+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11892 | |||||||||
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Title | Structure of native royal jelly filaments | |||||||||
Map data | native royal jelly filament | |||||||||
Sample |
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Function / homology | Function and homology information caste determination, influence by environmental factors / defense response to fungus / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | |||||||||
Biological species | Apis mellifera (honey bee) / Honeybee (honey bee) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Mattei S / Ban A / Picenoni A / Leibundgut M / Glockshuber R / Boehringer D | |||||||||
Funding support | European Union, 2 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structure of native glycolipoprotein filaments in honeybee royal jelly. Authors: Simone Mattei / Arvid Ban / Armin Picenoni / Marc Leibundgut / Rudi Glockshuber / Daniel Boehringer / Abstract: Royal jelly (RJ) is produced by honeybees (Apis mellifera) as nutrition during larval development. The high viscosity of RJ originates from high concentrations of long lipoprotein filaments that ...Royal jelly (RJ) is produced by honeybees (Apis mellifera) as nutrition during larval development. The high viscosity of RJ originates from high concentrations of long lipoprotein filaments that include the glycosylated major royal jelly protein 1 (MRJP1), the small protein apisimin and insect lipids. Using cryo-electron microscopy we reveal the architecture and the composition of RJ filaments, in which the MRJP1 forms the outer shell of the assembly, surrounding stacked apisimin tetramers harbouring tightly packed lipids in the centre. The structural data rationalize the pH-dependent disassembly of RJ filaments in the gut of the larvae. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11892.map.gz | 163.5 MB | EMDB map data format | |
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Header (meta data) | emd-11892-v30.xml emd-11892.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
Images | emd_11892.png | 264.8 KB | ||
Masks | emd_11892_msk_1.map | 178 MB | Mask map | |
Others | emd_11892_half_map_1.map.gz emd_11892_half_map_2.map.gz | 138.8 MB 138.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11892 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11892 | HTTPS FTP |
-Related structure data
Related structure data | 7asdMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_11892.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | native royal jelly filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.19467 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11892_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: native royal jelly filament
File | emd_11892_half_map_1.map | ||||||||||||
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Annotation | native royal jelly filament | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: native royal jelly filament
File | emd_11892_half_map_2.map | ||||||||||||
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Annotation | native royal jelly filament | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : native royal jelly filaments
Entire | Name: native royal jelly filaments |
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Components |
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-Supramolecule #1: native royal jelly filaments
Supramolecule | Name: native royal jelly filaments / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Apis mellifera (honey bee) |
-Macromolecule #1: Major royal jelly protein 1
Macromolecule | Name: Major royal jelly protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Honeybee (honey bee) |
Molecular weight | Theoretical: 48.934898 KDa |
Sequence | String: MTRLFMLVCL GIVCQGTTGN ILRGESLNKS LPILHEWKFF DYDFGSDERR QDAILSGEYD YKNNYPSDID QWHDKIFVTM LRYNGVPSS LNVISKKVGD GGPLLQPYPD WSFAKYDDCS GIVSASKLAI DKCDRLWVLD SGLVNNTQPM CSPKLLTFDL T TSQLLKQV ...String: MTRLFMLVCL GIVCQGTTGN ILRGESLNKS LPILHEWKFF DYDFGSDERR QDAILSGEYD YKNNYPSDID QWHDKIFVTM LRYNGVPSS LNVISKKVGD GGPLLQPYPD WSFAKYDDCS GIVSASKLAI DKCDRLWVLD SGLVNNTQPM CSPKLLTFDL T TSQLLKQV EIPHDVAVNA TTGKGRLSSL AVQSLDCNTN SDTMVYIADE KGEGLIVYHN SDDSFHRLTS NTFDYDPKFT KM TIDGESY TAQDGISGMA LSPMTNNLYY SPVASTSLYY VNTEQFRTSD YQQNDIHYEG VQNILDTQSS AKVVSKSGVL FFG LVGDSA LGCWNEHRTL ERHNIRTVAQ SDETLQMIAS MKIKEALPHV PIFDRYINRE YILVLSNKMQ KMVNNDFNFD DVNF RIMNA NVNELILNTR CENPDNDRTP FKISIHL |
-Macromolecule #2: Apisimin
Macromolecule | Name: Apisimin / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Honeybee (honey bee) |
Molecular weight | Theoretical: 7.949325 KDa |
Sequence | String: MSKIVAVVVL AAFCVAMLVS DVSAKTSISV KGESNVDVVS QINSLVSSIV SGANVSAVLL AQTLVNILQI LIDANVFA |
-Macromolecule #5: (3beta,14beta,17alpha)-ergosta-5,24(28)-dien-3-ol
Macromolecule | Name: (3beta,14beta,17alpha)-ergosta-5,24(28)-dien-3-ol / type: ligand / ID: 5 / Number of copies: 16 / Formula: 94R |
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Molecular weight | Theoretical: 398.664 Da |
Chemical component information | ChemComp-94R: |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 8 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #7: SULFATE ION
Macromolecule | Name: SULFATE ION / type: ligand / ID: 7 / Number of copies: 8 / Formula: SO4 |
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Molecular weight | Theoretical: 96.063 Da |
Chemical component information | ChemComp-SO4: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 4 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.7 sec. / Average electron dose: 82.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated magnification: 119050 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 105000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 54.0 Å Applied symmetry - Helical parameters - Δ&Phi: 64 ° Applied symmetry - Helical parameters - Axial symmetry: D2 (2x2 fold dihedral) Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 240483 |
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CTF correction | Software - Name: Gctf |
Startup model | Type of model: OTHER / Details: featureless cylindrical density |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION |