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- EMDB-12946: Cryo-EM reconstruction of dodecameric SlyB from Escherichia coli K12 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-12946
TitleCryo-EM reconstruction of dodecameric SlyB from Escherichia coli K12
Map dataSlyB12
Sample
  • Complex: Outer membrane lipoprotein SlyB
    • Protein or peptide: Outer membrane lipoprotein SlyB
KeywordsOuter membrane chaperon / 2TM glycine zipper / outer membrane lipoprotein SlyB / LPS-LP binding protein / MEMBRANE PROTEIN
Biological speciesEscherichia coli (E. coli) / Escherichia coli BW25113 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsNguyen VS / Remaut H
Funding support Belgium, 4 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0G0818N Belgium
Research Foundation - Flanders (FWO)G0H5916N Belgium
Research Foundation - Flanders (FWO)FWOTM903 Belgium
Research Foundation - Flanders (FWO)12ZM421N Belgium
CitationJournal: Nature / Year: 2023
Title: SlyB encapsulates outer membrane proteins in stress-induced lipid nanodomains
Authors: Janssens A / Nguyen VS / Cecil AJ / Van der Verren SE / Timmerman E / Deghelt M / Pak AJ / Collet JF / Impens F / Remaut H
History
DepositionMay 14, 2021-
Header (metadata) releaseJun 1, 2022-
Map releaseJun 1, 2022-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_12946.png

Downloads & links

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Map

FileDownload / File: emd_12946.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSlyB12
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.78 Å/pix.
x 360 pix.
= 282.24 Å		0.78 Å/pix.
x 360 pix.
= 282.24 Å		0.78 Å/pix.
x 360 pix.
= 282.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.784 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.009044827 - 0.017491745
Average (Standard dev.)0.00010932445 (±0.00071990915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 282.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Outer membrane lipoprotein SlyB

EntireName: Outer membrane lipoprotein SlyB
Components
  • Complex: Outer membrane lipoprotein SlyB
    • Protein or peptide: Outer membrane lipoprotein SlyB

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Supramolecule #1: Outer membrane lipoprotein SlyB

SupramoleculeName: Outer membrane lipoprotein SlyB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Dodecameric SlyB was purified from overexpression of SlyB-TEV-HIS in E. coli using using 2-step Ni-IMAC purification.
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BW25113 / Location in cell: Outer membrane
Molecular weightTheoretical: 220 KDa

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Macromolecule #1: Outer membrane lipoprotein SlyB

MacromoleculeName: Outer membrane lipoprotein SlyB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
(PLM)CVNNDTLSG DVYTASEAKQ VQNVSYGTIV NVRPVQIQGG DDSNVIGAIG GAVLGGFLGN TVGGGTGRSL ATAAGAVAGG VAGQGVQSAM NKTQGVELEI RKDDGNTIMV VQKQGNTRFS PGQRVVLASN GSQVTVSPRG GGENLYFQ

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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

Concentration0.04 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
20.0 mMTristris(hydroxymethyl)aminomethane
0.03 %DDMN-Dodecyl-beta-Maltoside
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: GATAN CRYOPLUNGE 3 / Details: Back-blotting for 4 seconds before plunging.

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6352 / Average exposure time: 3.0 sec. / Average electron dose: 61.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.55 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 60000
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C12 (12 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 70176
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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