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- EMDB-14170: Low resolution negative stain map of SslE -

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Basic information

Entry
Database: EMDB / ID: EMD-14170
TitleLow resolution negative stain map of SslE
Map dataLow resolution map of SslE
Sample
  • Complex: SslE
    • Protein or peptide: SslE
Keywordsmetalloprotease / biofilm formation / MEMBRANE PROTEIN
Biological speciesEscherichia coli W (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 22.0 Å
AuthorsFenn K / Darbari VC / Garnett JA / Corsini PM
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R000514/1 United Kingdom
CitationJournal: NPJ Biofilms Microbiomes / Year: 2022
Title: Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation.
Authors: Paula M Corsini / Sunjun Wang / Saima Rehman / Katherine Fenn / Amin Sagar / Slobodan Sirovica / Leanne Cleaver / Charlotte J C Edwards-Gayle / Giulia Mastroianni / Ben Dorgan / Lee M Sewell ...Authors: Paula M Corsini / Sunjun Wang / Saima Rehman / Katherine Fenn / Amin Sagar / Slobodan Sirovica / Leanne Cleaver / Charlotte J C Edwards-Gayle / Giulia Mastroianni / Ben Dorgan / Lee M Sewell / Steven Lynham / Dinu Iuga / W Trent Franks / James Jarvis / Guy H Carpenter / Michael A Curtis / Pau Bernadó / Vidya C Darbari / James A Garnett /
Abstract: Escherichia coli is a Gram-negative bacterium that colonises the human intestine and virulent strains can cause severe diarrhoeal and extraintestinal diseases. The protein SslE is secreted by a range ...Escherichia coli is a Gram-negative bacterium that colonises the human intestine and virulent strains can cause severe diarrhoeal and extraintestinal diseases. The protein SslE is secreted by a range of pathogenic and commensal E. coli strains. It can degrade mucins in the intestine, promotes biofilm maturation and it is a major determinant of infection in virulent strains, although how it carries out these functions is not well understood. Here, we examine SslE from the commensal E. coli Waksman and BL21 (DE3) strains and the enterotoxigenic H10407 and enteropathogenic E2348/69 strains. We reveal that SslE has a unique and dynamic structure in solution and in response to acidification within mature biofilms it can form a unique aggregate with amyloid-like properties. Furthermore, we show that both SslE monomers and aggregates bind DNA in vitro and co-localise with extracellular DNA (eDNA) in mature biofilms, and SslE aggregates may also associate with cellulose under certain conditions. Our results suggest that interactions between SslE and eDNA are important for biofilm maturation in many E. coli strains and SslE may also be a factor that drives biofilm formation in other SslE-secreting bacteria.
History
DepositionJan 19, 2022-
Header (metadata) releaseMar 16, 2022-
Map releaseMar 16, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00562
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.00562
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_14170.png

Downloads & links

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Map

FileDownload / File: emd_14170.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLow resolution map of SslE
Voxel sizeX=Y=Z: 2.6 Å
Density
Contour LevelBy AUTHOR: 0.00562 / Movie #1: 0.00562
Minimum - Maximum-0.01572856 - 0.100149855
Average (Standard dev.)0.00015534388 (±0.0026861483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 390.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.62.62.6
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z390.000390.000390.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ640640640
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.0160.1000.000

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Supplemental data

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Sample components

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Entire : SslE

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

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Supramolecule #1: SslE

SupramoleculeName: SslE / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli W (bacteria)
Molecular weightTheoretical: 160 KDa

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Macromolecule #1: SslE

MacromoleculeName: SslE / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Escherichia coli W (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: CDGGGSGSSS DTPPVDSGTG SLPEVKPDPT PNPEPTPEPT PDPEPTPEPT PDPEPTPEPE PEPVPTKTGY LTLGGSLRVT GDITCNDESS DGFTFTPGDK VTCVAGNNTT IATFDTQSEA ARSLRAVEKV SFSLEDAQEL AGSDNKKSNA LSLVTSMNSC PANTEQVCLE ...String:
CDGGGSGSSS DTPPVDSGTG SLPEVKPDPT PNPEPTPEPT PDPEPTPEPT PDPEPTPEPE PEPVPTKTGY LTLGGSLRVT GDITCNDESS DGFTFTPGDK VTCVAGNNTT IATFDTQSEA ARSLRAVEKV SFSLEDAQEL AGSDNKKSNA LSLVTSMNSC PANTEQVCLE FSSVIESKRF DSLYKQIDLA PEEFKKLVNE EVENNAATDK APSTHTSPVV PATTPGTKPD LNASFVSANA EQFYQYQPTE IILSEGRLVD SQGDGVVGVN YYTNSGRGVT GENGEFSFSW GETISFGIDT FELGSVRGNK STIALTELGD EVRGANIDQL IHRYSKAGQN HTRVVPDEVR KVFAEYPNVI NEIINLSLSN GATLGEGEQV VNLPNEFIEQ FKTGQAKEID TAICAKTDGC NEARWFSLTT RNVNDGQIQG VINKLWGVDT NYKSVSKFHV FHDSTNFYGS TGNARGQAVV NISNAAFPIL MARNDKNYWL AFGEKRAWDK NELAYITEAP SIVRPENVTR ETATFNLPFI SLGQVGDGKL MVIGNPHYNS ILRCPNGYSW NGGVNKDGQC TLNSDPDDMK NFMENVLRYL SNDRWLPDAK SSMTVGTNLD TVYFKKHGQV LGNSAPFAFH KDFTGITVKP MTSYGNLNPD EVPLLILNGF EYVTQWGSDP YSIPLRADTS KPKLTQQDVT DLIAYMNKGG SVLIMENVMS NLKEESASGF VRLLDAAGLS MALNKSVVNN DPQGYPDRVR QRRSTPIWVY ERYPAVDGKP PYTIDDTTKE VIWKYQQENK PDDKPKLEVA SWQEEVEGKQ VTQFAFIDEA DHKTPESLAA AKQRILDAFP GLEVCKDSDY HYEVNCLEYR PGTGVPVTGG MYVPQYTQLD LGADTAKAML QAADLGTNIQ RLYQHELYFR TNGRQGERLN SVDLERLYQN MSVWLWNETK YRYEEGKEDE LGFKTFTEFL NCYTNNAYVG TQCSAELKKS LIDNKMIYGE ESSKAGMMNP SYPLNYMEKP LTRLMLGRSW WDLNIKVDVE KYPGAVSEEG QNVTETISLY SNPTKWFAGN MQSTGLWAPA QKEVTIKSNA NVPVTVTVAL ADDLTGREKH EVALNRPPRV TKTYSLDASG TVKFKVPYGG LIYIKGDSKD NESASFTFTG VVKAPFYKDG AWKNDLNSPA PLGELESDAF VYTAPKKNLN ASNYTGGLKQ FANDLDTFAS SMNDFYGRNE EDGKHRMFTY KNLTGHKHRF ANDVQISIGD AHSGYPVMNS SFSTNSTTLP TTPLNDWLIW HEVGHNAAET PLTVPGATEV ANNVLALYMQ DRYLGKMNRV ADDITVAPEY LEESNGQAWA RGGAGDRLLM YAQLKEWAEK NFDIKKWYPE GELPKFFSDR EGMKGWNLFQ LMHRKARGDD VGDKTFGGKN YCAESNGNAA DTLMLCASWV AQTDLSEFFK KWNPGANAYQ LPGASEMSFE GGVSQSAYNT LASLKLPKPE QGPETINKVT EHKMSVE

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 8 / Component - Concentration: 50.0 mM / Component - Formula: Tris-HCl / Component - Name: Tris
StainingType: NEGATIVE / Material: Uranyl acetate
Details: 2% (v/v) uranyl acetate was applied for staining for 1 min. The excess liquid was blotted

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Electron microscopy

MicroscopeJEOL 2100
Image recordingFilm or detector model: OTHER / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: OTHER / Number images used: 11000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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