+Open data
-Basic information
Entry | Database: PDB / ID: 7asd | |||||||||
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Title | Structure of native royal jelly filaments | |||||||||
Components |
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Keywords | PROTEIN FIBRIL / protein filament / lipoprotein / glycosylation / royal jelly / major royal jelly protein / honeybee | |||||||||
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) | |||||||||
Method | ELECTRON MICROSCOPY / 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, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7asd.cif.gz | 648.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7asd.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7asd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/as/7asd ftp://data.pdbj.org/pub/pdb/validation_reports/as/7asd | HTTPS FTP |
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-Related structure data
Related structure data | 11892MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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-Components
-Protein , 2 types, 16 molecules AABACADAEAFAGAHAABBBCBDBEBFBGBHB
#1: Protein | Mass: 48934.898 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Apis mellifera (honey bee) / References: UniProt: O18330 #2: Protein | Mass: 7949.325 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Apis mellifera (honey bee) / Plasmid details: royal jelly / References: UniProt: Q8ISL8 |
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-Sugars , 3 types, 24 molecules
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / |
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-Non-polymers , 2 types, 24 molecules
#5: Chemical | ChemComp-94R / ( #7: Chemical | ChemComp-SO4 / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: native royal jelly filaments / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL |
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Source (natural) | Organism: Apis mellifera (honey bee) |
Buffer solution | pH: 4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 119050 X / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Image recording | Average exposure time: 1.7 sec. / Electron dose: 82 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 64 ° / Axial rise/subunit: 54 Å / Axial symmetry: D2 | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 240483 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL |