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- EMDB-12948: Cryo-EM reconstruction of SlyB14-BamA from Escherichia coli -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-12948
TitleCryo-EM reconstruction of SlyB14-BamA from Escherichia coli
Map dataSlyB14-BamA
Sample
  • Complex: Outer membrane lipoprotein SlyB
    • Protein or peptide: Outer membrane lipoprotein SlyB
    • Protein or peptide: Outer membrane protein assembly factor BamA
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: 6.7 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_12948.png

Downloads & links

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Map

FileDownload / File: emd_12948.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSlyB14-BamA
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: 0.012
Minimum - Maximum-0.012756235 - 0.026699824
Average (Standard dev.)0.00031114725 (±0.0017389361)
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
    • Protein or peptide: Outer membrane protein assembly factor BamA

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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: SlyB14-BamA was purified from overexpression of SlyB-TEV-HIS/BamA 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: 290 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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Macromolecule #2: Outer membrane protein assembly factor BamA

MacromoleculeName: Outer membrane protein assembly factor BamA / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli BW25113 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVKE RPTIASITFS GNKSVKDDML KQNLEASGVR VGESLDRTTI ADIEKGLEDF YYSVGKYSAS VKAVVTPLPR NRVDLKLVFQ EGVSAEIQQI NIVGNHAFTT ...String:
AEGFVVKDIH FEGLQRVAVG AALLSMPVRT GDTVNDEDIS NTIRALFATG NFEDVRVLRD GDTLLVQVKE RPTIASITFS GNKSVKDDML KQNLEASGVR VGESLDRTTI ADIEKGLEDF YYSVGKYSAS VKAVVTPLPR NRVDLKLVFQ EGVSAEIQQI NIVGNHAFTT DELISHFQLR DEVPWWNVVG DRKYQKQKLA GDLETLRSYY LDRGYARFNI DSTQVSLTPD KKGIYVTVNI TEGDQYKLSG VEVSGNLAGH SAEIEQLTKI EPGELYNGTK VTKMEDDIKK LLGRYGYAYP RVQSMPEIND ADKTVKLRVN VDAGNRFYVR KIRFEGNDTS KDAVLRREMR QMEGAWLGSD LVDQGKERLN RLGFFETVDT DTQRVPGSPD QVDVVYKVKE RNTGSFNFGI GYGTESGVSF QAGVQQDNWL GTGYAVGING TKNDYQTYAE LSVTNPYFTV DGVSLGGRLF YNDFQADDAD LSDYTNKSYG TDVTLGFPIN EYNSLRAGLG YVHNSLSNMQ PQVAMWRYLY SMGEHPSTSD QDNSFKTDDF TFNYGWTYNK LDRGYFPTDG SRVNLTGKVT IPGSDNEYYK VTLDTATYVP IDDDHKWVVL GRTRWGYGDG LGGKEMPFYE NFYAGGSSTV RGFQSNTIGP KAVYFPHQAS NYDPDYDYEC ATQDGAKDLC KSDDAVGGNA MAVASLEFIT PTPFISDKYA NSVRTSFFWD MGTVWDTNWD SSQYSGYPDY SDPSNIRMSA GIALQWMSPL GPLVFSYAQP FKKYDGDKAE QFQFNIGKTW

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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
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: 7352 / 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 56166
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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