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- EMDB-53287: Lymphostatin - conformation II - pH 6.5 phosphate buffer -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53287
TitleLymphostatin - conformation II - pH 6.5 phosphate buffer
Map data
Sample
  • Complex: Lymphostatin
    • Protein or peptide: Lymphostatin
KeywordsLymphostatin virulence factor A/E bacteria Toxin-like / 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 (E. coli) / Escherichia coli O127:H6 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGriessmann M / Rasmussen T / Bottcher B
Funding support Germany, United Kingdom, 6 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
German Research Foundation (DFG)411346541 Germany
Biotechnology and Biological Sciences Research Council (BBSRC)BBS/E/RL/230002C United Kingdom
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 29, 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_53287.png

Downloads & links

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Map

FileDownload / File: emd_53287.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 425.4 Å		1.06 Å/pix.
x 400 pix.
= 425.4 Å		1.06 Å/pix.
x 400 pix.
= 425.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0635 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.5798436 - 2.1323311
Average (Standard dev.)-0.00080973026 (±0.05912731)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 425.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53287_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53287_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53287_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

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 / Details: pH 6.5 Phosphate buffer
Source (natural)Organism: Escherichia coli (E. coli)
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

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 73.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 216178
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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