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- EMDB-53169: Lymphostatin - pH 8 - phosphate buffer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53169
TitleLymphostatin - pH 8 - 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 O127:H6 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsGriessmann M / Schneider R / 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 15, 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_53169.png

Downloads & links

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Map

FileDownload / File: emd_53169.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
AxesX (Sec.)Y (Row.)Z (Col.)
0.95 Å/pix.
x 400 pix.
= 378.4 Å		0.95 Å/pix.
x 400 pix.
= 378.4 Å		0.95 Å/pix.
x 400 pix.
= 378.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-16.27178 - 38.760080000000002
Average (Standard dev.)-0.008341267 (±0.8662337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 378.4 Å
α=β=γ: 90.0 °

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Supplemental data

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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 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O127:H6 (bacteria)
Molecular weightTheoretical: 366.421219 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRLPEKVLFP PVTSGLSGQE KQKKPKSITG FQENYQRNIR PIKTASEARL RFFDKMVSKE NSLEDVVSLG EMIQKEIYGH EQRTFSPVH HTGNWKSSLL HNALLGLANV YNGLRETEYP NTFNRDGIKS TNSFRDNLLT KTRTPRDNFE EGIKHPEHAT I PYDNDNES ...String:
MRLPEKVLFP PVTSGLSGQE KQKKPKSITG FQENYQRNIR PIKTASEARL RFFDKMVSKE NSLEDVVSLG EMIQKEIYGH EQRTFSPVH HTGNWKSSLL HNALLGLANV YNGLRETEYP NTFNRDGIKS TNSFRDNLLT KTRTPRDNFE EGIKHPEHAT I PYDNDNES NKLLKAGKIA GNNNELLMEI KKESQSDHQI PLSDKFLKRK KRSPVAEDKV QNSLTPENFV QKISLSDELK TK YANEIIE IKRIMGEYNL LPDKNSRNGL KLLQKQADLL KIIMEDTSVT ENTFKNIEIA ITDIKREYYS HTVDIEKNIH AIW VAGSPP ESISDYIKTF LKTYKEFTYY LWVDEKAFGA AKFTSVLKQI AFDLACRTIQ QNTPQKNIDF INLYNEIRKK YNNN PSGQQ EYLNKLRELY ATYQKISTPL KHMFNSFFLE NMIKLQDNFF NYCIVKGVTE INDELRINYL KNVIKLSDDD IGNYQ KTIN DNKDRVKKLI LDLQKQFGEN RISIKDVNSL TSLSKSENNH NYQTEMLLRW NYPAASDLLR MYILKEHGGI YTDTDM MPA YSKQVIFKIM MQTNGDNRFL EDLKLRRAIS DGVLRYVNNQ NIDEVNYNEI SDADKNIIKK ILTEISKMPE DSIFTKI NT RIPRDTMPIL RRYHLWPDGW NIRGLNGFML SHKGSEVIDA VIAGQNQAYR ELRRIRDNIH SEIYFKQTDE LSSLPDTD K IGGILVKKYL SGSLFSKFRQ DTIIPEALST LQISGPDLIQ RKMLQFFRSR GVLGEEFINE RKLSDKAYIG VYKTTGTGK YDWLTPESIG VNDVTPADES TWCIGKGRCV DDFLFKDVST LKTENLPELF LTKIDTDTFF SQWSTKTKKD LQKKIQDLTV RYNELIDSS TIDFKNLYEI DQMLHMIMLE MNDDIAKRSL FSLQVQISEK IRRMTIPVDN IINIYPDLHK KNDNDLSMSI K GFLASNPH TKINILYSNK TEHNIFIKDL FSFAVMENEL RDIINNMSKD KTPENWEGRV MLQRYLELKM KDHLSLQSSQ EA NEFLEIS TFIYENDFLR EKIEAVKNKM NSHELYFEKI KKEQNTWQDL STKEQKLQLI KALKEISGNT EKDSHYDRLL DAF FKKHNE NIHNKIQRIK DEFKEYSRVA IHNIDKVIFK GQTLDRLYHE GYVFSDINTL SRYTLHGLGI TGVHTEENLL PAPS SSLIN ILKEHYNEDE ISAKLPLAYD YILNKKESSS IPVEILNKLS ELPPHELLTP VLGQSVNPLG MGYSSDNGKI TEQVI VSGA DGFDNPISGL IYTYLEDLYN IHVRMREGTL NSQNLRQLLE NSVSSCFLTE QSINKLLSEA EKRPYQSLTE IHQHLT GLP TIADATLSLL SVGLPGTGKL LRREQDYGRP PVTAIQDSTF VLPYNFKGIG FNDNIISSAP VASSLHFIAE HAKYTLL SW PEFYRHHAQR WFEMAKGYGS QNIDFHPQSL LVTQEGRCMG LALLYLQTED TAHYSILQEN LMTVSALHQT SNRDKLPL S KDDNSLMTRT YSLIEMLQYQ GNKYITNESL LHKTAWNQER ITLLFNEKGV KRALISTPNH TLVLQQLEDI YRLTDPNFG HADFLSPIDA LKFIEAMIQL TPTLQEYYGL LNKDINKHIQ VHYAESDMVW NKLLPENDAG LSTRIQHTTT DRLANLAEPV AVAGISLPV KTLYDIGATL DGRRITSPPT SEQIPSLRLN GDVLNDYLSR TVLTPEQADN IRKILHTQGI RSGTRPIDPE M IRGTQDDL VSSQTRLQRQ ATRVKQQLAG VLDTLQQHFQ NIPRSSGRHL SVENIELADI GSGRFNLQIR DGETLHTTSV EV PEVVSRF QKLSTMLSAL PASGIMDFDL GMSVVGVVQY ARLLQQGHED STLAKINLAM DIKQLSEATL GSMIQIAGNK FLN TEGIQG FRLESAVAEG MRSVATRTGG TMGKALSASA RVLELPVLET VLGTWNLYNS VIQLQQATSY SETMAARVQI AFDS ISLGL TAASVAFPPL IIATGPIAAI GMGASSIARN VARKEERHTQ WLEYKKFLTD GSKHIVVASP ERGLLDFSGN KVFGK MVLD LRQSPPLLHG ESSFNADRKI GHRPDLGDWQ IREKVGYANS ISPYSSLAHG YANSKWPRTI PKIPSGEYDT IILGYG HQY QANTEIEYLS NWIVWREAVP DSTSRHKRPP LEVLNSQCTV IAGERKTTVL PLRVLSDLTP ECTEQAISLK DYKFILR GG SGGLAVQVGG AGYYDIDANL VAKENTLSFR GLPEEFPLTF DLSKQTQSVM LKTPDDEVPV MTITQKGINT LVGTAAGK D RLIGNDKDNT FHTSSGGGTV ISGGGNNRYI IPRDLKTPLT LTLSSNSVSH EIFLPETTLA ELKPVAFELS LIYWAGNNI NVQPEDEAKL NHFAGNFRVH TRDGMTLEAV SRENGIQLAI SLCDVQRWQA VYPEENNRPD AILDRLHDMG WSLTPEVRFQ GGETQVSYD PLTRQLVYQL QARYSEFQLA GSRHHTTAVT GTPGSRYIIM KPVTTQILPT QIILAGDNDH PETIDLLEAS P VLVEGKKD KNSVILTIAT IQYSLQLTIS GIEESLPETT RVAIQPQDTR LLGDVLRILP DNGNWVGIFR SGHTPTVNRL EN LMALNQV MTFLPRVSGS AEQVLCLENL GGVRKKVEGE LLSGKLKGAW KAEGEPTVPV NISDLSIPPY SRLYLIFEGK NNV LLRSKV HAAPLKITSA GEMQLSERQW QQQEHIIVKP DNEAPSLILS EFRRFTISSD KTFSLKLMCH QGMVRIDRRS LSVR LFYLR EQPGIGSLRL TFRDFFTEVM DTTDREILEK ELRPILIGDT HRFINAAYKN HLNIQLGDGV LNLADIVAEY ARIQK EETS KILYQYQGAM KKKTDGPSVV EDAIMTTTVT TDSGELFPTF HPWYTDDLSG RYKSVPMARK ADTLYHLTPK GDLQII YQV ATKMVNQAMI VSLPNYRHEW EKYNLSILSE IPQNNNTVVH SILRVNGPTM QVRTIDYRGT DENNPIVSFS DTTFING EQ MLSYDSHSSG RVYSREEYMM WELQQRVSEA SSARTQDYWL MDAAVRNGEW KITPELLRHT PGYIRSTVSK WSRGWLKT G TILQTPEDRN TDVYLTTIQN NVFSRQGGGY QVYYRIDGMA GADIADNAPG ETRCTLRPGT CFEVTSVDER HYEWNIIYV 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: 8
Details: 25 mM sodium phosphate pH 8, 100 mM NaCl, 0.075 mM MnCl2, 1.5 mM TCEP
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / 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: 1.2 µm / Nominal defocus min: 0.5 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: EMDB MAP
EMDB ID:

19984

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 1294835
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9qhh:
Lymphostatin - pH 8 - phosphate buffer

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