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- PDB-5ecg: Crystal structure of the BRCT domains of 53BP1 in complex with p5... -

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Basic information

Entry
Database: PDB / ID: 5ecg
TitleCrystal structure of the BRCT domains of 53BP1 in complex with p53 and H2AX-pSer139 (gammaH2AX)
Components
  • Cellular tumor antigen p53P53
  • SEP-GLN-GLU-TYR
  • Tumor suppressor p53-binding protein 1
KeywordsANTITUMOR PROTEIN / DNA Repair / NHEJ / H2AX / BRCT
Function / homology
Function and homology information


ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / DNA repair complex ...ubiquitin-modified histone reader activity / positive regulation of isotype switching / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / DNA repair complex / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / glucose catabolic process to lactate via pyruvate / regulation of tissue remodeling / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / bone marrow development / circadian behavior / histone deacetylase regulator activity / T cell proliferation involved in immune response / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / germ cell nucleus / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / negative regulation of neuroblast proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / negative regulation of glial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / negative regulation of double-strand break repair via homologous recombination / positive regulation of execution phase of apoptosis / mitochondrial DNA repair / T cell lineage commitment / telomeric DNA binding / negative regulation of DNA replication / ER overload response / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / entrainment of circadian clock by photoperiod / cardiac septum morphogenesis / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / Zygotic genome activation (ZGA) / necroptotic process / negative regulation of telomere maintenance via telomerase / positive regulation of release of cytochrome c from mitochondria / rRNA transcription / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / mitophagy / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / neuroblast proliferation / general transcription initiation factor binding / cellular response to actinomycin D / Transcriptional Regulation by VENTX / response to X-ray / DNA damage response, signal transduction by p53 class mediator / replicative senescence / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / chromosome organization / gastrulation / cellular response to UV-C / response to inorganic substance / hematopoietic stem cell differentiation / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of reactive oxygen species metabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / MDM2/MDM4 family protein binding / glial cell proliferation / embryonic organ development / cellular response to glucose starvation / Pyroptosis / cis-regulatory region sequence-specific DNA binding / hematopoietic progenitor cell differentiation / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / somitogenesis / type II interferon-mediated signaling pathway / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation
Similarity search - Function
: / BRCA1 C Terminus (BRCT) domain / Tumour suppressor p53-binding protein-1 Tudor domain / Tumour suppressor p53-binding protein-1 Tudor / : / : / BRCT domain / Immunoglobulin-like - #720 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 ...: / BRCA1 C Terminus (BRCT) domain / Tumour suppressor p53-binding protein-1 Tudor domain / Tumour suppressor p53-binding protein-1 Tudor / : / : / BRCT domain / Immunoglobulin-like - #720 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / breast cancer carboxy-terminal domain / p53-like transcription factor, DNA-binding / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ribosomal protein L2, domain 2 / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cellular tumor antigen p53 / TP53-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDay, M. / Oliver, A.W. / Pearl, L.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKC302/A14532 United Kingdom
CitationJournal: Cell Rep / Year: 2015
Title: ATM Localization and Heterochromatin Repair Depend on Direct Interaction of the 53BP1-BRCT2 Domain with gamma H2AX.
Authors: Baldock, R.A. / Day, M. / Wilkinson, O.J. / Cloney, R. / Jeggo, P.A. / Oliver, A.W. / Watts, F.Z. / Pearl, L.H.
History
DepositionOct 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellular tumor antigen p53
B: Cellular tumor antigen p53
C: Tumor suppressor p53-binding protein 1
D: Tumor suppressor p53-binding protein 1
E: SEP-GLN-GLU-TYR
F: SEP-GLN-GLU-TYR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9528
Polymers110,8216
Non-polymers1312
Water30617
1
A: Cellular tumor antigen p53
C: Tumor suppressor p53-binding protein 1
F: SEP-GLN-GLU-TYR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4764
Polymers55,4113
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cellular tumor antigen p53
D: Tumor suppressor p53-binding protein 1
E: SEP-GLN-GLU-TYR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4764
Polymers55,4113
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.264, 94.498, 131.742
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 Cellular tumor antigen p53 / P53 / Antigen NY-CO-13 / Phosphoprotein p53 / Tumor suppressor p53


Mass: 25180.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53, P53 / Plasmid: pTHREE-E / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P04637
#2: Protein Tumor suppressor p53-binding protein 1 / p53BP1


Mass: 29624.533 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53BP1 / Plasmid: pHIS-SUMO-GG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q12888
#3: Protein/peptide SEP-GLN-GLU-TYR


Mass: 605.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200mM NaF, 100mM Bis-Tris Propane pH 6.5, 20% (w/v) PEG 3,350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 3→48.06 Å / Num. obs: 18153 / % possible obs: 99.8 % / Redundancy: 4.3 % / Net I/σ(I): 11.6
Reflection shellResolution: 3→3.18 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KZY

1kzy


Resolution: 3→48.056 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 919 5.08 %Random Selection
Rwork0.2035 ---
obs0.2067 18104 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→48.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6295 0 2 17 6314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046458
X-RAY DIFFRACTIONf_angle_d0.5458807
X-RAY DIFFRACTIONf_dihedral_angle_d16.1623829
X-RAY DIFFRACTIONf_chiral_restr0.043989
X-RAY DIFFRACTIONf_plane_restr0.0051149
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.15810.39151310.31452410X-RAY DIFFRACTION100
3.1581-3.3560.37551160.2712416X-RAY DIFFRACTION100
3.356-3.6150.30321190.23762430X-RAY DIFFRACTION100
3.615-3.97860.28941240.19432432X-RAY DIFFRACTION100
3.9786-4.5540.23571490.172441X-RAY DIFFRACTION100
4.554-5.7360.22841490.1792456X-RAY DIFFRACTION100
5.736-48.0620.24051310.19782600X-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)
14.9375-1.72591.49813.5410.94242.36560.61520.02831.4636-0.0032-0.2974-0.5941-0.79842.00220.10271.0872-0.08370.33850.89980.2030.6862-23.00594.638-10.1086
24.7798-4.2515-3.11926.64872.22167.7366-0.0990.1837-1.1413-1.2792-0.30270.1690.4859-0.88770.55610.5365-0.11810.14820.55740.09150.4972-40.62696.7748-1.0167
32.43671.328-0.46893.69523.8385.2578-0.2297-0.265-0.3348-0.1395-0.12450.02410.3214-0.01670.36510.8752-0.08440.02980.5630.18930.5362-29.60758.997-0.3368
45.4822-0.34892.11758.0045-1.22978.3703-0.2041-1.79820.08020.30050.0276-0.3972-1.057-0.7060.14370.93010.2284-0.01491.02650.08010.5292-25.356811.155417.2319
55.96642.0651.32156.6555-1.16736.25310.0394-0.12010.171.085-0.22320.33811.0717-0.76760.26461.21230.04510.15310.88210.14870.6286-27.21980.1969.6977
63.2424-0.38-0.23794.6503-1.246.4653-0.075-1.2301-0.9160.7226-0.0528-1.589-1.07751.07030.37520.3089-0.0322-0.00270.8330.09480.6657-17.88985.72455.6896
71.0818-0.36771.65535.0067-0.19152.9803-0.1897-0.5976-1.0567-0.0832-0.23770.48861.0519-0.5051-1.58121.3336-0.22590.36740.47790.2661.2455-34.6661-3.3410.5299
81.2707-0.509-0.22041.03182.66946.6554-0.2877-0.10410.2102-0.16010.2486-0.2629-0.94580.32580.04460.801-0.1730.10940.630.07120.5325-25.547812.663.5704
92.8689-2.5617-0.45224.94423.92976.33630.4448-0.22970.5607-0.7824-0.1051-0.5636-0.0476-0.14640.4060.6443-0.13390.0420.36560.06390.5621-30.646711.3678-1.8798
103.9154-0.02541.81284.035-0.14758.9122-0.69171.18840.7167-0.68080.5667-1.4179-2.912-0.28470.60951.39670.20120.0050.8887-0.01550.7451-42.714622.8212-5.8713
114.5564-3.8202-3.23694.73594.67994.9745-0.38340.2140.41921.76250.4992-0.2318-0.0037-0.1771-0.02951.6978-0.16680.15140.69390.10090.6683-21.98137.6595-15.8178
122.4851-1.96342.14162.75510.40325.2287-0.8734-0.4613-0.4032-0.2517-0.38981.3732-0.6335-0.25551.07191.2502-0.15340.15210.56780.08230.9757-29.254531.9428-32.6987
133.1866-3.7551-0.64566.84434.73117.2603-0.48310.17940.0442-0.29390.528-0.1055-0.1737-0.0045-0.13121.0693-0.20280.05850.5610.1450.7508-18.151734.6631-26.2768
147.6056-0.1922-2.44788.42321.5848.8171-1.1851-0.45560.0852-0.99471.0389-1.8113-0.80911.06981.00580.9269-0.0084-0.12430.88650.05371.0035-8.374931.911-39.5069
154.47011.8715-0.49244.62221.58920.8343-0.74410.71760.13280.23490.77650.627-1.72210.1505-0.0241.1356-0.10540.19120.35040.03320.5447-10.576539.074-30.441
160.16140.56550.10474.8433-3.61236.54130.1248-0.3740.20620.7590.70441.3412-1.5865-1.3264-0.45781.33130.02070.05530.38320.1510.7982-22.920747.1694-28.6357
179.4244-5.8709-3.90223.57812.17544.30720.07621.1566-0.5249-0.4304-0.67670.47510.0606-0.12550.67871.065-0.05960.06650.6624-0.11860.4858-18.276828.1779-34.8084
189.28964.70722.7373.41840.13269.8536-0.05840.7861-0.82950.77590.689-0.76950.34370.89771.03151.27380.0783-0.03690.40330.26450.7525-20.319635.2001-24.5455
191.1686-1.22230.01012.30842.2264.8128-1.93221.215-1.3164-1.52020.3947-0.94050.9260.48550.25061.3358-0.52220.47321.18-0.28330.9201-32.817719.8394-34.7518
208.08842.01721.45198.2714-2.38981.24770.1842-0.39170.86620.2622-0.50110.60821.25550.13190.30271.07910.1175-0.08071.2664-0.070.3796-16.559827.242226.4197
219.893-1.121-0.26347.774-3.93917.06330.32440.6881.33340.8962-0.48870.1652-0.20270.28140.36170.99660.0208-0.00230.7048-0.15060.5278-17.191339.225219.7064
222.15310.9858-1.58294.2428-3.57735.93430.0829-0.0522-0.3339-0.84610.15460.12331.73730.2823-0.03560.62230.076-0.02230.5481-0.04960.4274-20.704433.832813.2168
234.55851.9164-0.2944.2989-5.01929.05090.5801-0.4152-0.01790.0164-0.2131-0.2114-0.22820.2435-0.16750.6802-0.03540.02220.55840.04470.7039-23.395549.60460.8646
244.27041.47671.97024.9181-1.25412.23340.3592-0.79820.9465-0.0591-0.3185-0.1749-0.84740.0713-0.49920.82710.05460.36920.51840.080.8193-25.927462.6901-4.8727
252.77920.0304-0.01953.717-5.26388.73440.0212-0.0201-0.1597-0.52050.70110.4690.2776-0.7462-0.89470.8930.06720.03250.46130.09720.7245-30.644352.5586-6.494
263.72832.8805-0.52288.99572.3531.6879-0.71730.7879-0.4728-1.05190.537-1.45640.2999-0.1731-0.1781.0988-0.18090.04820.6194-0.02770.46150.39618.6118-42.1403
272.94841.974-2.76243.4111-2.53742.6074-0.15630.2022-0.12260.04150.2123-0.13310.1145-0.059-0.0071.1318-0.0613-0.01950.5346-0.05260.6025-13.6622-4.0813-27.0319
285.1582-1.08061.79555.20183.76264.06840.0114-0.7435-0.20241.3116-0.6297-0.53520.0186-0.12780.30081.4914-0.4710.21260.72530.15570.8588-15.624-7.0494-38.0238
298.86012.41480.26229.5987-5.67733.7021.80961.23280.6426-1.7108-1.2873-0.6496-0.8727-0.2205-0.77361.62830.6260.2611.05820.2161.3068-30.698149.422912.1468
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 96 through 109 )
2X-RAY DIFFRACTION2chain 'A' and (resid 110 through 123 )
3X-RAY DIFFRACTION3chain 'A' and (resid 124 through 176 )
4X-RAY DIFFRACTION4chain 'A' and (resid 177 through 194 )
5X-RAY DIFFRACTION5chain 'A' and (resid 195 through 206 )
6X-RAY DIFFRACTION6chain 'A' and (resid 207 through 219 )
7X-RAY DIFFRACTION7chain 'A' and (resid 220 through 236 )
8X-RAY DIFFRACTION8chain 'A' and (resid 237 through 263 )
9X-RAY DIFFRACTION9chain 'A' and (resid 264 through 277 )
10X-RAY DIFFRACTION10chain 'A' and (resid 278 through 293 )
11X-RAY DIFFRACTION11chain 'B' and (resid 96 through 109 )
12X-RAY DIFFRACTION12chain 'B' and (resid 110 through 140 )
13X-RAY DIFFRACTION13chain 'B' and (resid 141 through 178 )
14X-RAY DIFFRACTION14chain 'B' and (resid 179 through 194 )
15X-RAY DIFFRACTION15chain 'B' and (resid 195 through 213 )
16X-RAY DIFFRACTION16chain 'B' and (resid 214 through 229 )
17X-RAY DIFFRACTION17chain 'B' and (resid 230 through 250 )
18X-RAY DIFFRACTION18chain 'B' and (resid 251 through 277 )
19X-RAY DIFFRACTION19chain 'B' and (resid 278 through 289 )
20X-RAY DIFFRACTION20chain 'C' and (resid 1714 through 1731 )
21X-RAY DIFFRACTION21chain 'C' and (resid 1732 through 1800 )
22X-RAY DIFFRACTION22chain 'C' and (resid 1801 through 1850 )
23X-RAY DIFFRACTION23chain 'C' and (resid 1851 through 1904 )
24X-RAY DIFFRACTION24chain 'C' and (resid 1905 through 1927 )
25X-RAY DIFFRACTION25chain 'C' and (resid 1928 through 1970 )
26X-RAY DIFFRACTION26chain 'D' and (resid 1719 through 1782 )
27X-RAY DIFFRACTION27chain 'D' and (resid 1783 through 1970 )
28X-RAY DIFFRACTION28chain 'E' and (resid 140 through 142 )
29X-RAY DIFFRACTION29chain 'F' and (resid 140 through 142 )

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Yorodumi

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  • 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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