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- PDB-7xqp: PSI-LHCI-LHCII-Lhcb9 supercomplex of Physcomitrella patens -

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Basic information

Entry
Database: PDB / ID: 7xqp
TitlePSI-LHCI-LHCII-Lhcb9 supercomplex of Physcomitrella patens
Components
  • (Chlorophyll a-b binding protein, ...) x 6
  • (Photosystem I P700 chlorophyll a apoprotein ...) x 2
  • (Photosystem I reaction center subunit ...) x 3
  • PSI subunit V
  • PSI-F
  • PSI-G
  • Photosystem I iron-sulfur center
  • Predicted protein PsaD
  • PsaE
  • PsaH photosystem I reaction center subunit
  • PsaK
  • PsaO
KeywordsPHOTOSYNTHESIS / Supercomplex / Membrane protein / State transitions
Function / homology
Function and homology information


chloroplast thylakoid lumen / photosynthesis, light harvesting / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane ...chloroplast thylakoid lumen / photosynthesis, light harvesting / photosynthesis, light harvesting in photosystem I / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
Photosystem I PsaO / PsaO transmembrane domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre ...Photosystem I PsaO / PsaO transmembrane domain / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaD / Chlorophyll A-B binding protein / Photosystem I, reaction centre subunit PsaD superfamily / Chlorophyll A-B binding protein / PsaD / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IX / PsaJ / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / : / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-NEX / PHYLLOQUINONE / IRON/SULFUR CLUSTER ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / Chem-NEX / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Chem-XAT / PSI subunit V / Uncharacterized protein / Photosystem I reaction center subunit III / Photosystem I reaction center subunit V, chloroplastic / Photosystem I subunit O / Photosystem I reaction center subunit II, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSI-K / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Uncharacterized protein / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1
Similarity search - Component
Biological speciesPhyscomitrium patens (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsZhang, S. / Tang, K.L. / Li, X.Y. / Wang, W.D. / Yan, Q.J. / Shen, L.L. / Kuang, T.Y. / Han, G.Y. / Shen, J.R. / Zhang, X.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0907600 China
Chinese Academy of SciencesYSBR-004 China
CitationJournal: Nat Plants / Year: 2023
Title: Structural insights into a unique PSI-LHCI-LHCII-Lhcb9 supercomplex from moss Physcomitrium patens.
Authors: Song Zhang / Kailu Tang / Qiujing Yan / Xingyue Li / Liangliang Shen / Wenda Wang / Yi-Kun He / Tingyun Kuang / Guangye Han / Jian-Ren Shen / Xing Zhang /
Abstract: Photosystem I (PSI) possesses a variable supramolecular organization among different photosynthetic organisms to adapt to different light environments. Mosses are evolutionary intermediates that ...Photosystem I (PSI) possesses a variable supramolecular organization among different photosynthetic organisms to adapt to different light environments. Mosses are evolutionary intermediates that diverged from aquatic green algae and evolved into land plants. The moss Physcomitrium patens (P. patens) has a light-harvesting complex (LHC) superfamily more diverse than those of green algae and higher plants. Here, we solved the structure of a PSI-LHCI-LHCII-Lhcb9 supercomplex from P. patens at 2.68 Å resolution using cryo-electron microscopy. This supercomplex contains one PSI-LHCI, one phosphorylated LHCII trimer, one moss-specific LHC protein, Lhcb9, and one additional LHCI belt with four Lhca subunits. The complete structure of PsaO was observed in the PSI core. One Lhcbm2 in the LHCII trimer interacts with PSI core through its phosphorylated N terminus, and Lhcb9 mediates assembly of the whole supercomplex. The complicated pigment arrangement provided important information for possible energy-transfer pathways from the peripheral antennae to the PSI core.
History
DepositionMay 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 3, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jun 7, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Photosystem I P700 chlorophyll a apoprotein A1
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Predicted protein PsaD
E: PsaE
F: PSI-F
G: PSI-G
H: PsaH photosystem I reaction center subunit
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
K: PsaK
L: PSI subunit V
M: Photosystem I reaction center subunit XII
O: PsaO
1: Chlorophyll a-b binding protein, chloroplastic
2: Chlorophyll a-b binding protein, chloroplastic
3: Chlorophyll a-b binding protein, chloroplastic
4: Chlorophyll a-b binding protein, chloroplastic
5: Chlorophyll a-b binding protein, chloroplastic
6: Chlorophyll a-b binding protein, chloroplastic
7: Chlorophyll a-b binding protein, chloroplastic
8: Chlorophyll a-b binding protein, chloroplastic
9: Chlorophyll a-b binding protein, chloroplastic
a: Chlorophyll a-b binding protein, chloroplastic
b: Chlorophyll a-b binding protein, chloroplastic
c: Chlorophyll a-b binding protein, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)857,081390
Polymers559,56326
Non-polymers297,517364
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I P700 chlorophyll a apoprotein ... , 2 types, 2 molecules AB

#1: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PSI-A / PsaA


Mass: 82313.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q8MFA3, photosystem I
#2: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PSI-B / PsaB


Mass: 82316.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q8MFA2, photosystem I

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Protein , 9 types, 9 molecules CDEFGHKLO

#3: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8649.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q6YXQ2, photosystem I
#4: Protein Predicted protein PsaD


Mass: 15654.927 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1JKF2
#5: Protein PsaE


Mass: 6895.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1IKE2
#6: Protein PSI-F / PsaF


Mass: 17465.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1J0L9
#7: Protein PSI-G / Photosystem I reaction center subunit V / chloroplastic


Mass: 10564.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1JC42
#8: Protein PsaH photosystem I reaction center subunit


Mass: 10468.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9SL09
#11: Protein PsaK


Mass: 8088.327 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1KU02
#12: Protein PSI subunit V


Mass: 17346.957 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1IAD0
#14: Protein PsaO


Mass: 9863.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1JDE1

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Photosystem I reaction center subunit ... , 3 types, 3 molecules IJM

#9: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 3791.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q6YXR3
#10: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4597.460 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q6YXM2
#13: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3412.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: Q6YXK4

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Chlorophyll a-b binding protein, ... , 6 types, 12 molecules 152637489abc

#15: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 20833.689 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1KU97
#16: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23039.275 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1K0C7
#17: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 23606.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1KGQ2
#18: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 22521.654 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1K0E4
#19: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 24760.443 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A0A2K1KKR9
#20: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 24457.379 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Physcomitrium patens (plant) / References: UniProt: A9RT62

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Sugars , 2 types, 6 molecules

#26: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
#27: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 10 types, 358 molecules

#21: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 221 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#22: Chemical ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H46O2
#23: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#24: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C40H56
#25: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe4S4
#28: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H86O10
#29: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: C55H70MgN4O6
#30: Chemical
ChemComp-LUT / (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / (3R,3'R)-BETA,BETA-CAROTENE-3,3'-DIOL / LUTEIN


Mass: 568.871 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C40H56O2
#31: Chemical
ChemComp-XAT / (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL / VIOLAXANTHIN


Mass: 600.870 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C40H56O4
#32: Chemical ChemComp-NEX / (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL / (3S,5R,6R,3'S,5'R,6'S)-5',6'-EPOXY-6,7-DIDEHYDRO- 5,6,5',6'-TETRAHYDRO-BETA,BETA-CAROTENE-3,5,3'-TRIOL / 9'-CIS-NEOXANTHIN


Mass: 600.870 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C40H56O4

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: PSI-LHCI-LHCII-Lhcb9 supercomplex of Physcomitrella patens
Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL
Source (natural)Organism: Physcomitrium patens (plant)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 1600 nm
Image recordingElectron dose: 78 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 83777 / Symmetry type: POINT

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