+Open data
-Basic information
Entry | Database: PDB / ID: 7ojf | ||||||
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Title | CRYO-EM STRUCTURE OF SLYB13-BAMA FROM ESCHERICHIA COLI | ||||||
Components | (Outer membrane ...) x 2 | ||||||
Keywords | MEMBRANE PROTEIN / OUTER MEMBRANE CHAPERON / 2TM GLYCINE ZIPPER / OUTER MEMBRANE LIPOPROTEIN SLYB / LPS-LP BINDING PROTEIN | ||||||
Function / homology | Function and homology information Bam protein complex / Gram-negative-bacterium-type cell outer membrane assembly / protein insertion into membrane / cell outer membrane Similarity search - Function | ||||||
Biological species | Escherichia coli BW25113 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Nguyen, V.S. / Remaut, H. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ojf.cif.gz | 433.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ojf.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ojf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ojf_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 7ojf_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 7ojf_validation.xml.gz | 98.2 KB | Display | |
Data in CIF | 7ojf_validation.cif.gz | 106.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oj/7ojf ftp://data.pdbj.org/pub/pdb/validation_reports/oj/7ojf | HTTPS FTP |
-Related structure data
Related structure data | 12949 7ojgC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Outer membrane ... , 2 types, 14 molecules ABCDEFGHIJKLMN
#1: Protein | 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 | | 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 / #4: Chemical | ChemComp-L8Z / ( #5: Chemical | ChemComp-LPP / #6: Chemical | ChemComp-GOL / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: 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 |
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Molecular weight | Value: 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 |
Specimen | Conc.: 0.04 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 90 % / Details: Back-blotting for 4 seconds before plunging |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 600 nm / Cs: 2.55 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER |
Image recording | Average 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 scans | Num. digital images: 7352 |
-Processing
EM software |
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3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73756 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 56 / Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Highest resolution: 3.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.14 Å2 |