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- PDB-7asd: Structure of native royal jelly filaments -

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Basic information

Entry
Database: PDB / ID: 7asd
TitleStructure of native royal jelly filaments
Components
  • Apisimin
  • Major royal jelly protein 1
KeywordsPROTEIN FIBRIL / protein filament / lipoprotein / glycosylation / royal jelly / major royal jelly protein / honeybee
Function / homology
Function and homology information


multicellular organism adhesion to substrate / caste determination, influence by environmental factors / rhabdomere / sterol binding / defense response to fungus / defense response to Gram-negative bacterium / killing of cells of another organism / cytoskeleton / defense response to Gram-positive bacterium / extracellular region / cytoplasm
Similarity search - Function
Major royal jelly protein/protein yellow / Major royal jelly protein / Six-bladed beta-propeller, TolB-like
Similarity search - Domain/homology
(3beta,14beta,17alpha)-ergosta-5,24(28)-dien-3-ol / Major royal jelly protein 1 / Apisimin
Similarity search - Component
Biological speciesApis mellifera (honey bee)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsMattei, S. / Ban, A. / Picenoni, A. / Leibundgut, M. / Glockshuber, R. / Boehringer, D.
Funding supportEuropean Union, 2items
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, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Assembly

Deposited unit
AA: Major royal jelly protein 1
AB: Apisimin
BA: Major royal jelly protein 1
BB: Apisimin
CA: Major royal jelly protein 1
CB: Apisimin
DA: Major royal jelly protein 1
DB: Apisimin
EA: Major royal jelly protein 1
EB: Apisimin
FA: Major royal jelly protein 1
FB: Apisimin
GA: Major royal jelly protein 1
GB: Apisimin
HA: Major royal jelly protein 1
HB: Apisimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,07864
Polymers455,07416
Non-polymers17,00448
Water00
1
AA: Major royal jelly protein 1
AB: Apisimin
BA: Major royal jelly protein 1
BB: Apisimin
CA: Major royal jelly protein 1
CB: Apisimin
DA: Major royal jelly protein 1
DB: Apisimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,03932
Polymers227,5378
Non-polymers8,50224
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
2
EA: Major royal jelly protein 1
EB: Apisimin
FA: Major royal jelly protein 1
FB: Apisimin
GA: Major royal jelly protein 1
GB: Apisimin
HA: Major royal jelly protein 1
HB: Apisimin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,03932
Polymers227,5378
Non-polymers8,50224
Water0
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 16 molecules AABACADAEAFAGAHAABBBCBDBEBFBGBHB

#1: Protein
Major royal jelly protein 1 / MRJP1 / 56-kDa protein 4 / p56kP-4 / Apalbumin 1 / Apisin subunit MRJP1 / Bee-milk protein / Royalactin


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
Apisimin / Apisin subunit Apisimin / Royal jelly protein RJP54


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


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 24 molecules

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


Mass: 398.664 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C28H46O
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: native royal jelly filaments / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Source (natural)Organism: Apis mellifera (honey bee)
Buffer solutionpH: 4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Calibrated magnification: 119050 X / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingAverage exposure time: 1.7 sec. / Electron dose: 82 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4GctfCTF correction
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
12RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 64 ° / Axial rise/subunit: 54 Å / Axial symmetry: D2
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 240483 / Algorithm: FOURIER SPACE / Symmetry type: HELICAL

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