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- PDB-5ja4: Crystal structure of human TONSL and MCM2 HBDs binding to a histo... -

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Basic information

Entry
Database: PDB / ID: 5ja4
TitleCrystal structure of human TONSL and MCM2 HBDs binding to a histone H3-H4 tetramer
Components
  • DNA replication licensing factor MCM2
  • Histone H3.3H3F3A
  • Histone H4
  • Tonsoku-like protein
KeywordsCHAPERONE / DNA repair and histone chaperone
Function / homology
Function and homology information


Switching of origins to a post-replicative state / Unwinding of DNA / nuclear origin of replication recognition complex / CMG complex / MCM complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / nucleosomal DNA binding / regulation of DNA-templated DNA replication initiation / replication fork processing ...Switching of origins to a post-replicative state / Unwinding of DNA / nuclear origin of replication recognition complex / CMG complex / MCM complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / nucleosomal DNA binding / regulation of DNA-templated DNA replication initiation / replication fork processing / cochlea development / DNA unwinding involved in DNA replication / nuclear replication fork / DNA replication origin binding / DNA replication initiation / Activation of the pre-replicative complex / RNA polymerase II core promoter sequence-specific DNA binding / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Replacement of protamines by nucleosomes in the male pronucleus / Activation of ATR in response to replication stress / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / cellular response to interleukin-4 / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / helicase activity / Defective pyroptosis / Assembly of the pre-replicative complex / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / double-strand break repair via homologous recombination / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / nucleosome / single-stranded DNA binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / DNA helicase / Estrogen-dependent gene expression / DNA replication / chromosome, telomeric region / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / apoptotic process / chromatin / enzyme binding / ATP hydrolysis activity / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane
Similarity search - Function
Domain of unknown function DUF3447 / : / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / MCM N-terminal domain / MCM N-terminal domain / Leucine Rich repeat / MCM OB domain ...Domain of unknown function DUF3447 / : / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / MCM N-terminal domain / MCM N-terminal domain / Leucine Rich repeat / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / Ankyrin repeat-containing domain / Histone, subunit A / Histone, subunit A / Tetratricopeptide repeat / TPR repeat region circular profile. / Tetratricopeptide repeats / Ankyrin repeat / Tetratricopeptide repeat / Leucine-rich repeat / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Ankyrin repeats (3 copies) / Histone H3 signature 1. / Ankyrin repeat profile. / Leucine-rich repeat domain superfamily / Ankyrin repeat region circular profile. / ankyrin repeats / Histone H3 signature 2. / Ankyrin repeat / Histone H3 / Histone H3/CENP-A / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA replication licensing factor MCM2 / Histone H4 / Histone H3.3 / Tonsoku-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.424 Å
AuthorsHuang, H. / Patel, D.
CitationJournal: Nature / Year: 2016
Title: H4K20me0 marks post-replicative chromatin and recruits the TONSL-MMS22L DNA repair complex.
Authors: Saredi, G. / Huang, H. / Hammond, C.M. / Alabert, C. / Bekker-Jensen, S. / Forne, I. / Reveron-Gomez, N. / Foster, B.M. / Mlejnkova, L. / Bartke, T. / Cejka, P. / Mailand, N. / Imhof, A. / ...Authors: Saredi, G. / Huang, H. / Hammond, C.M. / Alabert, C. / Bekker-Jensen, S. / Forne, I. / Reveron-Gomez, N. / Foster, B.M. / Mlejnkova, L. / Bartke, T. / Cejka, P. / Mailand, N. / Imhof, A. / Patel, D.J. / Groth, A.
History
DepositionApr 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Jul 13, 2016Group: Database references
Revision 1.3Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.3
B: Histone H4
C: DNA replication licensing factor MCM2
D: Tonsoku-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8987
Polymers48,5184
Non-polymers3793
Water1,56787
1
A: Histone H3.3
B: Histone H4
C: DNA replication licensing factor MCM2
D: Tonsoku-like protein
hetero molecules

A: Histone H3.3
B: Histone H4
C: DNA replication licensing factor MCM2
D: Tonsoku-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,79514
Polymers97,0368
Non-polymers7596
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_647y+1,x-1,-z+21
Buried area24010 Å2
ΔGint-97 kcal/mol
Surface area36680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.506, 139.506, 72.896
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Histone H3.3 / H3F3A


Mass: 9026.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P84243
#2: Protein Histone H4 /


Mass: 11263.231 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein DNA replication licensing factor MCM2 / Minichromosome maintenance protein 2 homolog / Nuclear protein BM28


Mass: 7860.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM2, BM28, CCNL1, CDCL1, KIAA0030 / Production host: Escherichia coli (E. coli) / References: UniProt: P49736, DNA helicase
#4: Protein Tonsoku-like protein / Inhibitor of kappa B-related protein / IkappaBR / NF-kappa-B inhibitor-like protein 2 / Nuclear ...Inhibitor of kappa B-related protein / IkappaBR / NF-kappa-B inhibitor-like protein 2 / Nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2


Mass: 20368.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TONSL, IKBR, NFKBIL2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96HA7

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Non-polymers , 3 types, 90 molecules

#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 4.22 Å3/Da / Density % sol: 70.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 0.1M MES pH 5.6, 7% isopropanol / PH range: 5.5-6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 31146 / % possible obs: 99.8 % / Redundancy: 5.5 % / Net I/σ(I): 23.1
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIXdev_1760refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BNV

5bnv


Resolution: 2.424→46.513 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.43
RfactorNum. reflection% reflection
Rfree0.2461 1446 4.64 %
Rwork0.2013 --
obs0.2033 31137 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.424→46.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2908 0 24 87 3019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092970
X-RAY DIFFRACTIONf_angle_d1.3163997
X-RAY DIFFRACTIONf_dihedral_angle_d16.961128
X-RAY DIFFRACTIONf_chiral_restr0.048441
X-RAY DIFFRACTIONf_plane_restr0.007526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4241-2.51070.3071570.27872831X-RAY DIFFRACTION97
2.5107-2.61120.29691520.27312945X-RAY DIFFRACTION100
2.6112-2.73010.32161320.26692959X-RAY DIFFRACTION100
2.7301-2.8740.28651320.25422948X-RAY DIFFRACTION100
2.874-3.0540.29611450.23912981X-RAY DIFFRACTION100
3.054-3.28980.25221630.22662945X-RAY DIFFRACTION100
3.2898-3.62070.25621390.21392984X-RAY DIFFRACTION100
3.6207-4.14440.22441260.18363015X-RAY DIFFRACTION100
4.1444-5.22030.21631470.16293015X-RAY DIFFRACTION100
5.2203-46.52130.22121530.17393068X-RAY DIFFRACTION99
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)
12.36250.888-0.70413.305-5.16918.5525-0.13731.024-0.464-0.8115-0.754-0.38220.52181.13890.61780.61520.12720.06980.6074-0.04060.4328132.9444-63.108866.8172
22.25680.4699-0.26678.3131-0.94817.36240.4183-0.27880.08840.5260.1281-0.23690.31160.3236-0.53910.44370.10920.0060.4173-0.00210.4581127.9335-69.907283.1764
35.1108-0.29090.49299.42297.29688.0125-0.0191-0.6047-1.00991.27560.0841-0.24060.4621-1.4075-0.03050.60990.08810.11370.30520.09280.6844122.8498-78.650685.1855
42.436-0.2752-0.02098.3244-3.20782.1186-0.06950.2342-0.0245-0.41030.0540.38440.25560.04450.00920.27380.02480.01940.3685-0.05240.3565121.787-56.758771.3312
59.55541.6402-2.06722.7835-2.25764.69290.0052-0.3170.70520.38620.11690.1115-0.21930.2829-0.18050.36640.05180.03710.352-0.06250.424120.0499-44.802276.1455
63.09371.82182.27044.3363.45633.39490.5115-0.2752-0.1840.4917-0.0534-0.03530.71030.3467-0.460.8740.10230.01280.7992-0.06690.3986135.5026-59.4474103.0983
73.3563-0.648-0.28612.817-1.60256.5997-0.10160.2160.25090.0396-0.0904-0.3286-0.00120.29970.16310.2810.0330.020.3892-0.030.4316132.1132-54.225272.6362
84.16441.9098-0.49167.9084-0.28492.5476-0.0946-0.2956-0.29460.54760.02030.64110.3161-0.08730.07990.30980.11110.0910.3445-0.01420.4184118.1199-67.088981.4501
93.31360.48491.04082.5349-1.02544.2109-0.83731.25170.6888-0.55770.30111.34360.51110.59460.38640.84490.0884-0.26551.2246-0.22270.9009113.9651-66.519870.5572
106.6893-0.2832-3.18241.85540.52352.40140.28960.1861.2086-0.55310.0371-0.6271-0.94271.6652-0.40820.4629-0.1257-0.00030.84780.01460.6889137.7081-45.932367.7421
113.047-0.5568-1.65093.2714-2.51023.59780.15510.93241.4183-0.33740.77-0.7803-0.6745-0.1631-0.39940.56690.05110.08650.66610.01260.6429139.8599-56.294465.28
123.2222.1329-2.65542.5175-1.09192.6581-0.06081.2725-1.59690.08330.0017-1.17980.58490.6473-0.03760.35810.09510.03680.6116-0.05580.6857141.3243-67.885670.3178
134.25984.387-2.88094.5011-3.07242.2418-0.3724-0.3834-0.6613-0.2332-0.2151-1.17590.4930.30070.36680.46690.05860.10430.3378-0.0270.7123131.4197-77.915677.2497
143.8871-1.74612.67062.1852-0.84931.9335-0.1001-0.3935-0.53650.42010.1311.3845-0.1646-0.65080.07890.52530.05490.08080.5207-0.05070.8172115.5051-86.159777.4034
153.59573.47853.69883.39593.9087.85810.0301-1.0557-0.32380.3074-0.81811.4518-0.7015-1.38420.56150.62320.08510.39230.8426-0.03951.4373104.2076-70.31586.7375
163.2916-0.0452-1.19082.0374-1.94322.2422-0.2178-0.6806-0.0727-0.1065-0.60680.3292-2.7833-2.49910.4381.47350.7598-0.03911.5075-0.27960.5444126.9272-51.142295.9377
170.6164-1.3868-0.19937.8816.47327.6246-0.7089-0.02541.0319-0.772-0.64431.2911-1.3647-0.83391.26051.53630.47320.26391.4038-0.21061.25123.7836-39.048899.0843
181.0504-0.5250.52051.16020.26250.6556-0.6316-0.40150.0212-0.02720.05310.5826-1.6028-3.56940.41971.32020.53450.04942.2402-0.33850.3727126.118-54.0505104.1236
194.3519-2.08851.8664.826-3.10162.2929-0.15340.0509-0.04050.03680.68610.276-1.1445-3.0699-0.42821.34950.09820.34152.1265-0.22830.6675122.0874-47.4996110.1344
207.39441.5862-2.73692.1675-2.73313.56530.1629-1.9470.53450.131-1.21820.4036-0.6368-3.31310.82410.91990.1309-0.04841.9063-0.25820.6566130.1423-54.9079115.2981
211.3013-0.34510.33281.7237-1.46851.28430.363-0.9767-0.5937-0.0237-0.53490.3284-0.2412-1.55070.15791.3573-0.29780.28782.7201-0.6437-0.093123.9112-57.8615119.8845
227.0222-1.8886-0.6376.02022.67646.7220.73-0.03260.17160.3456-0.3254-0.60.7677-0.1914-0.41030.8171-0.16450.04571.3225-0.02630.4503139.7446-57.2892122.8161
237.90251.3027-0.78745.54741.96584.9029-0.4653-0.8710.3113-0.207-0.34310.2893-1.0326-2.11320.691.34960.1189-0.10681.5865-0.21350.492133.3886-51.7076128.8696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 57 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 85 )
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 113 )
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 134 )
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 24 )
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 47 )
8X-RAY DIFFRACTION8chain 'B' and (resid 48 through 92 )
9X-RAY DIFFRACTION9chain 'B' and (resid 93 through 100 )
10X-RAY DIFFRACTION10chain 'C' and (resid 68 through 76 )
11X-RAY DIFFRACTION11chain 'C' and (resid 77 through 81 )
12X-RAY DIFFRACTION12chain 'C' and (resid 82 through 87 )
13X-RAY DIFFRACTION13chain 'C' and (resid 88 through 97 )
14X-RAY DIFFRACTION14chain 'C' and (resid 98 through 106 )
15X-RAY DIFFRACTION15chain 'C' and (resid 107 through 124 )
16X-RAY DIFFRACTION16chain 'D' and (resid 521 through 541 )
17X-RAY DIFFRACTION17chain 'D' and (resid 542 through 551 )
18X-RAY DIFFRACTION18chain 'D' and (resid 552 through 574 )
19X-RAY DIFFRACTION19chain 'D' and (resid 575 through 593 )
20X-RAY DIFFRACTION20chain 'D' and (resid 594 through 616 )
21X-RAY DIFFRACTION21chain 'D' and (resid 617 through 633 )
22X-RAY DIFFRACTION22chain 'D' and (resid 634 through 650 )
23X-RAY DIFFRACTION23chain 'D' and (resid 651 through 669 )

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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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