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- PDB-7ojf: CRYO-EM STRUCTURE OF SLYB13-BAMA FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 7ojf
TitleCRYO-EM STRUCTURE OF SLYB13-BAMA FROM ESCHERICHIA COLI
Components(Outer membrane ...) x 2
KeywordsMEMBRANE PROTEIN / OUTER MEMBRANE CHAPERON / 2TM GLYCINE ZIPPER / OUTER MEMBRANE LIPOPROTEIN SLYB / LPS-LP BINDING PROTEIN
Function / homology
Function and homology information


Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane
Similarity search - Function
Glycine zipper 2TM domain / Glycine zipper 2TM domain / Outer membrane protein assembly factor BamA / POTRA domain, BamA/TamA-like / Surface antigen variable number repeat / POTRA domain / POTRA domain profile. / Surface antigen D15-like / Bacterial surface antigen (D15) / Omp85 superfamily domain / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Chem-L8Z / Chem-LPP / PALMITIC ACID / Outer membrane protein assembly factor BamA / Outer membrane lipoprotein slyB
Similarity search - Component
Biological speciesEscherichia coli BW25113 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsNguyen, V.S. / Remaut, H.
CitationJournal: Nature / Year: 2023
Title: SlyB encapsulates outer membrane proteins in stress-induced lipid nanodomains
Authors: Janssens, A. / Nguyen, V.S. / Cecil, A.J. / Van der Verren, S.E. / Timmerman, E. / Deghelt, M. / Pak, A.J. / Collet, J.F. / Impens, F. / Remaut, H.
History
DepositionMay 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer membrane lipoprotein slyB
B: Outer membrane lipoprotein slyB
C: Outer membrane lipoprotein slyB
D: Outer membrane lipoprotein slyB
E: Outer membrane lipoprotein slyB
F: Outer membrane lipoprotein slyB
G: Outer membrane lipoprotein slyB
H: Outer membrane lipoprotein slyB
I: Outer membrane lipoprotein slyB
J: Outer membrane lipoprotein slyB
K: Outer membrane lipoprotein slyB
L: Outer membrane lipoprotein slyB
M: Outer membrane lipoprotein slyB
N: Outer membrane protein assembly factor BamA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)332,07465
Polymers293,62014
Non-polymers38,45451
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Outer membrane ... , 2 types, 14 molecules ABCDEFGHIJKLMN

#1: Protein
Outer membrane lipoprotein slyB


Mass: 15613.606 Da / Num. of mol.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Strain: 2002017 / Gene: slyB, SFxv_1871 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21AI / References: UniProt: D2AGE2
#2: Protein Outer membrane protein assembly factor BamA


Mass: 90643.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli BW25113 (bacteria) / Gene: bamA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21AI / References: UniProt: C3TPJ2

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Non-polymers , 4 types, 51 molecules

#3: Chemical
ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C16H32O2
#4: Chemical
ChemComp-L8Z / (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-5-[[(~{E},3~{R})-3-dodecanoyloxytetradec-5-enoyl]amino]-6-[[(2~{R},3~{S},4~{R},5~{R},6~{R})-3-oxidanyl-5-[[(~{E},3~{R})-3-oxidanyltetradec-11-enoyl]amino]-4-[(~{E},3~{R})-3-oxidanyltetradec-5-enoyl]oxy-6-phosphonooxy-oxan-2-yl]methoxy]-3-phosphonooxy-4-[(~{E},3~{R})-3-tetradecanoyloxytetradec-7-enoyl]oxy-oxan-2-yl]methoxy]-4,5-bis(oxidanyl)oxane-2-carboxylic acid


Mass: 2010.478 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C102H182N2O32P2
#5: Chemical
ChemComp-LPP / 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / L-B,G-DIPALMITOYL-A-PHOSPHATIDIC ACID DISODIUM SALT / 3-SN-PHOSPHATIDIC ACID / 1,2-DIPALMITOYLDISODIUM SALT


Mass: 648.891 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C35H69O8P / Comment: phospholipid*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of SlyB13-BamA from Escherichia coli
Type: COMPLEX
Details: SlyB13-BamA was purified from overexpression of SlyB-TEV-HIS/BamA in E. coli using using 2-step Ni-IMAC purification.
Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.27 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BW25113 / Cellular location: Outer membrane
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21AI / Plasmid: pASK-IBA
SpecimenConc.: 0.04 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Details: Back-blotting for 4 seconds before plunging

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 60000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm / Cs: 2.55 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER
Image recordingAverage exposure time: 3 sec. / Electron dose: 61 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 7352
Image scansNum. digital images: 7352

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Processing

EM software
IDNameVersionCategoryDetails
4RELION3.1CTF correctionParticle extraction, 3D classification, and 3D reconstruction
5cryoSPARC3.2.0CTF correction2D classification
6CTFFIND4CTF correctionCTF estimation
7MotionCorr21.3CTF correctionMotion correction
8SerialEMCTF correctionImage acquisition
11Cootmodel fitting
13PHENIXmodel refinementusing phenix.real_space_refine
16RELIONclassification
17RELION3.13D reconstruction
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73756 / Symmetry type: POINT
Atomic model buildingB value: 56 / Protocol: OTHER / Space: REAL
RefinementHighest resolution: 3.9 Å
Displacement parametersBiso mean: 60.14 Å2

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