[English] 日本語
Yorodumi
- EMDB-10035: Cryo-EM structure of Morganella morganii TcdA4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10035
TitleCryo-EM structure of Morganella morganii TcdA4
Map dataCryo-EM density map of Morganella morganii TcdA4
Sample
  • Complex: M. morganii TcdA4 pentamer
    • Protein or peptide: Insecticidal toxin protein TcdA4
Function / homology
Function and homology information


TcA receptor binding domain / TcA receptor binding domain / Insecticidal toxin complex/plasmid virulence protein / Tc toxin complex TcA, C-terminal TcB-binding domain / Neuraminidase-like domain / Salmonella virulence plasmid 28.1kDa A protein / Tc toxin complex TcA C-terminal TcB-binding domain / Neuraminidase-like domain
Similarity search - Domain/homology
Insecticidal toxin protein
Similarity search - Component
Biological speciesMorganella morganii subsp. morganii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsRoderer D / Leidreiter F / Gatsogiannis C / Meusch D / Benz R / Raunser S
Funding support Germany, 1 items
OrganizationGrant numberCountry
European Research Council615984 Germany
CitationJournal: Sci Adv / Year: 2019
Title: Common architecture of Tc toxins from human and insect pathogenic bacteria.
Authors: F Leidreiter / D Roderer / D Meusch / C Gatsogiannis / R Benz / S Raunser /
Abstract: Tc toxins use a syringe-like mechanism to penetrate the membrane and translocate toxic enzymes into the host cytosol. They are composed of three components: TcA, TcB, and TcC. Low-resolution ...Tc toxins use a syringe-like mechanism to penetrate the membrane and translocate toxic enzymes into the host cytosol. They are composed of three components: TcA, TcB, and TcC. Low-resolution structures of TcAs from different bacteria suggest a considerable difference in their architecture and possibly in their mechanism of action. Here, we present high-resolution structures of five TcAs from insect and human pathogens, which show a similar overall composition and domain organization. Essential structural features, including a trefoil protein knot, are present in all TcAs, suggesting a common mechanism of action. All TcAs form functional pores and can be combined with TcB-TcC subunits from other species to form active chimeric holotoxins. We identified a conserved ionic pair that stabilizes the shell, likely operating as a strong latch that only springs open after destabilization of other regions. Our results provide new insights into the architecture and mechanism of the Tc toxin family.
History
DepositionJun 4, 2019-
Header (metadata) releaseJun 12, 2019-
Map releaseOct 23, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.032
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.032
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6rw9
  • Surface level: 0.032
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10035.png

Downloads & links

-
Map

FileDownload / File: emd_10035.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM density map of Morganella morganii TcdA4
Voxel sizeX=Y=Z: 1.14 Å
Density
Contour LevelBy AUTHOR: 0.032 / Movie #1: 0.032
Minimum - Maximum-0.08405357 - 0.18358652
Average (Standard dev.)0.00052770635 (±0.0066100233)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 456.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.141.141.14
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z456.000456.000456.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0840.1840.001

-
Supplemental data

-
Sample components

-
Entire : M. morganii TcdA4 pentamer

EntireName: M. morganii TcdA4 pentamer
Components
  • Complex: M. morganii TcdA4 pentamer
    • Protein or peptide: Insecticidal toxin protein TcdA4

-
Supramolecule #1: M. morganii TcdA4 pentamer

SupramoleculeName: M. morganii TcdA4 pentamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Morganella morganii subsp. morganii (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 1.4 MDa

-
Macromolecule #1: Insecticidal toxin protein TcdA4

MacromoleculeName: Insecticidal toxin protein TcdA4 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Morganella morganii subsp. morganii (bacteria)
Molecular weightTheoretical: 275.658312 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDQITRILEK LNQQRSGETT VTLADFMPMS LAEIRSQNTG RLSREEAQLL HRAAQKEKQN NILYTARMLT RANPLLKKEM NTARYYGAT PYGYDDIIPP RAEKFVAPGA VSSMFSPAGY LTELYREARG LHPKDSDRNL DKRRQDLAKL VLSQDNLDNE I SALSLANE ...String:
MDQITRILEK LNQQRSGETT VTLADFMPMS LAEIRSQNTG RLSREEAQLL HRAAQKEKQN NILYTARMLT RANPLLKKEM NTARYYGAT PYGYDDIIPP RAEKFVAPGA VSSMFSPAGY LTELYREARG LHPKDSDRNL DKRRQDLAKL VLSQDNLDNE I SALSLANE QLETALMAQT GKTDKNKYYE TLATSRRSGV TPYNAPFEGI HNALAQRNFV LPDNILSNPA KFAILAAYDA GI SPKLYNI LTEDTESLTG SDLENSLKRN FPKVKIKDLM TLDALANYYE LPADDIQALI AAEITGRLPT PDVYNDDNKL VIP AINTGG KITFSELAKT QSDEKQADYI DLIPQGGNQF LVNFSVKKTK KDATHFSIGY NKSFNNLADK NGFVPLAGEH YSIP VTLDA KILEKKTKIG ITRKKPEPAS DENHYTSATF TIHPNAEPGI WLLRLNKTLR LAKVSGMTPH ETQHALIHVR NDSSE YELR RFTETLLYRK RYGIDTETAL MLCNAGISRI SYDGQLSHFD RLFNNPPLNG VTYTLGGDDI LMEPDAGDPR REVLKR AFR VDNTGLWQLL VITNRENKSK TIENKTEKLR GLLFVRLLAD VHNLTVAQLD ALLQISPYNS MNVYALDGKT RQKMLSF LS RITQWLNTQN ITVEQLMLLL DKISPAAPTK EMQVLLDLLR NGGIDKTNTK TLYTTMAPVI TAAMQLDITE SGEALLRW L DNNHPAGILT TSEARKLIIK KGQTAGDKEK LAAWCQALAQ RVLVIRTFTL SNAELQTLSQ GAPAGTITEL YNISDFHNL INRCGEQAGT VLDALQSGTL TVKILAQALN LSEEVITQAL TLAGQKPELT TWAQLAVLPP RLDLADTLHI TPKDITTLLT VSENVRPFY TDLSALAGLL QAGLNEQQTK QLQNQSEPRR NEALSGEYRS LVMNNPVADR DDIWRNLLVD GKVSAEITTT L LADAIAGI QLYINRTIAG DEPGADSDAL ERQFFKDWDA CNKRYSTWAG VSQLVYYPEN FVDPTLRTGQ TGMMNTMLEQ LS QSELNKD TLENGFRQYL TAFEQVADLK VVSGYHDTVN INQGNTWFIG TSQTEPKKYY WRKADHSKCQ NGRFAANAWS DWK EITCAV NPYGDMVRPV IFHSRLYLLW IEKQVQKDNT GKDTASFTLK LTHVKYDGSW ASPFSYDITE KNISGWKKTG LYCA ASQED NSLLIAWYQI EKETQPNSFG LHIQPDMSCK KEPNIAGILA TVTHQLDTET TVRVNTLLNR ISSFEFTLEK QEGNK EIDL VISHGDYTVK TENSISALIL NPTAYINITP YKLFSDIPDF YREKYITHLN SHSGTVYAPE SKKMEPANNA ISDKVN ACA VYTYNNKPPK KHISLSIGKN YPLITPLELV GRKLESFFIK HKETSALYYT YGDATDDRLT LEEDKYTIST GEKKLGT LS LGKMIAQVKT ISSDDISMEI ELNSTKFETI TGSDVGLRPP LYPTVSRETL AFPFGKLSIT IPAGADINNL DCTIKVRF K NTDVLAATTT YKLVIKKTDP VQKVISLYTT PDGAQYMEWD GYRTRLNTLF TRQLIERANN GIDAILSPET QYLPEPKPG QGTYVTLILK PYDKNTHGTN RAFTIYYSND ATGSGKFPVY SGSLSVTDNT EVKLFIPLIK PGKNAVSQSA GAQQDTLYLN ATYQKEATK QILLFRTDNN PEGWTLDKSV NNGTFAGLAE NGVTGLLQSG EPMDFSGANA LYFWELFYYT PMMVATRLLQ E QNFTEANR WLSYIWQPAA SGAGDWRVRP LKEDTSWNAD PLDSVDPDAV AQNDPMHYKV STLMKLLDLL IARGDKAYRM QE RDTLNEA KMWYMQALGL LGDKPVSIFS NGWENPSLSN AADKTQAKQF HDEISRIRSG GLLPDVRTAN TLTGLFRPQQ NEK LLGYWQ MLEMRLFNLR NNLSIDGQPL SLPVFAAPAD PAALLSAAAA ASGGSKPLPS ADIPAMRFPQ ALDSARSLTG QLMQ FGSTL LGLIERRDAE AMSELLQNQA GELMLSSLRM QEQALTELDA EKKILEQSRA GAQSRVDSYR ALYDENVSAE EKRTM DLYL SSAILSTSIG VLDMAAAAAD MAPNIFGVAV GGSRWGGIPK AIGAGMSLAA SATKITADNI SQSEAWRRRR QEWEIQ KNN AESEIRQIDA QLEALAVRRT ATEMQREHME IQQAQTQAQL EFLQRKFSNK ALYSWLRGRL ASIYYRFYDL TAARCMM AE KAYAWQTNDT ATRYIKSGAW QSNNAGLMAG ESLLLNLAEM EQAWLKRDSR SLEVTRTVSL AAVYRTDNVT LAEGIADL L KGNGSGNIPA STGLSMTADN QLHAAFNLKA LNIKDDYPEA LGTTRRIKQI SVTLPALVEP YQDMRAIFRY GGNSLPAGC KAIALSHGIN DDGLFRLDFN DGRWLPFEGI PVDDDNSLTL SFPDATGEKQ KPLLLSLTDI IIHIRYTIC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average exposure time: 1.5 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: OTHER / Software - Name: SPHIRE
Final angle assignmentType: OTHER / Software - Name: SPHIRE
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 247513

-
Atomic model buiding 1

Initial modelPDB ID:

1vw1
PDB Unreleased entry

Output model

PDB-6rw9:
Cryo-EM structure of Morganella morganii TcdA4

+
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