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- EMDB-11898: Tomographic reconstruction of native glycolipoprotein filaments i... -

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Basic information

Entry
Database: EMDB / ID: EMD-11898
TitleTomographic reconstruction of native glycolipoprotein filaments in honeybee royal jelly
Map dataTomographic reconstruction of native RJ filaments
Sample
  • Complex: Royal jelly glycolipoprotein filaments
Biological speciesApis mellifera (honey bee)
Methodelectron tomography / cryo EM
AuthorsMattei S / Ban A / Picenoni A / Leibundgut M / Glockshuber R / Boehringer D
CitationJournal: 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
DepositionOct 27, 2020-
Header (metadata) releaseDec 30, 2020-
Map releaseDec 30, 2020-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Movie viewer
Supplemental images

emd_11898.png

Downloads & links

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Map

FileDownload / File: emd_11898.map.gz / Format: CCP4 / Size: 40.9 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationTomographic reconstruction of native RJ filaments
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
11.1 Å/pix.
x 100 pix.
= 1109.6 Å		11.1 Å/pix.
x 463 pix.
= 5137.448 Å		11.1 Å/pix.
x 463 pix.
= 5137.448 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 11.096 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-31.0 - 37.0
Average (Standard dev.)1.0174522 (±3.4645584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions463463100
Spacing463463100
CellA: 5137.4478 Å / B: 5137.4478 Å / C: 1109.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z11.09611.09611.096
M x/y/z463463100
origin x/y/z0.0000.0000.000
length x/y/z5137.4485137.4481109.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS463463100
D min/max/mean-31.00037.0001.017

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Supplemental data

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Sample components

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Entire : Royal jelly glycolipoprotein filaments

EntireName: Royal jelly glycolipoprotein filaments
Components
  • Complex: Royal jelly glycolipoprotein filaments

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Supramolecule #1: Royal jelly glycolipoprotein filaments

SupramoleculeName: Royal jelly glycolipoprotein filaments / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Apis mellifera (honey bee)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statefilament

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Sample preparation

BufferpH: 4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: BBI / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-4 / Number grids imaged: 1 / Average exposure time: 1.6 sec. / Average electron dose: 2.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 6.3 µm / Calibrated defocus min: 4.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 41
CTF correctionSoftware - Name: CTFFIND (ver. 4)

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