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- EMDB-10036: Cryo-EM structure of Photorhabdus luminescens TcdA4 -

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Basic information

Entry
Database: EMDB / ID: EMD-10036
TitleCryo-EM structure of Photorhabdus luminescens TcdA4
Map dataCryo-EM density map of Photorhabdus luminescens TcdA4
Sample
  • Complex: P. luminescens TcdA4 pentamer
    • Protein or peptide: 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
Biological speciesPhotorhabdus luminescens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 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) releaseOct 23, 2019-
Map releaseOct 23, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6rwa
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10036.png

Downloads & links

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Map

FileDownload / File: emd_10036.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM density map of Photorhabdus luminescens TcdA4
Voxel sizeX=Y=Z: 1.12 Å
Density
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.045346726 - 0.11132428
Average (Standard dev.)0.00037561983 (±0.0040149735)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 448.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z448.000448.000448.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0450.1110.000

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Supplemental data

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Sample components

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Entire : P. luminescens TcdA4 pentamer

EntireName: P. luminescens TcdA4 pentamer
Components
  • Complex: P. luminescens TcdA4 pentamer
    • Protein or peptide: TcdA4

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Supramolecule #1: P. luminescens TcdA4 pentamer

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

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Macromolecule #1: TcdA4

MacromoleculeName: TcdA4 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 270.69525 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNSYVKEIPD VLQSQYGINC LTDICHYSFN EFRQQVSDHL SWSETNRLYR DAQQEQKENQ LYEARILKRA NPQLQNAVHL GITLPHAEL RGYNSEFGGR ASQYVAPGSV SSMFSPAAYL TELYREARNL HASDSVYHLD ERRPDLQSMT LSQQNMDTEL S TLSLSNEI ...String:
MNSYVKEIPD VLQSQYGINC LTDICHYSFN EFRQQVSDHL SWSETNRLYR DAQQEQKENQ LYEARILKRA NPQLQNAVHL GITLPHAEL RGYNSEFGGR ASQYVAPGSV SSMFSPAAYL TELYREARNL HASDSVYHLD ERRPDLQSMT LSQQNMDTEL S TLSLSNEI LLKGIKANQS NLDSDTKVME MLSTFRPSGT IPYHDAYENV RKAIQLQDPK LEQFQKSPAV AGLMHQASLL GI NNSISPE LFNILTEEIT EANAEAIYKQ NFGDIDPACL AMPEYLKSYY NFSDEELSQF IRKYPDNELN TQKIHLLKIN KII LLSQAV NLPFLKLDEI IPEQNITPTV LGKIFLVKYY MQKYNIGTET ALILCNDSIS QYSYSNQPSQ FDRLFNTSPL NGQY FVIED TNIDLSLNST DNWHKAVLKR AFNVDDISLY RLLHIANHNN TDGKIANNIK NLSNLYMTKL LADIHQLTID ELYLL LITI GEDKINLYDI DDKELEKLIN RLDTLSNWLH TQKWSIYQLF LMTTTNYDKT LTPEIQNLLD TVYNGLQNFD KNKTKL LAA IAPYIAATLQ LPSENVAHSI LLWADKIKPS ENKITAEKFW IWLQNRDTTE LSKPPEMQEQ IIQYCHCLAQ LTMIYRS SG INENAFRLFI EKPTIFGIPD EPNKATPAHN APTLIILTRF ANWVNSLGEK ASPILTAFEN KTLTAEKLAN AMNLDANL L EQASIQAQNY KQVTKENTFS NWQSIDIILQ WTNIASNLNI SPQGISPLIA LDYIKPAQKT PTYAQWENAA IALTAGLDT QQTHTLHVFL DESRSTALSN YYIGKVANRA ASIKSRDDLY QYLLIDNQVS AEIKTTRIAE AIASIQLYVN RALENIEIHA VSDVITRQF FIDWDKYNKR YSTWAGVSQL VYYPENYIDP TMRIGQTKMM DTLLQSVSQS QLNADTVEDA FKSYLTSFEQ V ANLEVISA YHDNVNNDQG LTYFIGNSKT EVNQYYWRSV DHSKFNDGKF AANAWSEWHK IDCAINPYQS TIRPVIYKSR LY LIWLEQK ETAKQKEDNK VTTDYHYELK LAHIRYDGTW NVPITFDVDE KILALELTKS QAPGLYCAGY QGEDTLLIMF YRK KEKLDD YKTAPMQGFY IFSDMSSKDM TNEQCNSYRD NGYTHFDTNS DTNSVIRINN RYAEDYEIPS LINHSNSHDW GEYN LSQVY GGNIVINYKV TSNDLKIYIS PKLRIIHDGK EGRERIQSNL IKKYGKLGDK FIIYTSLGIN PNNSSNRFMF YPVYQ YNGN TSGLAQGRLL FHRDTSYSSK VAAWIPGAGR SLINENANIG DDCAEDSVNK PDDLKQYIYM TDSKGTATDV SGPVDI NTA ISSEKVQITI KAGKEYSLTA NKDVSVQPSP SFEEMCYQFN ALEIDGSNLN FTNNSASIDV TFTALADDGR KLGYEIF NI PVIQKVKTDN ALTLFHDENG AQYMQWGAYR IRLNTLFARQ LVERANTGID TILSMETQNI QEPMMGIGAY IELILDKY N PDIHGTNKSF KIIYGDIFKA GDHFPIYQGA LSDITQTTVK LFLPRVDNAY GNKNNLYVYA AYQKVETNFI RFVKEDNNK PATFDTTYKN GTFPGLASAR VIQTVSEPMD FSGANSLYFW ELFYYTPMMV AQRLLHEQNF DEANRWLKYV WSPSGYIVRG QIKNYHWNV RPLLENTSWN SDPLDSVDPD AVAQHDPMHY KVATFMRTLD LLMARGDHAY RQLERDTLNE AKMWYMQALH L LGNKPYLP LSSVWNDPRL DNAAATTTQK AHAYAITSLR QGTQTPALLL RSANTLTDLF LPQINDVMLS YWNKLELRLY NL RHNLSID GQPLHLPIYA TPADPKALLS AAVATSQGGG KLPESFISLW RFPHMLENAR SMVTQLIQFG STLQNIIERQ DAE SLNALL QNQAKELILT TLSIQDKTIE EIDAEKTVLE KSKAGAKSRF DNYSKLYDED VNAGERQALD MRIASQSITS GLKG LHMAA AALEMVPNIY GFAVGGTRYG AIANAIAIGG GIAAEGLLIE AEKVSQSEIW RRRRQEWEIQ RNNAEAEMKQ IDAQL KSLT VRREAAVLQK TGLKTQQEQT QAQLAFLQRK FSNQALYNWL RGRLAAIYFQ FYDLVVARCL MAEQAYRWET NDSSAR FIK PGAWQGTYAG LLAGETLMLN LAQMEDAHLK QEQRALEVER TVSLAQVYQS LGEKSFALKD KIEALLQGDK ETSAGND GN QLKLTNNTLS ATLTLQDLKL KDDYPEEMQL GKTRRIKQIS VSLPALLGPY QDVQAVLSYG GDATGLAKGC KALAVSHG L NDNGQFQLDF NDGKFLPFEG IDINDKGTFT LSFPNAASKQ KNILQMLTDI ILHIRYTILE

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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: 8
VitrificationCryogen name: ETHANE

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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: 1.0 sec. / Average electron dose: 30.7 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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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: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 35857

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Atomic model buiding 1

Initial modelPDB ID:

1vw1
PDB Unreleased entry

Output model

PDB-6rwa:
Cryo-EM structure of Photorhabdus luminescens TcdA4

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