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- EMDB-19987: Lymphostatin, conformation 1 (composite structure) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-19987
TitleLymphostatin, conformation 1 (composite structure)
Map datacomposite map
Sample
  • Complex: Lymphostatin
    • Protein or peptide: Efa1/LifA protein
Keywordsbacterial virulence factor / glycosyltransferase / protease / 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 str. E2348/69 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGriessmann M / Rasmussen T / Bottcher B
Funding support Germany, 8 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)INST 93/903-1 Germany
German Research Foundation (DFG)INST 93/1042-1 Germany
German Research Foundation (DFG)INST 93/1143-1 Germany
German Research Foundation (DFG)BO1150/18-1 Germany
CitationJournal: to be published
Title: Structure of lymphostatin, a potent virulence factor from pathogenic Escherichia coli
Authors: Griessmann M / Rasmussen T / Flegler V / Kraft C / Schneider R / Spantzel L / Borsch M / Bottcher B
History
DepositionMar 28, 2024-
Header (metadata) releaseApr 9, 2025-
Map releaseApr 9, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19987.png

Downloads & links

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Map

FileDownload / File: emd_19987.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map
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: 5.0
Minimum - Maximum-26.682865 - 52.407474999999998
Average (Standard dev.)-0.004266597 (±1.0360255)
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: Efa1/LifA protein

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Supramolecule #1: Lymphostatin

SupramoleculeName: Lymphostatin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: C-terminal His6 tag
Source (natural)Organism: Escherichia coli O127:H6 str. E2348/69 (bacteria)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Efa1/LifA protein

MacromoleculeName: Efa1/LifA protein / type: protein_or_peptide / ID: 1 / Details: C-terminal His6 tag / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli O127:H6 str. E2348/69 (bacteria)
Molecular weightTheoretical: 367.234062 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 FSLQVQIAEK 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 LFNHHHHHH

UniProtKB: Efa1/LifA protein

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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

Concentration0.9 mg/mL
BufferpH: 4
Component:
ConcentrationFormulaName
25.0 mMNaH2PO4sodium dihydrogen phosphate
100.0 mMNaClsodium chloride
0.075 mMMnCl2manganese chloride
1.5 mMC9H15O6PHClTCEP

Details: pH was adjusted before vitrification to 4.0 with hydrochloric acid
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 150 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 5 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 41392 / Average exposure time: 6.1 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: 1.4000000000000001 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: 13373262
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0)
Details: This is a composite map from two original maps. One overall map was used until residue 2199 and for overall alignment. The second map was a local refinement for the C-terminal part from ...Details: This is a composite map from two original maps. One overall map was used until residue 2199 and for overall alignment. The second map was a local refinement for the C-terminal part from residue 2200. Phenix Combine focused maps tool was used (version 1.20.1)
Number images used: 120944
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: modelangelo was used for the initial model.
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: Cross-correlation coefficient
Output model

PDB-9euv:
Lymphostatin, conformation 1 (composite structure)

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