[English] 日本語
Yorodumi
- EMDB-18403: cryo-EM map of apo Clostridioides difficile toxin B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18403
Titlecryo-EM map of apo Clostridioides difficile toxin B
Map data
Sample
  • Organelle or cellular component: apo-structure of Clostridioides difficile toxin B
    • Organelle or cellular component: masked region-GTD/CPD domain
      • Other: apo-TcdB
Keywordsmicrobiology / pore forming region / CROP dynamics / TOXIN
Biological speciesClostridioides difficile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.21 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 government2021-00430
Other government2018-01562
Swedish Research Council2022-03681 Sweden
Swedish Research Council2018-03406 Sweden
Cancerfonden20 1287 PjF Sweden
Cancerfonden202 0264 PjF Sweden
Swedish Research Council2022-01398 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 7, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18403.png

Downloads & links

-
Map

FileDownload / File: emd_18403.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 500 pix.
= 579.6 Å		1.16 Å/pix.
x 500 pix.
= 579.6 Å		1.16 Å/pix.
x 500 pix.
= 579.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1592 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.288
Minimum - Maximum-0.6047986 - 1.2188528
Average (Standard dev.)-0.0005180077 (±0.023675384)
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

-
Half map: #2

Fileemd_18403_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_18403_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : apo-structure of Clostridioides difficile toxin B

EntireName: apo-structure of Clostridioides difficile toxin B
Components
  • Organelle or cellular component: apo-structure of Clostridioides difficile toxin B
    • Organelle or cellular component: masked region-GTD/CPD domain
      • Other: apo-TcdB

-
Supramolecule #1: apo-structure of Clostridioides difficile toxin B

SupramoleculeName: apo-structure of Clostridioides difficile toxin B / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridioides difficile (bacteria)

-
Supramolecule #2: masked region-GTD/CPD domain

SupramoleculeName: masked region-GTD/CPD domain / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Clostridioides difficile (bacteria)

-
Macromolecule #1: apo-TcdB

MacromoleculeName: apo-TcdB / type: other / ID: 1 / Classification: other
Source (natural)Organism: Clostridioides difficile (bacteria)
SequenceString: mdklvhlnqr gkctmslvnr kqlekmanvr frtqedeyva ildaleeyhn msentvveky lklkdinslt diyidtykks grnkalkkfk eylvtevl e lknnnltpve knlhfvwigg qindtainyi nqwkdvnsdy nvnvfydsna flintlkktv vesaindtle ...String:
mdklvhlnqr gkctmslvnr kqlekmanvr frtqedeyva ildaleeyhn msentvveky lklkdinslt diyidtykks grnkalkkfk eylvtevl e lknnnltpve knlhfvwigg qindtainyi nqwkdvnsdy nvnvfydsna flintlkktv vesaindtle sfrenlndpr fdynkffrkr meiiydk qk nfinyykaqr eenpeliidd ivktylsney skeidelnty ieeslnkitq nsgndvrnfe efkngesfnl yeqelverwn laaasdilri salkeigg m yldvdmlpgi qpdlfesiek pssvtvdfwe mtkleaimky keyipeytse hfdmldeevq ssfesvlask sdkseifssl gdmeasplev kiaf nskgi inqglisvkd sycsnlivkq ienrykilnn slnpaisedn dfntttntfi dsimaeanad ngrfmmelgk ylrvgffpdv kttinlsgpe ayaaa yqdl lmfkegsmni hlieadlrnf eisktnisqs teqemaslws fddarakaqf eeykrnyfeg slgeddnldf sqnivvdkey llekisslar sserg yihy ivqlqgdkis yeaacnlfak tpydsvlfqk niedseiayy ynpgdgeiqe idkykipsii sdrpkikltf ighgkdefnt difagfdvds lsteieaa i dlakedispk sieinllgcn mfsysinvee typgklllkv kdkiselmps isqdsiivsa nqyevrinse grrelldhsg ewinkeesii kdisskeyis f npkenkit vksknlpels tllqeirnns nssdieleek vmlteceinv isnidtqive erieeaknlt sdsinyikde fkliesisda lcdlkqqnel edsh fisfe disetdegfs irfinketge sifvetekti fseyanhite eiskikgtif dtvngklvkk vnldtthevn tlnaaffiqs lieynsskes lsnlsvamkv qvyaqlfst glntitdaak vvelvstald etidllptls eglpiiatii dgvslgaaik elsetsdpll rqeieakigi mavnlttatt aiitsslgia sgfsillvpl a gisagips lvnnelvlrd katkvvdyfk hvslvetegv ftllddkimm pqddlvisei dfnnnsivlg kceiwrmegg sghtvtddid hffsapsity r ephlsiyd vlevqkeeld lskdlmvlpn apnrvfawet gwtpglrsle ndgtklldri rdnyegefyw ryfafiadal ittlkpryed tnirinldsn trs fivpii tteyirekls ysfygsggty alslsqynmg inielsesdv wiidvdnvvr dvtiesdkik kgdliegils tlsieenkii lnsheinfsg evngsngfv sltfsilegi naiievdlls ksykllisge lkilmlnsnh iqqkidyigf nselqknipy sfvdsegken gfingstkeg lfvselpdvv liskvymdds kpsf gyysn nlkdvkvitk dnvniltgyy lkddikisls ltlqdektik lnsvhldesg vaeilkfmnr kgntntsdsl msflesmnik sifvnflqsn ikfildan f iisgttsigq feficdendn iqpyfikfnt letnytlyvg nrqnmivepn ydlddsgdis stvinfsqky lygidscvnk vvispniytd einitpvyet n ntypeviv ldanyineki nvnindlsir yvwsndgndf ilmstseenk vsqvkirfvn vfkdktlank lsfnfsdkqd vpvseiilsf tpsyyedgli gy dlglvsl ynekfyinnf gmmvsgliyi ndslyyfkpp vnnlitgfvt vgddkyyfnp inggaasige tiiddknyyf nqsgvlqtgv fstedgfkyf apa ntlden legeaidftg kliideniyy fddnyrgave wkeldgemhy fspetgkafk glnqigdyky yfnsdgvmqk gfvsindnkh yfddsgvmk vgyteidgkh fyfaengemq igvfntedgf kyfahhnedl gneegeeisy sgilnfnnki yyfddsftav vgwkdledgs kyyfdedtae ayiglsli n dgqyyfnddg imqvgfvtin dkvfyfsdsg iiesgvqnid dnyfyiddng ivqigvfdts dgykyfapan tvndniygqa veysglvrvg edvyyf get ytietgwiyd menesdkyyf npetkkackg inliddikyy fdekgimrtg lisfennnyy fnengemqfg yiniedkmfy fgedgvmqig vf ntpdgfk yfahqntlde nfegesinyt gwldldekry yftdeyiaat gsviidgeey yfdpdtaqlv isegyrphag lrgshhhhhh
Recombinant expressionOrganism: Priestia megaterium DSM 319 (bacteria)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.630 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
0.1 MTRIS-HCltris hydrochloride
0.2 MNaClsodium 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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 5240176
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 41523
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final 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)
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

+
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://pdbjlvh1.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