[English] 日本語
Yorodumi
- EMDB-18374: cryo-EM structure complex of Frizzled-7 and Clostridioides diffic... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18374
Titlecryo-EM structure complex of Frizzled-7 and Clostridioides difficile toxin B
Map data
Sample
  • Complex: Complex of Frizzled-7 and Clostridioides difficile toxin B
    • Organelle or cellular component: masked region--CROP domain
      • Protein or peptide: Toxin B
    • Organelle or cellular component: masked region-core domain
    • Organelle or cellular component: masked region-FZD7 CRD and leg of TcdB
      • Protein or peptide: Frizzled-7
  • Ligand: ZINC ION
Keywordsmicriobiology / class F G protein-coupled receptors / CROP dynamics / TOXIN
Function / homology
Function and homology information


negative regulation of ectodermal cell fate specification / negative regulation of cardiac muscle cell differentiation / mesenchymal to epithelial transition / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / Wnt receptor activity / somatic stem cell division / non-canonical Wnt signaling pathway / glucosyltransferase activity / Wnt-protein binding / positive regulation of epithelial cell proliferation involved in wound healing ...negative regulation of ectodermal cell fate specification / negative regulation of cardiac muscle cell differentiation / mesenchymal to epithelial transition / skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration / Wnt receptor activity / somatic stem cell division / non-canonical Wnt signaling pathway / glucosyltransferase activity / Wnt-protein binding / positive regulation of epithelial cell proliferation involved in wound healing / WNT5:FZD7-mediated leishmania damping / frizzled binding / PCP/CE pathway / regulation of canonical Wnt signaling pathway / Class B/2 (Secretin family receptors) / negative regulation of cell-substrate adhesion / Wnt signaling pathway, planar cell polarity pathway / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / stem cell population maintenance / canonical Wnt signaling pathway / cysteine-type peptidase activity / cellular response to retinoic acid / positive regulation of phosphorylation / phosphatidylinositol-4,5-bisphosphate binding / substrate adhesion-dependent cell spreading / host cell endosome membrane / Asymmetric localization of PCP proteins / PDZ domain binding / G protein-coupled receptor activity / positive regulation of JNK cascade / neuron differentiation / recycling endosome membrane / T cell differentiation in thymus / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / positive regulation of MAPK cascade / intracellular membrane-bounded organelle / lipid binding / regulation of DNA-templated transcription / host cell plasma membrane / positive regulation of DNA-templated transcription / proteolysis / extracellular region / membrane / metal ion binding / plasma membrane
Similarity search - Function
Frizzled-7, cysteine-rich Wnt-binding domain / Dermonecrotic/RTX toxin, membrane localization domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / Membrane Localization Domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Frizzled/Smoothened, transmembrane domain / TcdA/TcdB toxin, pore forming domain / Frizzled/Smoothened family membrane region ...Frizzled-7, cysteine-rich Wnt-binding domain / Dermonecrotic/RTX toxin, membrane localization domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / Membrane Localization Domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Frizzled/Smoothened, transmembrane domain / TcdA/TcdB toxin, pore forming domain / Frizzled/Smoothened family membrane region / TcdA/TcdB pore forming domain / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Frizzled-7 / Toxin B
Similarity search - Component
Biological speciesSpodoptera frugiperda (fall armyworm) / Priestia megaterium DSM 319 (bacteria) / Clostridioides difficile (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsKinsolving J / Bous J
Funding support Sweden, Denmark, 11 items
OrganizationGrant numberCountry
Swedish Research Council2019-01190 Sweden
Cancerfonden20 1102 PjF Sweden
Novo Nordisk FoundationNNF21OC0070008 Denmark
Novo Nordisk FoundationNNF22OC0078104 Denmark
Other government2018-01562
Swedish Research Council2022-03681 Sweden
Swedish Research Council2018-03406 Sweden
Cancerfonden20 1287 PjF Sweden
Swedish Research Council2022-01398 Sweden
Cancerfonden20 0264 PjF Sweden
Other government2021-00430 Sweden
CitationJournal: Cell Rep / Year: 2024
Title: Structural and functional insight into the interaction of Clostridioides difficile toxin B and FZD.
Authors: Julia Kinsolving / Julien Bous / Pawel Kozielewicz / Sara Košenina / Rawan Shekhani / Lukas Grätz / Geoffrey Masuyer / Yuankai Wang / Pål Stenmark / Min Dong / Gunnar Schulte /
Abstract: The G protein-coupled receptors of the Frizzled (FZD) family, in particular FZD, are receptors that are exploited by Clostridioides difficile toxin B (TcdB), the major virulence factor responsible ...The G protein-coupled receptors of the Frizzled (FZD) family, in particular FZD, are receptors that are exploited by Clostridioides difficile toxin B (TcdB), the major virulence factor responsible for pathogenesis associated with Clostridioides difficile infection. We employ a live-cell assay examining the affinity between full-length FZDs and TcdB. Moreover, we present cryoelectron microscopy structures of TcdB alone and in complex with full-length FZD, which reveal that large structural rearrangements of the combined repetitive polypeptide domain are required for interaction with FZDs and other TcdB receptors, constituting a first step for receptor recognition. Furthermore, we show that bezlotoxumab, an FDA-approved monoclonal antibody to treat Clostridioides difficile infection, favors the apo-TcdB structure and thus disrupts binding with FZD. The dynamic transition between the two conformations of TcdB also governs the stability of the pore-forming region. Thus, our work provides structural and functional insight into how conformational dynamics of TcdB determine receptor binding.
History
DepositionSep 1, 2023-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18374.png

Downloads & links

-
Map

FileDownload / File: emd_18374.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.1592 Å
Density
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-0.120876685 - 9.874971
Average (Standard dev.)0.014228614 (±0.03141671)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 579.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_18374_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_18374_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #3

Fileemd_18374_msk_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_18374_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_18374_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of Frizzled-7 and Clostridioides difficile toxin B

EntireName: Complex of Frizzled-7 and Clostridioides difficile toxin B
Components
  • Complex: Complex of Frizzled-7 and Clostridioides difficile toxin B
    • Organelle or cellular component: masked region--CROP domain
      • Protein or peptide: Toxin B
    • Organelle or cellular component: masked region-core domain
    • Organelle or cellular component: masked region-FZD7 CRD and leg of TcdB
      • Protein or peptide: Frizzled-7
  • Ligand: ZINC ION

-
Supramolecule #1: Complex of Frizzled-7 and Clostridioides difficile toxin B

SupramoleculeName: Complex of Frizzled-7 and Clostridioides difficile toxin B
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Spodoptera frugiperda (fall armyworm)

-
Supramolecule #2: masked region--CROP domain

SupramoleculeName: masked region--CROP domain / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Priestia megaterium DSM 319 (bacteria)

-
Supramolecule #3: masked region-core domain

SupramoleculeName: masked region-core domain / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Priestia megaterium DSM 319 (bacteria)

-
Supramolecule #4: masked region-FZD7 CRD and leg of TcdB

SupramoleculeName: masked region-FZD7 CRD and leg of TcdB / type: organelle_or_cellular_component / ID: 4 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Priestia megaterium DSM 319 (bacteria)

-
Macromolecule #1: Toxin B

MacromoleculeName: Toxin B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 273.551562 KDa
Recombinant expressionOrganism: Priestia megaterium DSM 319 (bacteria)
SequenceString: MDKLVHLNQR GKCTMSLVNR KQLEKMANVR FRTQEDEYVA ILDALEEYHN MSENTVVEKY LKLKDINSLT DIYIDTYKKS GRNKALKKF KEYLVTEVLE LKNNNLTPVE KNLHFVWIGG QINDTAINYI NQWKDVNSDY NVNVFYDSNA FLINTLKKTV V ESAINDTL ...String:
MDKLVHLNQR GKCTMSLVNR KQLEKMANVR FRTQEDEYVA ILDALEEYHN MSENTVVEKY LKLKDINSLT DIYIDTYKKS GRNKALKKF KEYLVTEVLE LKNNNLTPVE KNLHFVWIGG QINDTAINYI NQWKDVNSDY NVNVFYDSNA FLINTLKKTV V ESAINDTL ESFRENLNDP RFDYNKFFRK RMEIIYDKQK NFINYYKAQR EENPELIIDD IVKTYLSNEY SKEIDELNTY IE ESLNKIT QNSGNDVRNF EEFKNGESFN LYEQELVERW NLAAASDILR ISALKEIGGM YLDVDMLPGI QPDLFESIEK PSS VTVDFW EMTKLEAIMK YKEYIPEYTS EHFDMLDEEV QSSFESVLAS KSDKSEIFSS LGDMEASPLE VKIAFNSKGI INQG LISVK DSYCSNLIVK QIENRYKILN NSLNPAISED NDFNTTTNTF IDSIMAEANA DNGRFMMELG KYLRVGFFPD VKTTI NLSG PEAYAAAYQD LLMFKEGSMN IHLIEADLRN FEISKTNISQ STEQEMASLW SFDDARAKAQ FEEYKRNYFE GSLGED DNL DFSQNIVVDK EYLLEKISSL ARSSERGYIH YIVQLQGDKI SYEAACNLFA KTPYDSVLFQ KNIEDSEIAY YYNPGDG EI QEIDKYKIPS IISDRPKIKL TFIGHGKDEF NTDIFAGFDV DSLSTEIEAA IDLAKEDISP KSIEINLLGC NMFSYSIN V EETYPGKLLL KVKDKISELM PSISQDSIIV SANQYEVRIN SEGRRELLDH SGEWINKEES IIKDISSKEY ISFNPKENK ITVKSKNLPE LSTLLQEIRN NSNSSDIELE EKVMLTECEI NVISNIDTQI VEERIEEAKN LTSDSINYIK DEFKLIESIS DALCDLKQQ NELEDSHFIS FEDISETDEG FSIRFINKET GESIFVETEK TIFSEYANHI TEEISKIKGT IFDTVNGKLV K KVNLDTTH EVNTLNAAFF IQSLIEYNSS KESLSNLSVA MKVQVYAQLF STGLNTITDA AKVVELVSTA LDETIDLLPT LS EGLPIIA TIIDGVSLGA AIKELSETSD PLLRQEIEAK IGIMAVNLTT ATTAIITSSL GIASGFSILL VPLAGISAGI PSL VNNELV LRDKATKVVD YFKHVSLVET EGVFTLLDDK IMMPQDDLVI SEIDFNNNSI VLGKCEIWRM EGGSGHTVTD DIDH FFSAP SITYREPHLS IYDVLEVQKE ELDLSKDLMV LPNAPNRVFA WETGWTPGLR SLENDGTKLL DRIRDNYEGE FYWRY FAFI ADALITTLKP RYEDTNIRIN LDSNTRSFIV PIITTEYIRE KLSYSFYGSG GTYALSLSQY NMGINIELSE SDVWII DVD NVVRDVTIES DKIKKGDLIE GILSTLSIEE NKIILNSHEI NFSGEVNGSN GFVSLTFSIL EGINAIIEVD LLSKSYK LL ISGELKILML NSNHIQQKID YIGFNSELQK NIPYSFVDSE GKENGFINGS TKEGLFVSEL PDVVLISKVY MDDSKPSF G YYSNNLKDVK VITKDNVNIL TGYYLKDDIK ISLSLTLQDE KTIKLNSVHL DESGVAEILK FMNRKGNTNT SDSLMSFLE SMNIKSIFVN FLQSNIKFIL DANFIISGTT SIGQFEFICD ENDNIQPYFI KFNTLETNYT LYVGNRQNMI VEPNYDLDDS GDISSTVIN FSQKYLYGID SCVNKVVISP NIYTDEINIT PVYETNNTYP EVIVLDANYI NEKINVNIND LSIRYVWSND G NDFILMST SEENKVSQVK IRFVNVFKDK TLANKLSFNF SDKQDVPVSE IILSFTPSYY EDGLIGYDLG LVSLYNEKFY IN NFGMMVS GLIYINDSLY YFKPPVNNLI TGFVTVGDDK YYFNPINGGA ASIGETIIDD KNYYFNQSGV LQTGVFSTED GFK YFAPAN TLDENLEGEA IDFTGKLIID ENIYYFDDNY RGAVEWKELD GEMHYFSPET GKAFKGLNQI GDYKYYFNSD GVMQ KGFVS INDNKHYFDD SGVMKVGYTE IDGKHFYFAE NGEMQIGVFN TEDGFKYFAH HNEDLGNEEG EEISYSGILN FNNKI YYFD DSFTAVVGWK DLEDGSKYYF DEDTAEAYIG LSLINDGQYY FNDDGIMQVG FVTINDKVFY FSDSGIIESG VQNIDD NYF YIDDNGIVQI GVFDTSDGYK YFAPANTVND NIYGQAVEYS GLVRVGEDVY YFGETYTIET GWIYDMENES DKYYFNP ET KKACKGINLI DDIKYYFDEK GIMRTGLISF ENNNYYFNEN GEMQFGYINI EDKMFYFGED GVMQIGVFNT PDGFKYFA H QNTLDENFEG ESINYTGWLD LDEKRYYFTD EYIAATGSVI IDGEEYYFDP DTAQLVISEG YRPHAGLRGS HHHHHH

UniProtKB: Toxin B

-
Macromolecule #2: Frizzled-7

MacromoleculeName: Frizzled-7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 67.460859 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDQPYHGEK GISVPDHGFC QPISIPLCTD IAYNQTILPN LLGHTNQEDA GLEVHQFYPL VKVQCSPEL RFFLCSMYAP VCTVLDQAIP PCRSLCERAR QGCEALMNKF GFQWPERLRC ENFPVHGAGE ICVGQNTSDG S GGPGGGPT ...String:
MKTIIALSYI FCLVFADYKD DDDQPYHGEK GISVPDHGFC QPISIPLCTD IAYNQTILPN LLGHTNQEDA GLEVHQFYPL VKVQCSPEL RFFLCSMYAP VCTVLDQAIP PCRSLCERAR QGCEALMNKF GFQWPERLRC ENFPVHGAGE ICVGQNTSDG S GGPGGGPT AYPTAPYLPD LPFTALPPGA SDGRGRPAFP FSCPRQLKVP PYLGYRFLGE RDCGAPCEPG RANGLMYFKE EE RRFARLW VGVWSVLCCA STLFTVLTYL VDMRRFSYPE RPIIFLSGCY FMVAVAHVAG FLLEDRAVCV ERFSDDGYRT VAQ GTKKEG CTILFMVLYF FGMASSIWWV ILSLTWFLAA GMKWGHEAIE ANSQYFHLAA WAVPAVKTIT ILAMGQVDGD LLSG VCYVG LSSVDALRGF VLAPLFVYLF IGTSFLLAGF VSLFRIRTIM KHDGTKTEKL EKLMVRIGVF SVLYTVPATI VLACY FYEQ AFREHWERTW LLQTCKSYAV PCPPGHFPPM SPDFTVFMIK YLMTMIVGIT TGFWIWSGKT LQSWRRFYHR LSHSSK GET AVSRLEVLFQ GPWSHPQFEK GGGSGGGSGG GSWSHPQFEK

UniProtKB: Frizzled-7

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.272 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
0.1 MTRIS-HClTristris hydrochloride
0.2 MNaClSodium chloridesodium chloride
0.002 %LMNGlauryl maltose neopentyl glycol
0.0002 %CHScholesteryl hemisuccinate tris salt
0.0002 %GDNglyco diosgenin

Details: 100 mM TRIS-HCl pH 7.5 200 mM NaCl 0.002% LMNG 0.0002% CHS 0.0002% GDN
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.101 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 17269 / Average exposure time: 3.0 sec. / Average electron dose: 50.453 e/Å2
Details: Images collected in super-resolution mode, faster acquisition mode, with 4 exposures per hole
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 5240176
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 100000 / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final reconstructionNumber classes used: 1 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 151385
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8qeo:
cryo-EM structure complex of Frizzled-7 and Clostridioides difficile toxin B

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more