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- EMDB-64036: Cryo-EM structure of the Lhcp trimer from Ostreococcus tauri at 1... -

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Basic information

Entry
Database: EMDB / ID: EMD-64036
TitleCryo-EM structure of the Lhcp trimer from Ostreococcus tauri at 1.94 angstrom resolution
Map data
Sample
  • Complex: Lhcp trimer from Ostreococcus tauri
    • Protein or peptide: x 1 types
  • Ligand: x 12 types
KeywordsLHCp / Prasinophytes / green light absorption / carotenoid / photosynthesis / Light-harvesting complex / prasinoxanthin / micromonal / dihydrolutein / uriolide / acyl-antheraxanthin / DVP.
Function / homologyphotosynthesis, light harvesting / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / Chlorophyll a-b binding protein, chloroplastic
Function and homology information
Biological speciesOstreococcus tauri (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.94 Å
AuthorsSeki S / Kubota M / Ishii A / Kim E / Tanaka H / Miyata T / Namba K / Kurisu G / Minagawa J / Fujii R
Funding support Japan, 7 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP23ama121003 Japan
Japan Society for the Promotion of Science (JSPS)K23KJ1834 Japan
Japan Science and TechnologyJPMJFS2138 Japan
Japan Science and TechnologyJPMJCR20E1 Japan
Japan Society for the Promotion of Science (JSPS)23H04958 Japan
Japan Society for the Promotion of Science (JSPS)21H05040 Japan
Japan Society for the Promotion of Science (JSPS)23H04960 Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of the LHCp trimer from Ostreococcus tauri at 1.94 angstrom resolution
Authors: Soichiro S / Kubota M / Ishii A / Kim E / Tomoko M / Hideaki T / Keiichi N / Genji K / Minagawa J / Ritsuko F
History
DepositionApr 3, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64036.png

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Map

FileDownload / File: emd_64036.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 219.904 Å		0.86 Å/pix.
x 256 pix.
= 219.904 Å		0.86 Å/pix.
x 256 pix.
= 219.904 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.859 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.9038061 - 3.7714272
Average (Standard dev.)0.0009286732 (±0.08379095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 219.904 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_64036_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64036_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Lhcp trimer from Ostreococcus tauri

EntireName: Lhcp trimer from Ostreococcus tauri
Components
  • Complex: Lhcp trimer from Ostreococcus tauri
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Ligand: CHLOROPHYLL A
  • Ligand: CHLOROPHYLL B
  • Ligand: Mg-2,4-divinyl-phaeoporphyrin a5-monometyl ester
  • Ligand: (3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one
  • Ligand: (5~{Z})-3-[2-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]ethyl]-5-[(2~{E},4~{E},6~{E},8~{E},10~{E},12~{E})-2,7,11-trimethyl-13-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]trideca-2,4,6,8,10,12-hexaenylidene]furan-2-one
  • Ligand: (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
  • Ligand: (2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E})-6,11,15-trimethyl-17-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]-2-[2-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]ethyl]heptadeca-2,4,6,8,10,12,14,16-octaenal
  • Ligand: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15-octaenyl]cyclohex-3-en-1-ol
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: [(1~{S},3~{S},6~{R})-1,5,5-trimethyl-6-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]-7-oxabicyclo[4.1.0]heptan-3-yl] (~{Z})-oct-2-enoate
  • Ligand: water

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Supramolecule #1: Lhcp trimer from Ostreococcus tauri

SupramoleculeName: Lhcp trimer from Ostreococcus tauri / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Ostreococcus tauri (plant)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ostreococcus tauri (plant)
Molecular weightTheoretical: 21.417949 KDa
SequenceString: ADIYPEFGTY PGGGESPIIP FGSEKNAERE VIHGRWAMLG VTGAWAAENG TGIPWFTAGT LCTPDDCTAV ADKFPGAVAP LAPEGSGYP SFWNVLIIEI VLVGAAEAYR TGISDSPFDD GLTVGDVNPG GRFDPLGLAE SGDLEELKIK ELKHCRLSMF A WLGCIFQA ...String:
ADIYPEFGTY PGGGESPIIP FGSEKNAERE VIHGRWAMLG VTGAWAAENG TGIPWFTAGT LCTPDDCTAV ADKFPGAVAP LAPEGSGYP SFWNVLIIEI VLVGAAEAYR TGISDSPFDD GLTVGDVNPG GRFDPLGLAE SGDLEELKIK ELKHCRLSMF A WLGCIFQA LATQEGPIAN WQSHVADPVH SNVLTNAAKG FGFY

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #2: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 2 / Number of copies: 21 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #3: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 3 / Number of copies: 18 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #4: Mg-2,4-divinyl-phaeoporphyrin a5-monometyl ester

MacromoleculeName: Mg-2,4-divinyl-phaeoporphyrin a5-monometyl ester / type: ligand / ID: 4 / Number of copies: 3 / Formula: A1L0F
Molecular weightTheoretical: 610.941 Da

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Macromolecule #5: (3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4...

MacromoleculeName: (3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl- ...Name: (3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one
type: ligand / ID: 5 / Number of copies: 6 / Formula: IWJ
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-IWJ:
(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one

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Macromolecule #6: (5~{Z})-3-[2-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2...

MacromoleculeName: (5~{Z})-3-[2-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]ethyl]-5-[(2~{E},4~{E},6~{E},8~{E},10~{E},12~{E})-2,7,11-trimethyl-13-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7- ...Name: (5~{Z})-3-[2-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]ethyl]-5-[(2~{E},4~{E},6~{E},8~{E},10~{E},12~{E})-2,7,11-trimethyl-13-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]trideca-2,4,6,8,10,12-hexaenylidene]furan-2-one
type: ligand / ID: 6 / Number of copies: 3 / Formula: A1LYY
Molecular weightTheoretical: 614.854 Da

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Macromolecule #7: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...

MacromoleculeName: (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
type: ligand / ID: 7 / Number of copies: 3 / Formula: NEX
Molecular weightTheoretical: 600.87 Da
Chemical component information

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

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Macromolecule #8: (2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E})-6,11,15-tri...

MacromoleculeName: (2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E})-6,11,15-trimethyl-17-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]-2-[2-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl] ...Name: (2~{Z},4~{E},6~{E},8~{E},10~{E},12~{E},14~{E},16~{E})-6,11,15-trimethyl-17-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]-2-[2-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]ethyl]heptadeca-2,4,6,8,10,12,14,16-octaenal
type: ligand / ID: 8 / Number of copies: 3 / Formula: A1LYX
Molecular weightTheoretical: 584.871 Da

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Macromolecule #9: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},...

MacromoleculeName: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15- ...Name: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-1,3,5,7,9,11,13,15-octaenyl]cyclohex-3-en-1-ol
type: ligand / ID: 9 / Number of copies: 3 / Formula: A1L0E
Molecular weightTheoretical: 570.887 Da

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Macromolecule #10: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 10 / Number of copies: 3 / Formula: AV0
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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Macromolecule #11: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 11 / Number of copies: 3 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

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Macromolecule #12: [(1~{S},3~{S},6~{R})-1,5,5-trimethyl-6-[(1~{E},3~{E},5~{E},7~{E},...

MacromoleculeName: [(1~{S},3~{S},6~{R})-1,5,5-trimethyl-6-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca- ...Name: [(1~{S},3~{S},6~{R})-1,5,5-trimethyl-6-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenyl]-7-oxabicyclo[4.1.0]heptan-3-yl] (~{Z})-oct-2-enoate
type: ligand / ID: 12 / Number of copies: 3 / Formula: A1LYW
Molecular weightTheoretical: 709.051 Da

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Macromolecule #13: water

MacromoleculeName: water / type: ligand / ID: 13 / Number of copies: 186 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5.0 mg/mL
BufferpH: 7.5 / Component - Concentration: 25.0 mM / Component - Formula: C8H18N2O4S / Component - Name: HEPES / Details: 0.003% LMNG
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Pressure: 10000.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6144 / Average exposure time: 3.0 sec. / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 5408616
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 1.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 1153594
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8hg3


Chain - Chain ID: S / Chain - Residue range: 32-233 / Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9uc6:
Cryo-EM structure of the Lhcp trimer from Ostreococcus tauri at 1.94 angstrom resolution

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