[English] 日本語
![](img/lk-miru.gif)
- EMDB-12946: Cryo-EM reconstruction of dodecameric SlyB from Escherichia coli K12 -
+
Open data
-
Basic information
Entry | ![]() | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM reconstruction of dodecameric SlyB from Escherichia coli K12 | |||||||||||||||
![]() | SlyB12 | |||||||||||||||
![]() |
| |||||||||||||||
![]() | Outer membrane chaperon / 2TM glycine zipper / outer membrane lipoprotein SlyB / LPS-LP binding protein / MEMBRANE PROTEIN | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||||||||
![]() | Nguyen VS / Remaut H | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() 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 |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 18.6 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 12.5 KB 12.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 12.9 KB | Display | ![]() |
Images | ![]() | 171.1 KB | ||
Filedesc metadata | ![]() | 5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 386.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 386.5 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | SlyB12 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.784 Å | ||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-
Sample components
-Entire : Outer membrane lipoprotein SlyB
Entire | Name: Outer membrane lipoprotein SlyB |
---|---|
Components |
|
-Supramolecule #1: Outer membrane lipoprotein SlyB
Supramolecule | Name: 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: ![]() ![]() |
Molecular weight | Theoretical: 220 KDa |
-Macromolecule #1: Outer membrane lipoprotein SlyB
Macromolecule | Name: Outer membrane lipoprotein SlyB / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
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 |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 0.04 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 8 Component:
| ||||||||||||
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 |
---|---|
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: ![]() |
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 |