nat1, SPCC338.07c / Production host: Escherichia coli (E. coli) / References: UniProt: O74985
#2: Protein
N-terminal acetyltransferase A complex catalytic subunit ard1 / NatA complex subunit ARD1


Mass: 18030.750 Da / Num. of mol.: 4 / Fragment: unp residues 1-156
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: ard1, SPAC15E1.08 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UTI3, EC: 2.3.1.88

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Non-polymers , 5 types, 179 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 63 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein Buffer: 25 mM Hepes, 200 mM NaCl, 1 mM TCEP Crystallization well: 100 mM Hepes, 10% Peg 3350, 10% isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9896
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 2, 2012 / Details: Si(111) crystal
RadiationMonochromator: Si(111) crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9896 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. all: 153358 / Num. obs: 77244 / % possible obs: 99 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 17.2
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.602 / % possible all: 98.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 3.15→49.047 Å / SU ML: 0.39 / σ(F): 1.96 / Phase error: 27.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.246 3614 4.94 %
Rwork0.217 --
obs0.2184 73391 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→49.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27971 0 282 105 28358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00328844
X-RAY DIFFRACTIONf_angle_d0.7938947
X-RAY DIFFRACTIONf_dihedral_angle_d14.16910851
X-RAY DIFFRACTIONf_chiral_restr0.0624222
X-RAY DIFFRACTIONf_plane_restr0.0034966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1499-3.18570.34832220.34884648X-RAY DIFFRACTION95
3.1857-3.22320.40052200.3344987X-RAY DIFFRACTION98
3.2232-3.26250.32962690.30824779X-RAY DIFFRACTION98
3.2625-3.30370.30512780.30184813X-RAY DIFFRACTION98
3.3037-3.34720.34792770.29394830X-RAY DIFFRACTION98
3.3472-3.3930.34842590.29374877X-RAY DIFFRACTION98
3.393-3.44150.31122280.2784839X-RAY DIFFRACTION98
3.4415-3.49290.31042580.27274883X-RAY DIFFRACTION98
3.4929-3.54740.30922460.25974867X-RAY DIFFRACTION98
3.5474-3.60560.27982650.25214816X-RAY DIFFRACTION98
3.6056-3.66770.26882650.24184915X-RAY DIFFRACTION98
3.6677-3.73440.25122480.24794812X-RAY DIFFRACTION98
3.7344-3.80620.30312170.24224877X-RAY DIFFRACTION99
3.8062-3.88390.26192940.24384884X-RAY DIFFRACTION98
3.8839-3.96830.26742550.22854863X-RAY DIFFRACTION98
3.9683-4.06050.23872690.22354858X-RAY DIFFRACTION98
4.0605-4.1620.25322290.20764854X-RAY DIFFRACTION99
4.162-4.27450.21672640.2064919X-RAY DIFFRACTION98
4.2745-4.40020.24732380.19794818X-RAY DIFFRACTION99
4.4002-4.54210.23142740.18844886X-RAY DIFFRACTION98
4.5421-4.70430.20082470.18554900X-RAY DIFFRACTION98
4.7043-4.89250.23642570.18834823X-RAY DIFFRACTION99
4.8925-5.1150.25552350.19984907X-RAY DIFFRACTION98
5.115-5.38430.23452570.20684898X-RAY DIFFRACTION99
5.3843-5.72120.27132520.22464917X-RAY DIFFRACTION99
5.7212-6.16220.2822730.22074808X-RAY DIFFRACTION98
6.1622-6.78090.22382480.21354896X-RAY DIFFRACTION98
6.7809-7.75870.22652450.18874867X-RAY DIFFRACTION98
7.7587-9.76250.1482490.15134885X-RAY DIFFRACTION99
9.7625-49.05290.19512430.18684851X-RAY DIFFRACTION98
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)
15.0082-1.1256-0.83451.0612-0.21420.83090.2413-0.03920.27590.1349-0.1273-0.1741-0.19720.1471-0.12020.6754-0.1625-0.00990.3265-0.05060.2406-22.69249.0794-75.331
21.552-1.4696-0.53329.0048-2.18291.97270.1374-0.2877-0.2475-0.19790.43881.39240.1025-0.3603-0.49320.7542-0.0955-0.06210.5960.11010.4978-67.4514-4.3887-54.9958
32.02220.30850.08132.133-0.88031.2436-0.1883-0.1253-0.4879-0.43820.1087-0.16470.3860.02510.06310.7334-0.07610.08930.41310.00950.2885-37.0143-14.8875-63.7069
43.3224-0.46570.16964.74670.73832.9758-0.2896-0.6426-0.5670.95050.3698-0.48440.23870.3455-0.05750.83510.11430.01890.66940.14240.4929-23.3615-20.5706-46.3067
53.5362-0.5021-0.16173.13240.80262.2825-0.3693-0.09450.008-0.06130.2025-0.5638-0.752-0.07750.04040.606-0.28350.11810.3480.09550.5179-11.486768.9003-78.837
61.6170.70110.6560.31070.23360.46880.02020.7012-0.8031-0.6170.7384-1.9118-0.04970.8886-0.04170.8121-0.10090.63311.2952-0.4432.017715.800229.8013-99.3483
71.28340.36710.15493.64010.83840.44920.02680.0971-0.09720.144-0.1209-0.01080.1261-0.01940.13110.5726-0.14760.13410.4430.07640.2951-14.65440.6261-90.4319
83.48950.8708-0.54154.5812-0.68792.7036-0.15010.68790.1443-1.37760.06540.8964-0.7649-0.3661-0.04981.0103-0.139-0.10480.76530.06220.3894-29.064544.7511-107.6968
93.27140.30630.03983.42540.93172.2822-0.55120.1562-0.01710.11190.4908-0.57490.6085-0.0547-0.15440.45860.2043-0.24860.3589-0.00580.5638-41.1916-48.7234-140.1847
102.7936-0.4087-0.41550.0909-0.13811.65140.2826-0.3290.58310.49950.6518-1.6515-0.03081.01630.49640.6923-0.0313-0.50471.3223-0.74651.9664-15.1033-8.8385-120.3488
111.7484-1.1738-1.15653.76651.55561.18290.21760.03230.22110.0437-0.0607-0.2916-0.01330.0985-0.14510.39320.1057-0.12570.38830.02210.2733-45.1146-20.7698-129.5084
123.1808-1.4752-0.00844.32170.08842.3412-0.2688-0.34140.08471.23410.05080.72691.04260.0415-0.08140.89940.13120.06530.47110.04220.3949-59.7137-24.7641-112.4463
134.8871.06481.2272.3718-0.47151.58830.17550.0366-0.1649-0.5448-0.217-0.59690.13480.3112-0.00660.74890.16330.24020.3717-0.00990.4893-23.414324.2483-15.8542
142.55050.4081.60896.1555-1.56161.98340.40460.10990.08730.15370.01790.60950.1195-0.3624-0.34040.7765-0.00310.02630.50670.06910.3376-68.630137.6497-36.1702
151.8444-0.56710.32982.4818-1.0951.1293-0.26660.00340.23340.00810.029-0.0534-0.17570.06470.23650.71970.04120.04190.3862-0.04460.3436-37.976647.9608-27.3707
163.01170.5686-0.31494.85770.28472.7814-0.41880.49450.3906-1.42310.3347-0.53650.13070.28760.01011.1108-0.0920.09210.60940.0390.5245-24.499654.079-44.7859
173.9361-0.37490.56483.8316-0.11280.13560.04280.2089-0.14130.0669-0.08070.20380.1801-0.1735-0.01640.7056-0.13910.07040.42-0.07130.2454-45.9148-1.7797-74.8303
183.0143-0.05050.07439.40550.63633.4786-0.02440.4516-0.5081-0.6580.09250.94130.6364-0.5162-0.16770.791-0.10810.05870.5727-0.12190.473-52.311-6.8263-87.3481
194.6645-0.43320.62055.62551.00052.6847-0.1174-0.017-0.78750.05170.2825-1.32510.22470.4023-0.13430.3538-0.10070.08270.43620.07570.83580.680345.3704-79.1735
203.54233.04420.12178.258-0.56641.43640.1631-0.6796-1.8650.536-0.23-1.43770.38450.28030.0030.96770.0232-0.31780.82120.24011.39852.349436.9868-66.6383
215.11950.7849-0.6154.7120.25452.5748-0.00180.08761.0975-0.06490.3658-1.4005-0.23930.4039-0.2380.33160.0541-0.01740.4679-0.1190.9403-29.5932-25.206-140.6275
221.1424-2.5081-0.16398.7536-0.95461.89830.44111.00451.6286-0.68810.0867-0.084-0.6969-0.1323-0.63940.9564-0.04060.45240.85950.31061.7103-28.0284-17.1029-153.3582
234.69650.567-0.49534.8995-0.36880.7463-0.0584-0.06250.1656-0.47350.04380.4305-0.0867-0.0701-0.04560.57390.0809-0.04980.4054-0.07920.2521-46.899434.8416-16.1854
244.7131-0.3754-1.02664.2008-1.16635.06460.4418-0.29621.31740.50590.18421.4349-1.3822-0.6012-0.59910.71480.10520.12540.7758-0.06510.8987-53.137140.0045-3.4652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:269 )A5 - 269
2X-RAY DIFFRACTION2( CHAIN A AND RESID 270:428 )A270 - 428
3X-RAY DIFFRACTION3( CHAIN A AND RESID 429:572 )A429 - 572
4X-RAY DIFFRACTION4( CHAIN A AND RESID 573:731 )A573 - 731
5X-RAY DIFFRACTION5( CHAIN B AND RESID 5:266 )B5 - 266
6X-RAY DIFFRACTION6( CHAIN B AND RESID 267:428 )B267 - 428
7X-RAY DIFFRACTION7( CHAIN B AND RESID 429:572 )B429 - 572
8X-RAY DIFFRACTION8( CHAIN B AND RESID 573:731 )B573 - 731
9X-RAY DIFFRACTION9( CHAIN C AND RESID 5:269 )C5 - 269
10X-RAY DIFFRACTION10( CHAIN C AND RESID 270:428 )C270 - 428
11X-RAY DIFFRACTION11( CHAIN C AND RESID 429:572 )C429 - 572
12X-RAY DIFFRACTION12( CHAIN C AND RESID 573:730 )C573 - 730
13X-RAY DIFFRACTION13( CHAIN D AND RESID 5:269 )D5 - 269
14X-RAY DIFFRACTION14( CHAIN D AND RESID 270:428 )D270 - 428
15X-RAY DIFFRACTION15( CHAIN D AND RESID 429:572 )D429 - 572
16X-RAY DIFFRACTION16( CHAIN D AND RESID 573:730 )D573 - 730
17X-RAY DIFFRACTION17( CHAIN E AND RESID 1:97 )E1 - 97
18X-RAY DIFFRACTION18( CHAIN E AND RESID 98:153 )E98 - 153
19X-RAY DIFFRACTION19( CHAIN F AND RESID 1:99 )F1 - 99
20X-RAY DIFFRACTION20( CHAIN F AND RESID 100:153 )F100 - 153
21X-RAY DIFFRACTION21( CHAIN G AND RESID 1:99 )G1 - 99
22X-RAY DIFFRACTION22( CHAIN G AND RESID 100:153 )G100 - 153
23X-RAY DIFFRACTION23( CHAIN H AND RESID 1:98 )H1 - 98
24X-RAY DIFFRACTION24( CHAIN H AND RESID 99:153 )H99 - 153

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  • 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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