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- PDB-9luu: PSI-4 LHCI dimer supercomplex from M. polymorpha -

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Basic information

Entry
Database: PDB / ID: 9luu
TitlePSI-4 LHCI dimer supercomplex from M. polymorpha
Components
  • (Chlorophyll a-b binding protein, ...) x 4
  • (Photosystem I ...) x 11
  • PSI subunit V
  • PSI-K
KeywordsPHOTOSYNTHESIS / Photosystem I
Function / homology
Function and homology information


photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / response to low light intensity stimulus / plastid thylakoid membrane / thylakoid membrane / response to high light intensity / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / photosystem I reaction center ...photosynthetic NADP+ reduction / photosystem I stabilization / chloroplast photosystem I / response to low light intensity stimulus / plastid thylakoid membrane / thylakoid membrane / response to high light intensity / photosynthesis, light harvesting in photosystem I / chloroplast thylakoid lumen / 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 / response to cold / chloroplast / 4 iron, 4 sulfur cluster binding / electron transfer activity / oxidoreductase activity / protein stabilization / protein domain specific binding / mRNA binding / magnesium ion binding / metal ion binding
Similarity search - Function
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 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 / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / 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 / Photosystem I PsaD / Photosystem I, reaction centre subunit PsaD superfamily / PsaD / Photosystem I PsaE, reaction centre subunit IV / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I reaction centre subunit IV / PsaE / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I reaction centre subunit IX / PsaJ / 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 ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / EICOSANE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE ...BETA-CAROTENE / CHLOROPHYLL B / CHLOROPHYLL A ISOMER / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / EICOSANE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-LUT / PHYLLOQUINONE / IRON/SULFUR CLUSTER / Photosystem I reaction center subunit II, chloroplastic / PSI-K / Photosystem I reaction center subunit XI, chloroplastic / Photosystem I reaction center subunit III / Uncharacterized protein / Photosystem I reaction center subunit V, chloroplastic / Photosystem I reaction center subunit VI, chloroplastic / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I iron-sulfur center / Photosystem I P700 chlorophyll a apoprotein A1 / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem I reaction center subunit VIII / Photosystem I reaction center subunit IX / Photosystem I reaction center subunit XII
Similarity search - Component
Biological speciesMarchantia polymorpha (common liverwort)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.52 Å
AuthorsTsai, P.-C. / La Rocca, R. / Shen, J.-R. / Akita, F.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP22H04916 Japan
CitationJournal: Commun Biol / Year: 2026
Title: Structural study of monomeric and dimeric photosystem I-LHCI supercomplexes from a bryophyte.
Authors: Pi-Cheng Tsai / Romain La Rocca / Hiroyasu Motose / Jian-Ren Shen / Fusamichi Akita /
Abstract: Photosystem I (PSI) is one of the two photosystems conserved from cyanobacteria to vascular plants, and associates with multiple light-harvesting complexes (LHCs) that capture and transfer solar ...Photosystem I (PSI) is one of the two photosystems conserved from cyanobacteria to vascular plants, and associates with multiple light-harvesting complexes (LHCs) that capture and transfer solar energy. Liverworts such as Marchantia polymorpha occupy an early evolutionary position among land plants and faced major challenges during terrestrial adaptation, including desiccation, strong light, and UV radiation. We reveal the cryo-electron microscopic structures of PSI-LHCI monomer and homodimer from the liverwort M. polymorpha at resolutions of 1.94 and 2.52 Å, respectively. The high-resolution map allows identification of the cofactors of the monomer and reveal differences between the liverwort and moss, another clade of bryophytes. The PSI-LHCI monomer-monomer is stabilized by PsaG and PsaH interactions on the stromal side, which causes the bending and twisting of the homodimer. PsaM interacts with PsaB tightly, indicating a key role of PsaM in mediating the dimerization.
History
DepositionFeb 10, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Photosystem I P700 chlorophyll a apoprotein A2
C: Photosystem I iron-sulfur center
D: Photosystem I reaction center subunit II, chloroplastic
E: Photosystem I reaction centre subunit IV
F: Photosystem I reaction center subunit III
G: Photosystem I reaction center subunit V, chloroplastic
H: Photosystem I reaction center subunit VI, chloroplastic
I: Photosystem I reaction center subunit VIII
J: Photosystem I reaction center subunit IX
L: PSI subunit V
M: Photosystem I reaction center subunit XII
b: Photosystem I P700 chlorophyll a apoprotein A2
c: Photosystem I iron-sulfur center
d: Photosystem I reaction center subunit II, chloroplastic
e: Photosystem I reaction centre subunit IV
f: Photosystem I reaction center subunit III
g: Photosystem I reaction center subunit V, chloroplastic
h: Photosystem I reaction center subunit VI, chloroplastic
i: Photosystem I reaction center subunit VIII
j: Photosystem I reaction center subunit IX
l: PSI subunit V
m: Photosystem I reaction center subunit XII
A: Photosystem I P700 chlorophyll a apoprotein A1
2a: Chlorophyll a-b binding protein, chloroplastic
3a: Chlorophyll a-b binding protein, chloroplastic
5a: Chlorophyll a-b binding protein, chloroplastic
6a: Chlorophyll a-b binding protein, chloroplastic
K: PSI-K
a: Photosystem I P700 chlorophyll a apoprotein A1
2b: Chlorophyll a-b binding protein, chloroplastic
3b: Chlorophyll a-b binding protein, chloroplastic
5b: Chlorophyll a-b binding protein, chloroplastic
6b: Chlorophyll a-b binding protein, chloroplastic
k: PSI-K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,193,374446
Polymers859,09734
Non-polymers334,278412
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem I ... , 11 types, 22 molecules BbCcDdEeFfGgHhIiJjMmAa

#1: Protein Photosystem I P700 chlorophyll a apoprotein A2 / PsaB


Mass: 82484.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: A0A3Q9R072, photosystem I
#2: Protein Photosystem I iron-sulfur center / 9 kDa polypeptide / PSI-C / Photosystem I subunit VII / PsaC


Mass: 8866.216 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: A0A3Q9R1I6, photosystem I
#3: Protein Photosystem I reaction center subunit II, chloroplastic


Mass: 22614.096 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: A0A2R6W6G7
#4: Protein Photosystem I reaction centre subunit IV


Mass: 13821.722 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: A0A2R6WSQ6
#5: Protein Photosystem I reaction center subunit III / PSI-F


Mass: 26025.164 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: A0A2R6WM91
#6: Protein Photosystem I reaction center subunit V, chloroplastic / PSI-G


Mass: 16912.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: A0A2R6X3Q4
#7: Protein Photosystem I reaction center subunit VI, chloroplastic


Mass: 14660.665 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: A0A2R6XLB4
#8: Protein/peptide Photosystem I reaction center subunit VIII / PSI-I


Mass: 4017.787 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: P12185
#9: Protein/peptide Photosystem I reaction center subunit IX / PSI-J


Mass: 4778.650 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: P12191
#11: Protein/peptide Photosystem I reaction center subunit XII / PSI-M


Mass: 3568.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: P31590
#12: Protein Photosystem I P700 chlorophyll a apoprotein A1 / PsaA


Mass: 83299.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: A0A3Q9R2J6, photosystem I

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Protein , 2 types, 4 molecules LlKk

#10: Protein PSI subunit V


Mass: 23152.729 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: A0A2R6WE99
#17: Protein PSI-K


Mass: 13483.683 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: A0A2R6W993

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Chlorophyll a-b binding protein, ... , 4 types, 8 molecules 2a2b3a3b5a5b6a6b

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


Mass: 28576.648 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: I7JD56
#14: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 30133.443 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: I7KJM4
#15: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 27114.066 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: I7IIM0
#16: Protein Chlorophyll a-b binding protein, chloroplastic


Mass: 26038.801 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Marchantia polymorpha (common liverwort) / References: UniProt: I7JWJ2

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Sugars , 2 types, 8 molecules

#21: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15 / Feature type: SUBJECT OF INVESTIGATION
#28: Sugar
ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 10 types, 404 molecules

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


Mass: 893.489 Da / Num. of mol.: 276 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#19: Chemical
ChemComp-PQN / PHYLLOQUINONE / VITAMIN K1 / 2-METHYL-3-PHYTYL-1,4-NAPHTHOQUINONE


Mass: 450.696 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C31H46O2 / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical...
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 42 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical
ChemComp-LFA / EICOSANE / LIPID FRAGMENT


Mass: 282.547 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H42 / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#25: 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.: 20 / Source method: obtained synthetically / Formula: C40H56O2 / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical ChemComp-CL0 / CHLOROPHYLL A ISOMER


Mass: 893.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#29: Chemical...
ChemComp-CHL / CHLOROPHYLL B


Mass: 907.472 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION

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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: Photosystem I-4 LHCI dimer supercomplex from liverwort
Type: COMPLEX / Entity ID: #1-#17 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Marchantia polymorpha (common liverwort)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 1.46 mg Chl a per mL
Specimen supportDetails: 10 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 17907
EM imaging opticsEnergyfilter name: TFS Selectris X / Phase plate: VOLTA PHASE PLATE
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2EPU3image acquisition
4cryoSPARC4.6.0CTF correction
7Coot0.9.8.7model fitting
12cryoSPARC4.6.03D reconstruction
13PHENIX1.20.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2164638
3D reconstructionResolution: 2.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27750 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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