[English] 日本語
Yorodumi
- PDB-9be1: CG-centric NF-kappaB RelA binding DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9be1
TitleCG-centric NF-kappaB RelA binding DNA
Components(DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')) x 2
KeywordsDNA / kappaB DNA / Promoter / Transcription / RelA
Function / homologyACETATE ION / DNA / DNA (> 10)
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBiswas, T. / Shahabi, S. / Tsodikov, O.V. / Wang, V. / Ghosh, G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM085490-11 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2024
Title: Transient interactions modulate the affinity of NF-kappa B transcription factors for DNA.
Authors: Li, T. / Shahabi, S. / Biswas, T. / Tsodikov, O.V. / Pan, W. / Huang, D.B. / Wang, V.Y. / Wang, Y. / Ghosh, G.
History
DepositionApr 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2024Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
P: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
E: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
T: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
G: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
X: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
I: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
b: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
K: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
d: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
N: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
f: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
Y: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
h: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
W: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
j: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
U: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
l: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
S: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
n: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
Q: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
p: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
M: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
r: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,013133
Polymers87,92124
Non-polymers7,091109
Water8,539474
1
A: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
P: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,84410
Polymers7,3272
Non-polymers5178
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
T: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,03413
Polymers7,3272
Non-polymers70711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
X: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,97512
Polymers7,3272
Non-polymers64810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
b: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,85010
Polymers7,3272
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
K: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
d: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,97512
Polymers7,3272
Non-polymers64810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
N: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
f: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91511
Polymers7,3272
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
Y: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
h: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91511
Polymers7,3272
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
W: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
j: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,85010
Polymers7,3272
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
U: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
l: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91511
Polymers7,3272
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
S: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
n: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91511
Polymers7,3272
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
Q: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
p: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,91511
Polymers7,3272
Non-polymers5899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
M: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
r: DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,90911
Polymers7,3272
Non-polymers5829
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.999, 47.031, 98.682
Angle α, β, γ (deg.)90.03, 89.96, 59.99
Int Tables number1
Space group name H-MP1

-
Components

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


Mass: 3663.392 Da / Num. of mol.: 12 / Source method: obtained synthetically
Details: Each chain is two separate complimentary DNA oligomers with sequences CGGGAACTTCCG and CGGAAGTTCCCG
Source: (synth.) Homo sapiens (human)
#2: DNA chain
DNA (5'-D(*CP*GP*GP*GP*AP*AP*TP*TP*TP*CP*CP*GP*CP*GP*GP*AP*AP*AP*TP*TP*CP*CP*CP*G)-3')


Mass: 3663.392 Da / Num. of mol.: 12 / Source method: obtained synthetically
Details: Each chain is two separate complimentary DNA oligomers with sequences CGGGAACTTCCG and CGGAAGTTCCCG
Source: (synth.) Homo sapiens (human)
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 103 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 474 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: PEG3350 8%, Sodium Acetate pH 3.5 100 mM, 50 mM Zinc Acetate

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 20414 / % possible obs: 92 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Χ2: 0.067 / Net I/σ(I): 15
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 1680 / Χ2: 0.404 / % possible all: 95.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.911 / SU B: 13.882 / SU ML: 0.293 / Cross valid method: THROUGHOUT / ESU R Free: 0.523 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.34887 961 4.6 %RANDOM
Rwork0.29833 ---
obs0.30072 19780 92.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.479 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.21 Å20.79 Å2
2---0.08 Å2-0.2 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 5451 127 474 6052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0116405
X-RAY DIFFRACTIONr_bond_other_d0.0010.022970
X-RAY DIFFRACTIONr_angle_refined_deg0.7671.179387
X-RAY DIFFRACTIONr_angle_other_deg1.442.9927044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.050.2792
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023264
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021392
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2374.326
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3874.5936399
X-RAY DIFFRACTIONr_scbond_other2.3874.5936398
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6246.9179388
X-RAY DIFFRACTIONr_long_range_B_refined4.79738.6847804
X-RAY DIFFRACTIONr_long_range_B_other4.79738.6827805
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.539 101 -
Rwork0.381 1417 -
obs--95.89 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more