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Yorodumi- EMDB-12947: Cryo-EM structure of tridecameric SlyB from Escherichia coli K12 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12947 | |||||||||||||||
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Title | Cryo-EM structure of tridecameric SlyB from Escherichia coli K12 | |||||||||||||||
Map data | SlyB13 | |||||||||||||||
Sample |
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Keywords | Outer membrane chaperon / 2TM glycine zipper / outer membrane lipoprotein SlyB / LPS-LP binding protein / MEMBRANE PROTEIN | |||||||||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli BW25113 (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 5.8 Å | |||||||||||||||
Authors | Nguyen VS / Remaut H | |||||||||||||||
Funding support | Belgium, 4 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_12947.map.gz | 18.8 MB | EMDB map data format | |
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Header (meta data) | emd-12947-v30.xml emd-12947.xml | 12.4 KB 12.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_12947_fsc.xml | 12.9 KB | Display | FSC data file |
Images | emd_12947.png | 129.3 KB | ||
Filedesc metadata | emd-12947.cif.gz | 4.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12947 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12947 | HTTPS FTP |
-Validation report
Summary document | emd_12947_validation.pdf.gz | 377.5 KB | Display | EMDB validaton report |
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Full document | emd_12947_full_validation.pdf.gz | 377 KB | Display | |
Data in XML | emd_12947_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | emd_12947_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12947 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12947 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_12947.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | SlyB13 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.784 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Outer membrane lipoprotein SlyB
Entire | Name: Outer membrane lipoprotein SlyB |
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Components |
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-Supramolecule #1: Outer membrane lipoprotein SlyB
Supramolecule | Name: Outer membrane lipoprotein SlyB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Tricameric SlyB was purified from overexpression of SlyB-TEV-HIS in E. coli using using 2-step Ni-IMAC purification. |
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Source (natural) | Organism: Escherichia coli (E. coli) / Strain: BW25113 / Location in cell: Outer membrane |
Molecular weight | Theoretical: 185 KDa |
-Macromolecule #1: Outer membrane lipoprotein SlyB
Macromolecule | Name: Outer membrane lipoprotein SlyB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli BW25113 (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: (PLM)CVNNDTLSG DVYTASEAKQ VQNVSYGTIV NVRPVQIQGG DDSNVIGAIG GAVLGGFLGN TVGGGTGRSL ATAAGAVAGG VAGQGVQSAM NKTQGVELEI RKDDGNTIMV VQKQGNTRFS PGQRVVLASN GSQVTVSPRG GGENLYFQ |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.04 mg/mL | ||||||||||||
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Buffer | pH: 8 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Instrument: GATAN CRYOPLUNGE 3 / Details: Back-blotting for 4 seconds before plunging. |
-Electron microscopy
Microscope | JEOL CRYO ARM 300 |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 stage | Specimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN |