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- EMDB-38011: Cryo-EM structure of the TcsL at pH 5.0 in its open conformation -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-38011
TitleCryo-EM structure of the TcsL at pH 5.0 in its open conformation
Map dataAuthor stated: the relative low model inclusion of map was due to the flexible mobile nature of the molecule. We modeled the C-terminus of the TcsL by rigid docking in to the low-pass filtered map.
Sample
  • Complex: TcsL
    • Protein or peptide: Cytotoxin-L
  • Ligand: ZINC ION
KeywordsTcsL / CROP / TOXIN
Function / homology
Function and homology information


host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis ...host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / membrane / metal ion binding
Similarity search - Function
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 / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily ...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 / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Biological speciesPaeniclostridium sordellii (strain ATCC 9714 / DSM 2141 / JCM 3814 / LMG 15708 / NCIMB 10717 / 211) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsZhan X / Tao L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2023
Title: Structural dynamics of CROPs control stability and toxicity of Paeniclostridium sordellii lethal toxin
Authors: Yao Z / Xiechao Z / Liang T
History
DepositionNov 9, 2023-
Header (metadata) releaseDec 13, 2023-
Map releaseDec 13, 2023-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38011.png

Downloads & links

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Map

FileDownload / File: emd_38011.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAuthor stated: the relative low model inclusion of map was due to the flexible mobile nature of the molecule. We modeled the C-terminus of the TcsL by rigid docking in to the low-pass filtered map.
Voxel sizeX=Y=Z: 1.087 Å
Density
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-8.28098 - 12.371257999999999
Average (Standard dev.)-0.0002732941 (±0.10710035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 434.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_38011_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38011_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : TcsL

EntireName: TcsL
Components
  • Complex: TcsL
    • Protein or peptide: Cytotoxin-L
  • Ligand: ZINC ION

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Supramolecule #1: TcsL

SupramoleculeName: TcsL / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Paeniclostridium sordellii (strain ATCC 9714 / DSM 2141 / JCM 3814 / LMG 15708 / NCIMB 10717 / 211) (bacteria)

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Macromolecule #1: Cytotoxin-L

MacromoleculeName: Cytotoxin-L / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
Source (natural)Organism: Paeniclostridium sordellii (strain ATCC 9714 / DSM 2141 / JCM 3814 / LMG 15708 / NCIMB 10717 / 211) (bacteria)
Molecular weightTheoretical: 271.827531 KDa
Recombinant expressionOrganism: Bacillus subtilis (bacteria)
SequenceString: MNLVNKAQLQ KMAYVKFRIQ EDEYVAILNA LEEYHNMSES SVVEKYLKLK DINNLTDNYL NTYKKSGRNK ALKKFKEYLT MEVLELKNN SLTPVEKNLH FIWIGGQIND TAINYINQWK DVNSDYTVKV FYDSNAFLIN TLKKTIVESA TNNTLESFRE N LNDPEFDY ...String:
MNLVNKAQLQ KMAYVKFRIQ EDEYVAILNA LEEYHNMSES SVVEKYLKLK DINNLTDNYL NTYKKSGRNK ALKKFKEYLT MEVLELKNN SLTPVEKNLH FIWIGGQIND TAINYINQWK DVNSDYTVKV FYDSNAFLIN TLKKTIVESA TNNTLESFRE N LNDPEFDY NKFYRKRMEI IYDKQKHFID YYKSQIEENP EFIIDNIIKT YLSNEYSKDL EALNKYIEES LNKITANNGN DI RNLEKFA DEDLVRLYNQ ELVERWNLAA ASDILRISML KEDGGVYLDV DMLPGIQPDL FKSINKPDSI TNTSWEMIKL EAI MKYKEY IPGYTSKNFD MLDEEVQRSF ESALSSKSDK SEIFLPLDDI KVSPLEVKIA FANNSVINQA LISLKDSYCS DLVI NQIKN RYKILNDNLN PSINEGTDFN TTMKIFSDKL ASISNEDNMM FMIKITNYLK VGFAPDVRST INLSGPGVYT GAYQD LLMF KDNSTNIHLL EPELRNFEFP KTKISQLTEQ EITSLWSFNQ ARAKSQFEEY KKGYFEGALG EDDNLDFAQN TVLDKD YVS KKILSSMKTR NKEYIHYIVQ LQGDKISYEA SCNLFSKDPY SSILYQKNIE GSETAYYYSV ADAEIKEIDK YRIPYQI SN KRKIKLTFIG HGKSEFNTDT FANLDVDSLS SEIETILNLA KADISPKYIE INLLGCNMFS YSISAEETYP GKLLLKIK D RVSELMPSIS QDSITVSANQ YEVRINEEGK REILDHSGKW INKEESIIKD ISSKEYISFN PKENKIIVKS KYLHELSTL LQEIRNNANS SDIDLEKKVM LTECEINVAS NIDRQIVEGR IEEAKNLTSD SINYIKNEFK LIESISDSLY DLKHQNGLDD SHFISFEDI SKTENGFRIR FINKETGNSI FIETEKEIFS EYATHISKEI SNIKDTIFDN VNGKLVKKVN LDAAHEVNTL N SAFFIQSL IEYNTTKESL SNLSVAMKVQ VYAQLFSTGL NTITDASKVV ELVSTALDET IDLLPTLSEG LPIIATIIDG VS LGAAIKE LSETNDPLLR QEIEAKIGIM AVNLTAASTA IVTSALGIAS GFSILLVPLA GISAGIPSLV NNELILQDKA TKV IDYFKH ISLAETEGAF TLLDDKIIMP QDDLVLSEID FNNNSITLGK CEIWRAEGGS GHTLTDDIDH FFSSPSITYR KPWL SIYDV LNIKKEKIDF SKDLMVLPNA PNRVFGYEMG WTPGFRSLDN DGTKLLDRIR DHYEGQFYWR YFAFIADALI TKLKP RYED TNVRINLDGN TRSFIVPVIT TEQIRKNLSY SFYGSGGSYS LSLSPYNMNI DLNLVENDTW VIDVDNVVKN ITIESD EIQ KGELIENILS KLNIEDNKII LNNHTINFYG DINESNRFIS LTFSILEDIN IIIEIDLVSK SYKILLSGNC MKLIENS SD IQQKIDHIGF NGEHQKYIPY SYIDNETKYN GFIDYSKKEG LFTAEFSNES IIRNIYMPDS NNLFIYSSKD LKDIRIIN K GDVKLLIGNY FKDDMKVSLS FTIEDTNTIK LNGVYLDENG VAQILKFMNN AKSALNTSNS LMNFLESINI KNIFYNNLD PNIEFILDTN FIISGSNSIG QFELICDKDK NIQPYFIKFK IKETSYTLYV GNRQNLIVEP SYHLDDSGNI SSTVINFSQK YLYGIDRYV NKVIIAPNLY TDEINITPVY KPNYICPEVI ILDANYINEK INVNINDLSI RYVWDNDGSD LILIANSEED N QPQVKIRF VNVFKSDTAA DKLSFNFSDK QDVSVSKIIS TFSLAAYSDG FFDYEFGLVS LDNDYFYINS FGNMVSGLIY IN DSLYYFK PPKNNLITGF TTIDGNKYYF DPTKSGAASI GEITIDGKDY YFNKQGILQV GVINTSDGLK YFAPAGTLDE NLE GESVNF IGKLNIDGKI YYFEDNYRAA VEWKLLDDET YYFNPKTGEA LKGLHQIGDN KYYFDDNGIM QTGFITINDK VFYF NNDGV MQVGYIEVNG KYFYFGKNGE RQLGVFNTPD GFKFFGPKDD DLGTEEGELT LYNGILNFNG KIYFFDISNT AVVGW GTLD DGSTYYFDDN TAEACIGLTV INDCKYYFDD NGIRQLGFIT INDNIFYFSE SGKIELGYQN INGNYFYIDE SGLVLI GVF DTPDGYKYFA PLNTVNDNIY GQAVKYSGLV RVNEDVYYFG ETYKIETGWI ENETDKYYFD PETKKAYKGI NVVDDIK YY FDENGIMRTG LISFENNNYY FNEDGKMQFG YLNIKDKMFY FGKDGKMQIG VFNTPDGFKY FAHQNTLDEN FEGESINY T GWLDLDGKRY YFTDEYIAAT GSLTIDGYNY YFDPDTAELV VSEHHHHHHH H

UniProtKB: Cytotoxin-L

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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: 5
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: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1045888
FSC plot (resolution estimation)

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