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- PDB-4i7z: Crystal structure of cytochrome b6f in DOPG, with disordered Ries... -

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Basic information

Entry
Database: PDB / ID: 4i7z
TitleCrystal structure of cytochrome b6f in DOPG, with disordered Rieske Iron-Sulfur Protein soluble domain
Components
  • (Cytochrome b6-f complex subunit ...) x 5
  • Apocytochrome f
  • Cytochrome b6-f complex iron-sulfur subunit
  • Cytochrome b6Cytochrome b
KeywordsPHOTOSYNTHESIS / CYTOCHROME / MEMBRANE PROTEIN / PLASTOQUINOL:PLASTOCYANIN OXIDOREDUCTASE / PLASTOCYANIN / THYLAKOID MEMBRANE
Function / homology
Function and homology information


plastoquinol--plastocyanin reductase activity / cytochrome b6f complex / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / photosynthetic electron transport chain / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / respiratory electron transport chain ...plastoquinol--plastocyanin reductase activity / cytochrome b6f complex / plastoquinol-plastocyanin reductase / electron transporter, transferring electrons within cytochrome b6/f complex of photosystem II activity / cytochrome complex assembly / photosynthetic electron transport chain / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / iron ion binding / intracellular membrane-bounded organelle / heme binding / metal ion binding
Similarity search - Function
Single helix bin / plastocyanin oxidoreductase / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily ...Single helix bin / plastocyanin oxidoreductase / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6/f complex, subunit 5 / Cytochrome b6-f complex, subunit 8 / Cytochrome b6/f complex, subunit IV / PetM of cytochrome b6/f complex subunit 7 / Cytochrome b6, PetB / Cytochrome b6/f complex, subunit 5 superfamily / Cytochrome b6-f complex, subunit 8 superfamily / Cytochrome B6-F complex subunit 5 / PetN / PetM family of cytochrome b6f complex subunit 7 / Cytochrome f large domain / Cytochrome f transmembrane anchor / Cytochrome f / Cytochrome f large domain / Cytochrome f large domain superfamily / Apocytochrome F, C-terminal / Apocytochrome F, N-terminal / Cytochrome f family profile. / Single helix bin / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / : / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Rieske iron-sulphur protein / Rudiment single hybrid motif / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Helix Hairpins / Up-down Bundle / Immunoglobulin-like / Beta Barrel / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-1E2 / Octadecane / BETA-CAROTENE / : / CHLOROPHYLL A / PROTOPORPHYRIN IX CONTAINING FE / PENTADECANE / N-OCTANE / Chem-OZ2 / Cytochrome b6 ...Chem-1E2 / Octadecane / BETA-CAROTENE / : / CHLOROPHYLL A / PROTOPORPHYRIN IX CONTAINING FE / PENTADECANE / N-OCTANE / Chem-OZ2 / Cytochrome b6 / Cytochrome b6-f complex subunit 4 / Cytochrome f / Cytochrome b6-f complex iron-sulfur subunit / Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit 8
Similarity search - Component
Biological speciesMastigocladus laminosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.803 Å
AuthorsHasan, S.S. / Stofleth, J.T. / Yamashita, E. / Cramer, W.A.
CitationJournal: Biochemistry / Year: 2013
Title: Lipid-induced conformational changes within the cytochrome b6f complex of oxygenic photosynthesis.
Authors: Hasan, S.S. / Stofleth, J.T. / Yamashita, E. / Cramer, W.A.
History
DepositionDec 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 2.0Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.formula / _database_2.pdbx_DOI ..._chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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 / _pdbx_struct_conn_angle.value / _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_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_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: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,43127
Polymers107,6518
Non-polymers8,78019
Water23413
1
A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules

A: Cytochrome b6
B: Cytochrome b6-f complex subunit 4
C: Apocytochrome f
D: Cytochrome b6-f complex iron-sulfur subunit
E: Cytochrome b6-f complex subunit 6
F: Cytochrome b6-f complex subunit 7
G: Cytochrome b6-f complex subunit 5
H: Cytochrome b6-f complex subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,86254
Polymers215,30316
Non-polymers17,55938
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area75070 Å2
ΔGint-804 kcal/mol
Surface area68500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.451, 159.451, 362.746
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 3 types, 3 molecules ACD

#1: Protein Cytochrome b6 / Cytochrome b


Mass: 24245.529 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83791
#3: Protein Apocytochrome f


Mass: 31655.088 Da / Num. of mol.: 1 / Fragment: UNP residues 45-333 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83793
#4: Protein Cytochrome b6-f complex iron-sulfur subunit / Plastohydroquinone:plastocyanin oxidoreductase iron-sulfur protein / ISP / RISP / Rieske iron-sulfur protein


Mass: 19422.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83794, EC: 1.10.9.1

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Cytochrome b6-f complex subunit ... , 5 types, 5 molecules BEFGH

#2: Protein Cytochrome b6-f complex subunit 4 / 17 kDa polypeptide


Mass: 17687.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83792
#5: Protein/peptide Cytochrome b6-f complex subunit 6 / Cytochrome b6-f complex subunit PetL / Cytochrome b6-f complex subunit VI


Mass: 3504.444 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83795
#6: Protein/peptide Cytochrome b6-f complex subunit 7 / Cytochrome b6-f complex subunit PetM / Cytochrome b6-f complex subunit VII


Mass: 3843.595 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83796
#7: Protein/peptide Cytochrome b6-f complex subunit 5 / Cytochrome b6-f complex subunit PetG / Cytochrome b6-f complex subunit V


Mass: 4016.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83797
#8: Protein/peptide Cytochrome b6-f complex subunit 8 / Cytochrome b6-f complex subunit PetN / Cytochrome b6-f complex subunit VIII


Mass: 3276.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mastigocladus laminosus (bacteria) / References: UniProt: P83798

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Non-polymers , 11 types, 32 molecules

#9: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#10: Chemical ChemComp-MYS / PENTADECANE / Pentadecane


Mass: 212.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H32
#11: Chemical ChemComp-8K6 / Octadecane / N-Octadecane / Octadecane


Mass: 254.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38
#12: Chemical ChemComp-UMQ / UNDECYL-MALTOSIDE / UNDECYL-BETA-D-MALTOPYRANOSIDE


Mass: 496.589 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H44O11 / Comment: detergent*YM
#13: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#14: Chemical ChemComp-CLA / CHLOROPHYLL A / Chlorophyll a


Mass: 893.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#15: Chemical ChemComp-OZ2 / (2R)-3-{[(R)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-2-[(6Z)-tridec-6-enoyloxy]propyl (9Z)-octadec-9-enoate


Mass: 704.912 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C37H69O10P
#16: Chemical ChemComp-1E2 / (2S)-3-(acetyloxy)-2-hydroxypropyl 6-deoxy-6-sulfo-beta-D-glucopyranoside


Mass: 360.335 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20O11S
#17: Chemical ChemComp-OCT / N-OCTANE / Octane


Mass: 114.229 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18
#18: Chemical ChemComp-BCR / BETA-CAROTENE / Β-Carotene


Mass: 536.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56
#19: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2

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Sample preparation

CrystalDensity Matthews: 6.18 Å3/Da / Density % sol: 80.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15-20 MG/ML B6F DIMER MIXED WITH EQUAL VOLUME OF CRYSTALLIZATION BUFFER, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-B11.0332
SYNCHROTRONAPS 23-ID-B21.0332
Detector
TypeIDDetector
MARMOSAIC 300 mm CCD1CCD
MAR scanner 300 mm plate2IMAGE PLATE
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.8→48.52 Å / Num. all: 67115 / Num. obs: 67054 / % possible obs: 99.2 %
Reflection shellResolution: 2.8→2.85 Å / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
JBluIce-EPICSdata collection
RefinementResolution: 2.803→48.517 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.897 / SU ML: 0.43 / σ(F): 1.45 / Phase error: 26.09 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2718 3405 5.08 %
Rwork0.2484 --
obs0.2496 67054 99.21 %
all-67115 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.647 Å2
Baniso -1Baniso -2Baniso -3
1-0.57 Å20.57 Å20 Å2
2--0.57 Å20 Å2
3----1.84 Å2
Refinement stepCycle: LAST / Resolution: 2.803→48.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6386 0 560 13 6959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057158
X-RAY DIFFRACTIONf_angle_d1.0589782
X-RAY DIFFRACTIONf_dihedral_angle_d15.0712608
X-RAY DIFFRACTIONf_chiral_restr0.1871077
X-RAY DIFFRACTIONf_plane_restr0.0041158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8026-2.84270.37661240.37352474X-RAY DIFFRACTION94
2.8427-2.88510.371290.36342547X-RAY DIFFRACTION97
2.8851-2.93020.37021600.34312549X-RAY DIFFRACTION99
2.9302-2.97820.37331500.34892598X-RAY DIFFRACTION99
2.9782-3.02960.34351220.33412602X-RAY DIFFRACTION99
3.0296-3.08460.33651650.31192579X-RAY DIFFRACTION99
3.0846-3.1440.3181420.30222640X-RAY DIFFRACTION99
3.144-3.20810.27891510.29972606X-RAY DIFFRACTION100
3.2081-3.27790.27791480.27712606X-RAY DIFFRACTION99
3.2779-3.35410.26151450.26362632X-RAY DIFFRACTION100
3.3541-3.43790.25631320.25492628X-RAY DIFFRACTION100
3.4379-3.53090.2761250.24812662X-RAY DIFFRACTION100
3.5309-3.63470.27051400.23542671X-RAY DIFFRACTION100
3.6347-3.7520.24571250.21522628X-RAY DIFFRACTION100
3.752-3.88610.22161610.20172656X-RAY DIFFRACTION100
3.8861-4.04160.23511380.20462643X-RAY DIFFRACTION100
4.0416-4.22540.24441410.20762673X-RAY DIFFRACTION100
4.2254-4.4480.22681380.19932686X-RAY DIFFRACTION100
4.448-4.72650.22581190.19132704X-RAY DIFFRACTION100
4.7265-5.09110.22051400.19732697X-RAY DIFFRACTION100
5.0911-5.60280.25891410.22022716X-RAY DIFFRACTION100
5.6028-6.41190.27781690.25022738X-RAY DIFFRACTION100
6.4119-8.07230.23791710.23092762X-RAY DIFFRACTION100
8.0723-48.52430.32441290.28772952X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -48.0265 Å / Origin y: 67.0967 Å / Origin z: 4.4455 Å
111213212223313233
T0.4129 Å20.08 Å20.0307 Å2-0.7724 Å2-0.0068 Å2--0.5144 Å2
L1.2874 °20.1516 °20.2274 °2-1.1064 °20.2039 °2--1.084 °2
S0.0986 Å °0.6112 Å °0.0262 Å °-0.1304 Å °-0.0408 Å °0.0986 Å °0.0132 Å °0.133 Å °-0.0484 Å °
Refinement TLS groupSelection details: all

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