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- EMDB-47933: CryoEM map of the mLST8-Rag-Ragultor subcomplex -

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Basic information

Entry
Database: EMDB / ID: EMD-47933
TitleCryoEM map of the mLST8-Rag-Ragultor subcomplex
Map data
Sample
  • Complex: mLST8-Rag-Ragultor subcomplex
    • Protein or peptide: x 8 types
  • Ligand: x 3 types
KeywordsmTORC1 / cell growth / singaling protein / membrane / SIGNALING PROTEIN
Function / homology
Function and homology information


regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / regulation of cholesterol efflux / Gtr1-Gtr2 GTPase complex / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / positive regulation of pentose-phosphate shunt / TORC2 signaling ...regulation of cholesterol import / positive regulation of protein localization to lysosome / regulation of cell-substrate junction organization / regulation of cholesterol efflux / Gtr1-Gtr2 GTPase complex / FNIP-folliculin RagC/D GAP / Ragulator complex / protein localization to cell junction / positive regulation of pentose-phosphate shunt / TORC2 signaling / TORC2 complex / regulation of TORC1 signaling / protein localization to lysosome / TORC1 complex / regulation of TOR signaling / MTOR signalling / fibroblast migration / Amino acids regulate mTORC1 / lysosome localization / Energy dependent regulation of mTOR by LKB1-AMPK / endosome organization / TORC1 signaling / serine/threonine protein kinase complex / kinase activator activity / cellular response to osmotic stress / protein localization to membrane / endosomal transport / azurophil granule membrane / lysosome organization / small GTPase-mediated signal transduction / Macroautophagy / regulation of cell size / RHOJ GTPase cycle / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of actin filament polymerization / RHOQ GTPase cycle / TOR signaling / mTORC1-mediated signalling / CDC42 GTPase cycle / tertiary granule membrane / RHOH GTPase cycle / ficolin-1-rich granule membrane / RHOG GTPase cycle / regulation of receptor recycling / CD28 dependent PI3K/Akt signaling / RAC2 GTPase cycle / HSF1-dependent transactivation / RAC3 GTPase cycle / positive regulation of TOR signaling / enzyme-substrate adaptor activity / response to amino acid / positive regulation of lipid biosynthetic process / cellular response to nutrient levels / specific granule membrane / protein-membrane adaptor activity / RAC1 GTPase cycle / cytoskeleton organization / positive regulation of TORC1 signaling / negative regulation of autophagy / cellular response to amino acid starvation / RNA splicing / viral genome replication / guanyl-nucleotide exchange factor activity / cholesterol homeostasis / positive regulation of glycolytic process / cellular response to starvation / protein serine/threonine kinase activator activity / Regulation of PTEN gene transcription / tumor necrosis factor-mediated signaling pathway / VEGFR2 mediated vascular permeability / positive regulation of interleukin-8 production / TP53 Regulates Metabolic Genes / regulation of actin cytoskeleton organization / cellular response to amino acid stimulus / phosphoprotein binding / regulation of cell growth / MAP2K and MAPK activation / positive regulation of protein localization to nucleus / response to virus / GDP binding / late endosome membrane / Regulation of TP53 Degradation / intracellular protein localization / late endosome / glucose homeostasis / PIP3 activates AKT signaling / E3 ubiquitin ligases ubiquitinate target proteins / GTPase binding / positive regulation of cell growth / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / protein-macromolecule adaptor activity / cellular response to hypoxia / molecular adaptor activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / lysosome / positive regulation of canonical NF-kappaB signal transduction / endosome membrane / positive regulation of MAPK cascade / intracellular signal transduction / membrane raft
Similarity search - Function
Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / RagA/B ...Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / Ragulator complex protein LAMTOR5 / Mitogen-activated protein kinase kinase 1 interacting / LAMTOR1/MEH1 / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / Late endosomal/lysosomal adaptor and MAPK and MTOR activator / RagA/B / RagC/D / Gtr1/RagA G protein / Gtr1/RagA G protein conserved region / Ragulator complex protein LAMTOR2-like / Target of rapamycin complex subunit LST8 / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Quinoprotein alcohol dehydrogenase-like superfamily / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ragulator complex protein LAMTOR5 / Ragulator complex protein LAMTOR4 / Ragulator complex protein LAMTOR1 / Ras-related GTP-binding protein A / Target of rapamycin complex subunit LST8 / Ras-related GTP-binding protein C / Ragulator complex protein LAMTOR3 / Ragulator complex protein LAMTOR2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.98 Å
AuthorsCui Z / Hurley J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA285366 United States
CitationJournal: Nature / Year: 2025
Title: Structural basis for mTORC1 activation on the lysosomal membrane.
Authors: Zhicheng Cui / Alessandra Esposito / Gennaro Napolitano / Andrea Ballabio / James H Hurley /
Abstract: The mechanistic target of rapamycin complex 1 (mTORC1) integrates growth factor (GF) and nutrient signals to stimulate anabolic processes connected to cell growth and inhibit catabolic processes such ...The mechanistic target of rapamycin complex 1 (mTORC1) integrates growth factor (GF) and nutrient signals to stimulate anabolic processes connected to cell growth and inhibit catabolic processes such as autophagy. GF signalling through the tuberous sclerosis complex regulates the lysosomally localized small GTPase RAS homologue enriched in brain (RHEB). Direct binding of RHEB-GTP to the mTOR kinase subunit of mTORC1 allosterically activates the kinase by inducing a large-scale conformational change. Here we reconstituted mTORC1 activation on membranes by RHEB, RAGs and Ragulator. Cryo-electron microscopy showed that RAPTOR and mTOR interact directly with the membrane. Full engagement of the membrane anchors is required for optimal alignment of the catalytic residues in the mTOR kinase active site. Converging signals from GFs and nutrients drive mTORC1 recruitment to and activation on lysosomal membrane in a four-step process, consisting of (1) RAG-Ragulator-driven recruitment to within ~100 Å of the lysosomal membrane; (2) RHEB-driven recruitment to within ~40 Å; (3) RAPTOR-membrane engagement and intermediate enzyme activation; and (4) mTOR-membrane engagement and full enzyme activation. RHEB and membrane engagement combined leads to full catalytic activation and structurally explains GF and nutrient signal integration at the lysosome.
History
DepositionNov 15, 2024-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateOct 1, 2025-
Current statusOct 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47933.png

Downloads & links

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Map

FileDownload / File: emd_47933.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 448 pix.
= 465.92 Å		1.04 Å/pix.
x 448 pix.
= 465.92 Å		1.04 Å/pix.
x 448 pix.
= 465.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.46583465 - 0.7032586
Average (Standard dev.)-0.00015605202 (±0.009931812)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 465.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47933_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47933_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mLST8-Rag-Ragultor subcomplex

EntireName: mLST8-Rag-Ragultor subcomplex
Components
  • Complex: mLST8-Rag-Ragultor subcomplex
    • Protein or peptide: Ras-related GTP-binding protein A
    • Protein or peptide: Ragulator complex protein LAMTOR2
    • Protein or peptide: Ragulator complex protein LAMTOR3
    • Protein or peptide: Ragulator complex protein LAMTOR5
    • Protein or peptide: Target of rapamycin complex subunit LST8
    • Protein or peptide: Ras-related GTP-binding protein C
    • Protein or peptide: Ragulator complex protein LAMTOR1
    • Protein or peptide: Ragulator complex protein LAMTOR4
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: mLST8-Rag-Ragultor subcomplex

SupramoleculeName: mLST8-Rag-Ragultor subcomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ras-related GTP-binding protein A

MacromoleculeName: Ras-related GTP-binding protein A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 36.600195 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPNTAMKKKV LLMGKSGSGK TSMRSIIFAN YIARDTRRLG ATIDVEHSHV RFLGNLVLNL WDCGGLDTFM ENYFTSQRDN IFRNVEVLI YVFDVESREL EKDMHYYQSC LEAILQNSPD AKIFCLVHKM DLVQEDQRDL IFKEREEDLR RLSRPLECAC F RTSIWDET ...String:
MPNTAMKKKV LLMGKSGSGK TSMRSIIFAN YIARDTRRLG ATIDVEHSHV RFLGNLVLNL WDCGGLDTFM ENYFTSQRDN IFRNVEVLI YVFDVESREL EKDMHYYQSC LEAILQNSPD AKIFCLVHKM DLVQEDQRDL IFKEREEDLR RLSRPLECAC F RTSIWDET LYKAWSSIVY QLIPNVQQLE MNLRNFAQII EADEVLLFER ATFLVISHYQ CKEQRDVHRF EKISNIIKQF KL SCSKLAA SFQSMEVRNS NFAAFIDIFT SNTYVMVVMS DPSIPSAATL INIRNARKHF EKLERVDGPK HSLLMR

UniProtKB: Ras-related GTP-binding protein A

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Macromolecule #2: Ragulator complex protein LAMTOR2

MacromoleculeName: Ragulator complex protein LAMTOR2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.51745 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MLRPKALTQV LSQANTGGVQ STLLLNNEGS LLAYSGYGDT DARVTAAIAS NIWAAYDRNG NQAFNEDNLK FILMDCMEGR VAITRVANL LLCMYAKETV GFGMLKAKAQ ALVQYLEEPL TQVAAS

UniProtKB: Ragulator complex protein LAMTOR2

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Macromolecule #3: Ragulator complex protein LAMTOR3

MacromoleculeName: Ragulator complex protein LAMTOR3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.637678 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MADDLKRFLY KKLPSVEGLH AIVVSDRDGV PVIKVANDNA PEHALRPGFL STFALATDQG SKLGLSKNKS IICYYNTYQV VQFNRLPLV VSFIASSSAN TGLIVSLEKE LAPLFEELRQ VVEVS

UniProtKB: Ragulator complex protein LAMTOR3

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Macromolecule #4: Ragulator complex protein LAMTOR5

MacromoleculeName: Ragulator complex protein LAMTOR5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.6229 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MEATLEQHLE DTMKNPSIVG VLCTDSQGLN LGCRGTLSDE HAGVISVLAQ QAAKLTSDPT DIPVVCLESD NGNIMIQKHD GITVAVHKM AS

UniProtKB: Ragulator complex protein LAMTOR5

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Macromolecule #5: Target of rapamycin complex subunit LST8

MacromoleculeName: Target of rapamycin complex subunit LST8 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.91009 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNTSPGTVGS DPVILATAGY DHTVRFWQAH SGICTRTVQH QDSQVNALEV TPDRSMIAAA GYQHIRMYDL NSNNPNPIIS YDGVNKNIA SVGFHEDGRW MYTGGEDCTA RIWDLRSRNL QCQRIFQVNA PINCVCLHPN QAELIVGDQS GAIHIWDLKT D HNEQLIPE ...String:
MNTSPGTVGS DPVILATAGY DHTVRFWQAH SGICTRTVQH QDSQVNALEV TPDRSMIAAA GYQHIRMYDL NSNNPNPIIS YDGVNKNIA SVGFHEDGRW MYTGGEDCTA RIWDLRSRNL QCQRIFQVNA PINCVCLHPN QAELIVGDQS GAIHIWDLKT D HNEQLIPE PEVSITSAHI DPDASYMAAV NSTGNCYVWN LTGGIGDEVT QLIPKTKIPA HTRYALQCRF SPDSTLLATC SA DQTCKIW RTSNFSLMTE LSIKSGNPGE SSRGWMWGCA FSGDSQYIVT ASSDNLARLW CVETGEIKRE YGGHQKAVVC LAF NDSVLG

UniProtKB: Target of rapamycin complex subunit LST8

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Macromolecule #6: Ras-related GTP-binding protein C

MacromoleculeName: Ras-related GTP-binding protein C / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.298859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSLQYGAEET PLAGSYGAAD SFPKDFGYGV EEEEEEAAAA GGGVGAGAGG GCGPGGADSS KPRILLMGLR RSGKNSIQKV VFHKMSPNE TLFLESTNKI YKDDISNSSF VNFQIWDFPG QMDFFDPTFD YEMIFRGTGA LIYVIDAQDD YMEALTRLHI T VSKAYKVN ...String:
MSLQYGAEET PLAGSYGAAD SFPKDFGYGV EEEEEEAAAA GGGVGAGAGG GCGPGGADSS KPRILLMGLR RSGKNSIQKV VFHKMSPNE TLFLESTNKI YKDDISNSSF VNFQIWDFPG QMDFFDPTFD YEMIFRGTGA LIYVIDAQDD YMEALTRLHI T VSKAYKVN PDMNFEVFIH KVDGLSDDHK IETQRDIHQR ANDDLADAGL EKLHLSFYLT SIYDHSIFEA FSKVVQKLIP QL PTLENLL NIFISNSGIE KAFLFDVVSK IYIATDSSPV DMQSYELCCD MIDVVIDVSC IYGLKEDGSG SAYDKESMAI IKL NNTTVL YLKEVTKFLA LVCILREESF ERKGLIDYNF HCFRKAIHEV FEVGVTSHRS CGHQTSASSL KALTHNGTPR NAI

UniProtKB: Ras-related GTP-binding protein C

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Macromolecule #7: Ragulator complex protein LAMTOR1

MacromoleculeName: Ragulator complex protein LAMTOR1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.762775 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MGCCYSSENE DSDQDREERK LLLDPSSPPT KALNGAEPNY HSLPSARTDE QALLSSILAK TASNIIDVSA ADSQGMEQHE YMDRARQYS TRLAVLSSSL THWKKLPPLP SLTSQPHQVL ASEPIPFSDL QQVSRIAAYA YSALSQIRVD AKEELVVQFG I P

UniProtKB: Ragulator complex protein LAMTOR1

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Macromolecule #8: Ragulator complex protein LAMTOR4

MacromoleculeName: Ragulator complex protein LAMTOR4 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.753236 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MTSALTQGLE RIPDQLGYLV LSEGAVLASS GDLENDEQAA SAISELVSTA CGFRLHRGMN VPFKRLSVVF GEHTLLVTVS GQRVFVVKR QNRGREPIDV

UniProtKB: Ragulator complex protein LAMTOR4

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Macromolecule #9: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #11: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab-initio reconstruction by cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 190751
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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