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- EMDB-11892: Structure of native royal jelly filaments -

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Basic information

Entry
Database: EMDB / ID: EMD-11892
TitleStructure of native royal jelly filaments
Map datanative royal jelly filament
Sample
  • Complex: native royal jelly filaments
    • Protein or peptide: Major royal jelly protein 1
    • Protein or peptide: Apisimin
  • Ligand: (3beta,14beta,17alpha)-ergosta-5,24(28)-dien-3-ol
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SULFATE IONSulfate
Function / homology
Function and homology information


caste determination, influence by environmental factors / defense response to fungus / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function
Major royal jelly protein/protein yellow / Major royal jelly protein / Six-bladed beta-propeller, TolB-like
Similarity search - Domain/homology
Major royal jelly protein 1 / Apisimin
Similarity search - Component
Biological speciesApis mellifera (honey bee) / Honeybee (honey bee)
Methodhelical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMattei S / Ban A / Picenoni A / Leibundgut M / Glockshuber R / Boehringer D
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 793-2017European Union
Human Frontier Science Program (HFSP)LT000008/2018-LEuropean Union
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-
UpdateDec 30, 2020-
Current statusDec 30, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7asd
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7asd
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11892.png

Downloads & links

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Map

FileDownload / File: emd_11892.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationnative royal jelly filament
Voxel sizeX=Y=Z: 1.19467 Å
Density
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.03491768 - 0.08494006
Average (Standard dev.)-1.6316179e-05 (±0.0033898372)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 430.08118 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.19466944444441.19466944444441.1946694444444
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z430.081430.081430.081
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0350.085-0.000

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Supplemental data

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Mask #1

Fileemd_11892_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: native royal jelly filament

Fileemd_11892_half_map_1.map
Annotationnative royal jelly filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: native royal jelly filament

Fileemd_11892_half_map_2.map
Annotationnative royal jelly filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : native royal jelly filaments

EntireName: native royal jelly filaments
Components
  • Complex: native royal jelly filaments
    • Protein or peptide: Major royal jelly protein 1
    • Protein or peptide: Apisimin
  • Ligand: (3beta,14beta,17alpha)-ergosta-5,24(28)-dien-3-ol
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: SULFATE IONSulfate

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Supramolecule #1: native royal jelly filaments

SupramoleculeName: native royal jelly filaments / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Apis mellifera (honey bee)

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Macromolecule #1: Major royal jelly protein 1

MacromoleculeName: Major royal jelly protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Honeybee (honey bee)
Molecular weightTheoretical: 48.934898 KDa
SequenceString: 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

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Macromolecule #2: Apisimin

MacromoleculeName: Apisimin / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Honeybee (honey bee)
Molecular weightTheoretical: 7.949325 KDa
SequenceString:
MSKIVAVVVL AAFCVAMLVS DVSAKTSISV KGESNVDVVS QINSLVSSIV SGANVSAVLL AQTLVNILQI LIDANVFA

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Macromolecule #5: (3beta,14beta,17alpha)-ergosta-5,24(28)-dien-3-ol

MacromoleculeName: (3beta,14beta,17alpha)-ergosta-5,24(28)-dien-3-ol / type: ligand / ID: 5 / Number of copies: 16 / Formula: 94R
Molecular weightTheoretical: 398.664 Da
Chemical component information

ChemComp-94R:
(3beta,14beta,17alpha)-ergosta-5,24(28)-dien-3-ol

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #7: SULFATE ION

MacromoleculeName: SULFATE ION / type: ligand / ID: 7 / Number of copies: 8 / Formula: SO4
Molecular weightTheoretical: 96.063 Da
Chemical component information

ChemComp-SO4:
SULFATE ION / Sulfate

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
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
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 119050 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.7 sec. / Average electron dose: 82.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: featureless cylindrical density
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION
Final reconstructionApplied 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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