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Open data
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Basic information
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Title | Cryo-EM structure of undecameric SlyB from Escherichia coli K12 | |||||||||||||||
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![]() | OUTER MEMBRANE CHAPERONE / 2TM GLYCINE ZIPPER / OUTER MEMBRANE LIPOPROTEIN SLYB / LPS-LP BINDING PROTEIN / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Glycine zipper 2TM domain / Glycine zipper 2TM domain / cell outer membrane / Prokaryotic membrane lipoprotein lipid attachment site profile. / Outer membrane lipoprotein slyB![]() | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||
![]() | Nguyen VS / Remaut H | |||||||||||||||
Funding support | ![]()
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![]() | ![]() 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 | ![]() | 85.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15.3 KB 15.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.3 KB | Display | ![]() |
Images | ![]() | 174.4 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 487.9 KB | Display | ![]() |
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Full document | ![]() | 487.5 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 15.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7ojgMC ![]() 7ojfC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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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: #1 Details: Undecameric 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: ![]() ![]() |
Molecular weight | Theoretical: 200 KDa |
-Macromolecule #1: Outer membrane lipoprotein slyB
Macromolecule | Name: Outer membrane lipoprotein slyB / type: protein_or_peptide / ID: 1 / Number of copies: 11 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 15.613606 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MIKRVLVVSM VGLSLVGCVN NDTLSGDVYT ASEAKQVQNV SYGTIVNVRP VQIQGGDDSN VIGAIGGAVL GGFLGNTVGG GTGRSLATA AGAVAGGVAG QGVQSAMNKT QGVELEIRKD DGNTIMVVQK QGNTRFSPGQ RVVLASNGSQ VTVSPR UniProtKB: Outer membrane lipoprotein slyB |
-Macromolecule #2: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 2 / Number of copies: 33 / Formula: PLM |
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Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ![]() ChemComp-PLM: |
-Macromolecule #3: GLYCEROL
Macromolecule | Name: GLYCEROL / type: ligand / ID: 3 / Number of copies: 11 / Formula: GOL |
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Molecular weight | Theoretical: 92.094 Da |
Chemical component information | ![]() ChemComp-GOL: |
-Macromolecule #4: (2~{R},4~{R},5~{R},6~{R})-6-[(1~{R})-1,2-bis(oxidanyl)ethyl]-2-[[...
Macromolecule | Name: (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- ...Name: (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 type: ligand / ID: 4 / Number of copies: 11 / Formula: L8Z |
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Molecular weight | Theoretical: 2.010478 KDa |
Chemical component information | ![]() ChemComp-L8Z: |
-Macromolecule #5: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
Macromolecule | Name: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE type: ligand / ID: 5 / Number of copies: 11 / Formula: LPP |
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Molecular weight | Theoretical: 648.891 Da |
Chemical component information | ![]() ChemComp-LPP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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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. |
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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: ![]() |
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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 35 |
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Output model | ![]() PDB-7ojg: |