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- EMDB-0154: Retromer-Vps5: low-resolution overview map centred on the Vps26 dimer. -

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Basic information

Entry
Database: EMDB / ID: EMD-0154
TitleRetromer-Vps5: low-resolution overview map centred on the Vps26 dimer.
Map dataLow-resolution overview map of retromer-Vps5 centered on the Vps26 dimer.
Sample
  • Complex: Retromer-Vps5 complex assembled on the membrane.
    • Protein or peptide: Vacuolar protein sorting-associated protein 26-like protein
    • Protein or peptide: Putative vacuolar protein sorting-associated protein
    • Protein or peptide: Putative vacuolar protein sorting-associated protein
    • Protein or peptide: Putative vacuolar protein sorting-associated protein
    • Protein or peptide: Vacuolar protein sorting-associated protein 29
    • Protein or peptide: Vacuolar protein sorting-associated protein 35
Keywordsretromer / endosome / sorting nexin / BAR / membrane trafficking / PROTEIN TRANSPORT
Function / homology
Function and homology information


ascospore-type prospore membrane formation / prospore membrane / retromer, cargo-selective complex / retromer complex / retrograde transport, endosome to Golgi / phosphatidylinositol binding / intracellular protein transport / late endosome / endosome / identical protein binding / cytosol
Similarity search - Function
Vacuolar protein sorting-associated protein 5-like / Sorting nexin Vps5, BAR domain / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29 ...Vacuolar protein sorting-associated protein 5-like / Sorting nexin Vps5, BAR domain / Sorting nexin Vps5-like, C-terminal / Vps5 C terminal like / Vacuolar protein sorting protein 26 related / Vacuolar protein sorting-associated protein 26 / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 35, C-terminal / Vacuolar protein sorting-associated protein 35 / Vacuolar protein sorting-associated protein 29 / Phosphodiesterase MJ0936/Vps29 / Calcineurin-like phosphoesterase domain, lpxH-type / Calcineurin-like phosphoesterase superfamily domain / Arrestin-like, C-terminal / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / AH/BAR domain superfamily / Metallo-dependent phosphatase-like
Similarity search - Domain/homology
Vacuolar protein sorting-associated protein 29 / Vacuolar protein sorting-associated protein 26-like protein / Vacuolar protein sorting-associated protein 35 / Putative vacuolar protein sorting-associated protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsubtomogram averaging / cryo EM / Resolution: 11.4 Å
AuthorsKovtun O / Leneva N / Ariotti N / Rohan TS / Owen DJ / Briggs JAG / Collins BM
Funding support United Kingdom, Australia, 7 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_UP_1201/16 United Kingdom
Wellcome Trust207455/Z/17/Z United Kingdom
Australian Research CouncilDP160101743 Australia
National Health and Medical Research Council (Australia)APP1042082 Australia
National Health and Medical Research Council (Australia)APP1058734 Australia
National Health and Medical Research Council (Australia)APP1041929 Australia
National Health and Medical Research Council (Australia)APP1136021 Australia
CitationJournal: Nature / Year: 2018
Title: Structure of the membrane-assembled retromer coat determined by cryo-electron tomography.
Authors: Oleksiy Kovtun / Natalya Leneva / Yury S Bykov / Nicholas Ariotti / Rohan D Teasdale / Miroslava Schaffer / Benjamin D Engel / David J Owen / John A G Briggs / Brett M Collins /
Abstract: Eukaryotic cells traffic proteins and lipids between different compartments using protein-coated vesicles and tubules. The retromer complex is required to generate cargo-selective tubulovesicular ...Eukaryotic cells traffic proteins and lipids between different compartments using protein-coated vesicles and tubules. The retromer complex is required to generate cargo-selective tubulovesicular carriers from endosomal membranes. Conserved in eukaryotes, retromer controls the cellular localization and homeostasis of hundreds of transmembrane proteins, and its disruption is associated with major neurodegenerative disorders. How retromer is assembled and how it is recruited to form coated tubules is not known. Here we describe the structure of the retromer complex (Vps26-Vps29-Vps35) assembled on membrane tubules with the bin/amphiphysin/rvs-domain-containing sorting nexin protein Vps5, using cryo-electron tomography and subtomogram averaging. This reveals a membrane-associated Vps5 array, from which arches of retromer extend away from the membrane surface. Vps35 forms the 'legs' of these arches, and Vps29 resides at the apex where it is free to interact with regulatory factors. The bases of the arches connect to each other and to Vps5 through Vps26, and the presence of the same arches on coated tubules within cells confirms their functional importance. Vps5 binds to Vps26 at a position analogous to the previously described cargo- and Snx3-binding site, which suggests the existence of distinct retromer-sorting nexin assemblies. The structure provides insight into the architecture of the coat and its mechanism of assembly, and suggests that retromer promotes tubule formation by directing the distribution of sorting nexin proteins on the membrane surface while providing a scaffold for regulatory-protein interactions.
History
DepositionJul 31, 2018-
Header (metadata) releaseSep 5, 2018-
Map releaseSep 26, 2018-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6h7w
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6h7w
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0154.png

Downloads & links

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Map

FileDownload / File: emd_0154.map.gz / Format: CCP4 / Size: 11.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLow-resolution overview map of retromer-Vps5 centered on the Vps26 dimer.
Voxel sizeX=Y=Z: 2.7 Å
Density
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.15
Minimum - Maximum-0.5354475 - 0.764921
Average (Standard dev.)0.0027230864 (±0.058002256)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions144144144
Spacing144144144
CellA=B=C: 388.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z388.800388.800388.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS144144144
D min/max/mean-0.5350.7650.003

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Supplemental data

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Sample components

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Entire : Retromer-Vps5 complex assembled on the membrane.

EntireName: Retromer-Vps5 complex assembled on the membrane.
Components
  • Complex: Retromer-Vps5 complex assembled on the membrane.
    • Protein or peptide: Vacuolar protein sorting-associated protein 26-like protein
    • Protein or peptide: Putative vacuolar protein sorting-associated protein
    • Protein or peptide: Putative vacuolar protein sorting-associated protein
    • Protein or peptide: Putative vacuolar protein sorting-associated protein
    • Protein or peptide: Vacuolar protein sorting-associated protein 29
    • Protein or peptide: Vacuolar protein sorting-associated protein 35

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Supramolecule #1: Retromer-Vps5 complex assembled on the membrane.

SupramoleculeName: Retromer-Vps5 complex assembled on the membrane. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Vps26/Vps35/Vps29 trimer recruited to the membrane via Vps5 PX-BAR protein.
Source (natural)Organism: Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)

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Macromolecule #1: Vacuolar protein sorting-associated protein 26-like protein

MacromoleculeName: Vacuolar protein sorting-associated protein 26-like protein
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 34.308449 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: FSTPVDIDIV LADADKRAMV DVKLDKNRRE KVPLYMDGES VKGCVTVRPK DGKRLEHTGI KVQFIGTIEM FFDRGNHYEF LSLVQELAA PGELQHPQTF DFNFKNVEKQ YESYNGINVK LRYFVRVTVS RRMADVIREK DIWVYSYRIP PELNSSIKMD V GIEDCLHI ...String:
FSTPVDIDIV LADADKRAMV DVKLDKNRRE KVPLYMDGES VKGCVTVRPK DGKRLEHTGI KVQFIGTIEM FFDRGNHYEF LSLVQELAA PGELQHPQTF DFNFKNVEKQ YESYNGINVK LRYFVRVTVS RRMADVIREK DIWVYSYRIP PELNSSIKMD V GIEDCLHI EFEYSKSKYH LKDVIVGRIY FLLVRLKIKH MELSIIRRET TGVAPNQYNE SETLVRFEIM DGSPSRGETI PI RLFLGGF DLTPTFRDVN KKFSTRYYLS LVLIDEDARR YFKQSEIILY RQPPE

UniProtKB: Vacuolar protein sorting-associated protein 26-like protein

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Macromolecule #2: Putative vacuolar protein sorting-associated protein

MacromoleculeName: Putative vacuolar protein sorting-associated protein / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 42.060762 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ARPTFHITVG DPHKVGDLAT SHIVYSVRTK TTSKAYKQPE FEVKRRYRDF LWLYNTLHSN NPGVVVPPPP EKQAVGRFES NFVESRRAA LEKMLNKIAA HPTLQLDADL KLFLESESFN IDVKHKERKE PPLGESKGVF GSLGFGGGGN KFVEQDDWFH D RRVYLDAL ...String:
ARPTFHITVG DPHKVGDLAT SHIVYSVRTK TTSKAYKQPE FEVKRRYRDF LWLYNTLHSN NPGVVVPPPP EKQAVGRFES NFVESRRAA LEKMLNKIAA HPTLQLDADL KLFLESESFN IDVKHKERKE PPLGESKGVF GSLGFGGGGN KFVEQDDWFH D RRVYLDAL ENQLKALLKA MDNMVAQRKA MAEAAADFSA SLHALSTVEL SPTLSGPLDA LSELQLAIRD VYERQAQQDV LT FGIIIEE YIRLIGSVKQ AFSQRQKAFH SWHSAESELM KKKAAQDKLL RQGKTQQDRL NQVNAEVIDA ERKVHQARLL FED MGRLLR SELDRFEREK VEDFKSGVET FLESAVEAQK ELIEKWETFL MQ

UniProtKB: Putative vacuolar protein sorting-associated protein

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Macromolecule #3: Putative vacuolar protein sorting-associated protein

MacromoleculeName: Putative vacuolar protein sorting-associated protein / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 14.897982 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARPTFHITVG DPHKVGDLAT SHIVYSVRTK TTSKAYKQPE FEVKRRYRDF LWLYNTLHSN NPGVVVPPPP EKQAVGRFES NFVESRRAA LEKMLNKIAA HPTLQLDADL KLFLESESFN IDVKHKERKE

UniProtKB: Putative vacuolar protein sorting-associated protein

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Macromolecule #4: Putative vacuolar protein sorting-associated protein

MacromoleculeName: Putative vacuolar protein sorting-associated protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 25.477904 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: NKFVEQDDWF HDRRVYLDAL ENQLKALLKA MDNMVAQRKA MAEAAADFSA SLHALSTVEL SPTLSGPLDA LSELQLAIRD VYERQAQQD VLTFGIIIEE YIRLIGSVKQ AFSQRQKAFH SWHSAESELM KKKAAQDKLL RQGKTQQDRL NQVNAEVIDA E RKVHQARL ...String:
NKFVEQDDWF HDRRVYLDAL ENQLKALLKA MDNMVAQRKA MAEAAADFSA SLHALSTVEL SPTLSGPLDA LSELQLAIRD VYERQAQQD VLTFGIIIEE YIRLIGSVKQ AFSQRQKAFH SWHSAESELM KKKAAQDKLL RQGKTQQDRL NQVNAEVIDA E RKVHQARL LFEDMGRLLR SELDRFEREK VEDFKSGVET FLESAVEAQK ELIEKWETFL MQ

UniProtKB: Putative vacuolar protein sorting-associated protein

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Macromolecule #5: Vacuolar protein sorting-associated protein 29

MacromoleculeName: Vacuolar protein sorting-associated protein 29 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 21.470654 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AFLILVIGNL HIPDRALDIP PKFKKLLSPG KISQTLCLGN LTDRATYDYL RSISPDLKIV RGRMDVEATS LPLMQVVTHG SLRIGFLEG FTLVSEEPDV LLAEANKLDV DVLCWAGGSH RFECFEYMDK FFVNPGSATG AFTTDWLAEG EEVVPSFCLM D VQGISLTL ...String:
AFLILVIGNL HIPDRALDIP PKFKKLLSPG KISQTLCLGN LTDRATYDYL RSISPDLKIV RGRMDVEATS LPLMQVVTHG SLRIGFLEG FTLVSEEPDV LLAEANKLDV DVLCWAGGSH RFECFEYMDK FFVNPGSATG AFTTDWLAEG EEVVPSFCLM D VQGISLTL YVYQLRKDEN GTENVAVEKV TYTKP

UniProtKB: Vacuolar protein sorting-associated protein 29

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Macromolecule #6: Vacuolar protein sorting-associated protein 35

MacromoleculeName: Vacuolar protein sorting-associated protein 35 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Molecular weightTheoretical: 96.140016 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: RLLEDALIAV RQQTAMMRKF LDTPGKLMDA LKCCSTLVSE LRTSSLSPKQ YYELYMAVFD ALRYLSAHLR ENHPVNHLAD LYELVQYAG NIIPRLYLMI TVGTAYMSID GAPVKELMKD MMDMSRGVQH PVRGLFLRYY LSGQARDYLP TGDSDGPEGN L QDSINFIL ...String:
RLLEDALIAV RQQTAMMRKF LDTPGKLMDA LKCCSTLVSE LRTSSLSPKQ YYELYMAVFD ALRYLSAHLR ENHPVNHLAD LYELVQYAG NIIPRLYLMI TVGTAYMSID GAPVKELMKD MMDMSRGVQH PVRGLFLRYY LSGQARDYLP TGDSDGPEGN L QDSINFIL TNFVEMNKLW VRLQHQGHSR ERDLRTQERR ELQLLVGSNI VRLSQLVDLP TYRDSILGPL LEQIVQCRDI LA QEYLLEV ITQVFPDEYH LHTLDQFLGA VSRLNPHVNV KAIVIGMMNR LSDYAERESQ NEPEEDRAKL EEEALAKLLE KTK LGQNSE LEPQNGDHPD TEVSSTTDSA QAPSTADSDT TAVNGEEEPV RKRRGIPVNV PLYDIFFDQV QHLVQAQHLP IQDT IALCC SLANLSLNIY PERLDYVDGI LAYALAKVKE HANSADLHSQ PAQQSLLSLL QSPLRRYVSI FTALSLPTYV SLFQA QTYP TRRAIAGEIV RTLLKNQTLI STPAHLENVL EILKVLIKEG SQPPAGYPGV VQPRARPLET DETMEEQGWL ARLVHL IHS DDNDTQFRLL QMTRKAYAEG NERIRTTTPP LITAGLKLAR RFKAREHYDD NWSSQSSSLF KFLHSAISTL YTRVNGP GV ADLCLRLFCS CGQVADMTEF EEVAYEFFAQ AFTVYEESIS DSKAQFQAVC VIASALHRTR NFGRENYDTL ITKCAQHA S KLLRKPDQCR AVYLASHLWW ATPIAARGET EDTELYRDGK RVLECLQRAL RVADSCMETA TSIELFVEIL DRYVYYFDQ RNESVTTKYL NGLIELIHSN LAGNQQDSAS VEASRKHFIQ TLEMIQ

UniProtKB: Vacuolar protein sorting-associated protein 35

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state3D array

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Sample preparation

Concentration1.1 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMC8H19KN2O5SHEPES-KOH
200.0 mMNaClsodium chloride
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 292 K / Instrument: LEICA EM GP
DetailsThe solution-assembled complex was incubated with Folch liposomes at room temperature.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Average electron dose: 3.17 e/Å2
Details: Tomographic tilt series were acquired with the dose-symmetric tilt-scheme (Hagen et al., J Struct Biol. 2017)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.5 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsAfter motion correction in "alignframes" (IMOD), each of the images in the tilt series was low-pass filtered according to the electron-dose acquired by the sample (Grant and Grigorieff, 2015).
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 11.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 16037
ExtractionNumber tomograms: 71 / Number images used: 194885 / Reference model: reference-free
Method: geometrical seeding alogn the surface of manually traced tubules
Final angle assignmentType: OTHER / Software: (Name: AV3, TOM)
Details: Image processing was performed in TOM Toolbox, AV3 and Dynamo toolboxes.

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Atomic model buiding 1

DetailsNote that the associated PDB model was not generated by fitting into this map! It was generated by fitting into the associated local high-resolution maps and then combined. Initial global ridgid body fitting was done using Chimera, followed by MDFF within NAMD for flexible fitting. Note that side chain positions are not reliable in model generated by refinement into a map at this resolution.
RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6h7w:
Model of retromer-Vps5 complex assembled on membrane.

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