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- EMDB-52994: Lymphostatin - conformation III - pH 8 focussed on N-term -

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Basic information

Entry
Database: EMDB / ID: EMD-52994
TitleLymphostatin - conformation III - pH 8 focussed on N-term
Map data
Sample
  • Complex: Lymphostatin
    • Protein or peptide: Lymphostatin
KeywordsVirulence Factor Lymphostatin LifA Conformation III / TOXIN
Function / homology
Function and homology information


glycosyltransferase activity / cysteine-type endopeptidase activity
Similarity search - Function
Protein of unknown function DUF3491 / Protein of unknown function (DUF3491) / Peptidase C58, YopT-type domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Biological speciesEscherichia coli O127:H6 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsBottcher B / Schneider R / Griessmann M / Ramussen T
Funding support Germany, 4 items
OrganizationGrant numberCountry
German Research Foundation (DFG)359471283 Germany
German Research Foundation (DFG)456578072 Germany
German Research Foundation (DFG)525040890 Germany
German Research Foundation (DFG)428774170 Germany
CitationJournal: Nat Commun / Year: 2025
Title: Structure of lymphostatin, a large multi-functional virulence factor of pathogenic Escherichia coli.
Authors: Matthias Griessmann / Tim Rasmussen / Vanessa J Flegler / Christian Kraft / Ronja Schneider / Max Hateley / Lukas Spantzel / Mark P Stevens / Michael Börsch / Bettina Böttcher /
Abstract: Lymphostatin is a key virulence factor of enteropathogenic and enterohaemorrhagic Escherichia coli, playing roles in bacterial colonisation of the gut and in the inhibition of lymphocyte ...Lymphostatin is a key virulence factor of enteropathogenic and enterohaemorrhagic Escherichia coli, playing roles in bacterial colonisation of the gut and in the inhibition of lymphocyte proliferation and proinflammatory responses. The protein's glycosyltransferase and cysteine protease motifs are required for activity against lymphocytes, but high-resolution structural information has proven elusive. Here, we describe the structure of lymphostatin from enteropathogenic E. coli O127:H6, determined by electron cryo-microscopy at different pH values. We observe three conformations of a highly complex molecule with two glycosyltransferase domains, one PaToxP-like protease domain, an ADP-ribosyltransferase domain, a vertex domain and a delivery domain. Long linkers hold these domains together and occlude the catalytic sites of the N-terminal glycosyltransferase and protease domains. Lymphostatin binds to bovine T-lymphocytes and HEK-293T cells, forming clusters at the plasma membrane that are internalized. With six distinct domains, lymphostatin can be regarded as a multitool of pathogenic Escherichia coli, enabling complex interactions with host cells.
History
DepositionMar 1, 2025-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52994.png

Downloads & links

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Map

FileDownload / File: emd_52994.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 192 pix.
= 181.632 Å		0.95 Å/pix.
x 192 pix.
= 181.632 Å		0.95 Å/pix.
x 192 pix.
= 181.632 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0025
Minimum - Maximum-0.013378779 - 0.017922103
Average (Standard dev.)0.000015765843 (±0.0007633984)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 181.63199 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52994_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52994_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52994_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Lymphostatin

EntireName: Lymphostatin
Components
  • Complex: Lymphostatin
    • Protein or peptide: Lymphostatin

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Supramolecule #1: Lymphostatin

SupramoleculeName: Lymphostatin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli O127:H6 (bacteria)
Molecular weightTheoretical: 366 KDa

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Macromolecule #1: Lymphostatin

MacromoleculeName: Lymphostatin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O127:H6 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRLPEKVLFP PVTSGLSGQE KQKKPKSITG FQENYQRNIR PIKTASEARL RFFDKMVSKE NSLEDVVSLG EMIQKEIYGH EQRTFSPVHH TGNWKSSLLH NALLGLANVY NGLRETEYPN TFNRDGIKST NSFRDNLLTK TRTPRDNFEE GIKHPEHATI PYDNDNESNK ...String:
MRLPEKVLFP PVTSGLSGQE KQKKPKSITG FQENYQRNIR PIKTASEARL RFFDKMVSKE NSLEDVVSLG EMIQKEIYGH EQRTFSPVHH TGNWKSSLLH NALLGLANVY NGLRETEYPN TFNRDGIKST NSFRDNLLTK TRTPRDNFEE GIKHPEHATI PYDNDNESNK LLKAGKIAGN NNELLMEIKK ESQSDHQIPL SDKFLKRKKR SPVAEDKVQN SLTPENFVQK ISLSDELKTK YANEIIEIKR IMGEYNLLPD KNSRNGLKLL QKQADLLKII MEDTSVTENT FKNIEIAITD IKREYYSHTV DIEKNIHAIW VAGSPPESIS DYIKTFLKTY KEFTYYLWVD EKAFGAAKFT SVLKQIAFDL ACRTIQQNTP QKNIDFINLY NEIRKKYNNN PSGQQEYLNK LRELYATYQK ISTPLKHMFN SFFLENMIKL QDNFFNYCIV KGVTEINDEL RINYLKNVIK LSDDDIGNYQ KTINDNKDRV KKLILDLQKQ FGENRISIKD VNSLTSLSKS ENNHNYQTEM LLRWNYPAAS DLLRMYILKE HGGIYTDTDM MPAYSKQVIF KIMMQTNGDN RFLEDLKLRR AISDGVLRYV NNQNIDEVNY NEISDADKNI IKKILTEISK MPEDSIFTKI NTRIPRDTMP ILRRYHLWPD GWNIRGLNGF MLSHKGSEVI DAVIAGQNQA YRELRRIRDN IHSEIYFKQT DELSSLPDTD KIGGILVKKY LSGSLFSKFR QDTIIPEALS TLQISGPDLI QRKMLQFFRS RGVLGEEFIN ERKLSDKAYI GVYKTTGTGK YDWLTPESIG VNDVTPADES TWCIGKGRCV DDFLFKDVST LKTENLPELF LTKIDTDTFF SQWSTKTKKD LQKKIQDLTV RYNELIDSST IDFKNLYEID QMLHMIMLEM NDDIAKRSLF SLQVQISEKI RRMTIPVDNI INIYPDLHKK NDNDLSMSIK GFLASNPHTK INILYSNKTE HNIFIKDLFS FAVMENELRD IINNMSKDKT PENWEGRVML QRYLELKMKD HLSLQSSQEA NEFLEISTFI YENDFLREKI EAVKNKMNSH ELYFEKIKKE QNTWQDLSTK EQKLQLIKAL KEISGNTEKD SHYDRLLDAF FKKHNENIHN KIQRIKDEFK EYSRVAIHNI DKVIFKGQTL DRLYHEGYVF SDINTLSRYT LHGLGITGVH TEENLLPAPS SSLINILKEH YNEDEISAKL PLAYDYILNK KESSSIPVEI LNKLSELPPH ELLTPVLGQS VNPLGMGYSS DNGKITEQVI VSGADGFDNP ISGLIYTYLE DLYNIHVRMR EGTLNSQNLR QLLENSVSSC FLTEQSINKL LSEAEKRPYQ SLTEIHQHLT GLPTIADATL SLLSVGLPGT GKLLRREQDY GRPPVTAIQD STFVLPYNFK GIGFNDNIIS SAPVASSLHF IAEHAKYTLL SWPEFYRHHA QRWFEMAKGY GSQNIDFHPQ SLLVTQEGRC MGLALLYLQT EDTAHYSILQ ENLMTVSALH QTSNRDKLPL SKDDNSLMTR TYSLIEMLQY QGNKYITNES LLHKTAWNQE RITLLFNEKG VKRALISTPN HTLVLQQLED IYRLTDPNFG HADFLSPIDA LKFIEAMIQL TPTLQEYYGL LNKDINKHIQ VHYAESDMVW NKLLPENDAG LSTRIQHTTT DRLANLAEPV AVAGISLPVK TLYDIGATLD GRRITSPPTS EQIPSLRLNG DVLNDYLSRT VLTPEQADNI RKILHTQGIR SGTRPIDPEM IRGTQDDLVS SQTRLQRQAT RVKQQLAGVL DTLQQHFQNI PRSSGRHLSV ENIELADIGS GRFNLQIRDG ETLHTTSVEV PEVVSRFQKL STMLSALPAS GIMDFDLGMS VVGVVQYARL LQQGHEDSTL AKINLAMDIK QLSEATLGSM IQIAGNKFLN TEGIQGFRLE SAVAEGMRSV ATRTGGTMGK ALSASARVLE LPVLETVLGT WNLYNSVIQL QQATSYSETM AARVQIAFDS ISLGLTAASV AFPPLIIATG PIAAIGMGAS SIARNVARKE ERHTQWLEYK KFLTDGSKHI VVASPERGLL DFSGNKVFGK MVLDLRQSPP LLHGESSFNA DRKIGHRPDL GDWQIREKVG YANSISPYSS LAHGYANSKW PRTIPKIPSG EYDTIILGYG HQYQANTEIE YLSNWIVWRE AVPDSTSRHK RPPLEVLNSQ CTVIAGERKT TVLPLRVLSD LTPECTEQAI SLKDYKFILR GGSGGLAVQV GGAGYYDIDA NLVAKENTLS FRGLPEEFPL TFDLSKQTQS VMLKTPDDEV PVMTITQKGI NTLVGTAAGK DRLIGNDKDN TFHTSSGGGT VISGGGNNRY IIPRDLKTPL TLTLSSNSVS HEIFLPETTL AELKPVAFEL SLIYWAGNNI NVQPEDEAKL NHFAGNFRVH TRDGMTLEAV SRENGIQLAI SLCDVQRWQA VYPEENNRPD AILDRLHDMG WSLTPEVRFQ GGETQVSYDP LTRQLVYQLQ ARYSEFQLAG SRHHTTAVTG TPGSRYIIMK PVTTQILPTQ IILAGDNDHP ETIDLLEASP VLVEGKKDKN SVILTIATIQ YSLQLTISGI EESLPETTRV AIQPQDTRLL GDVLRILPDN GNWVGIFRSG HTPTVNRLEN LMALNQVMTF LPRVSGSAEQ VLCLENLGGV RKKVEGELLS GKLKGAWKAE GEPTVPVNIS DLSIPPYSRL YLIFEGKNNV LLRSKVHAAP LKITSAGEMQ LSERQWQQQE HIIVKPDNEA PSLILSEFRR FTISSDKTFS LKLMCHQGMV RIDRRSLSVR LFYLREQPGI GSLRLTFRDF FTEVMDTTDR EILEKELRPI LIGDTHRFIN AAYKNHLNIQ LGDGVLNLAD IVAEYARIQK EETSKILYQY QGAMKKKTDG PSVVEDAIMT TTVTTDSGEL FPTFHPWYTD DLSGRYKSVP MARKADTLYH LTPKGDLQII YQVATKMVNQ AMIVSLPNYR HEWEKYNLSI LSEIPQNNNT VVHSILRVNG PTMQVRTIDY RGTDENNPIV SFSDTTFING EQMLSYDSHS SGRVYSREEY MMWELQQRVS EASSARTQDY WLMDAAVRNG EWKITPELLR HTPGYIRSTV SKWSRGWLKT GTILQTPEDR NTDVYLTTIQ NNVFSRQGGG YQVYYRIDGM AGADIADNAP GETRCTLRPG TCFEVTSVDE RHYEWNIIYV TLKTCGWSRN GQSKTPNGDN LFN

UniProtKB: Lymphostatin

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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

Concentration1.25 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 5 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Number grids imaged: 3 / Number real images: 70899 / Average exposure time: 9.9 sec. / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 17027499
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6) / Software - details: Live session / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 169449
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9euw


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT

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