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- PDB-9enr: Vitellogenin from the honey bee hemolymph -

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Basic information

Entry
Database: PDB / ID: 9enr
TitleVitellogenin from the honey bee hemolymph
ComponentsVitellogenin
KeywordsLIPID BINDING PROTEIN / Yolk / LLTP / vWD / CTCK
Function / homology
Function and homology information


nutrient reservoir activity / lipid transporter activity / extracellular region
Similarity search - Function
: / Vitellinogen, open beta-sheet / Vitellinogen, open beta-sheet / DUF1943 / Vitellogenin, N-terminal / Lipovitellin-phosvitin complex, superhelical domain / Vitellinogen, beta-sheet N-terminal / Lipid transport protein, beta-sheet shell / Lipoprotein amino terminal region / Vitellogenin domain profile. ...: / Vitellinogen, open beta-sheet / Vitellinogen, open beta-sheet / DUF1943 / Vitellogenin, N-terminal / Lipovitellin-phosvitin complex, superhelical domain / Vitellinogen, beta-sheet N-terminal / Lipid transport protein, beta-sheet shell / Lipoprotein amino terminal region / Vitellogenin domain profile. / Lipoprotein N-terminal Domain / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain
Similarity search - Domain/homology
Chem-43Y / Vitellogenin
Similarity search - Component
Biological speciesApis cerana (Asiatic honeybee)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMontserrat-Canals, M. / Schnelle, K. / Moeller, A. / Cunha, E. / Luecke, H.
Funding support Norway, Germany, 5items
OrganizationGrant numberCountry
Norwegian Research Council262137 Norway
Norwegian Research Council335244 Norway
German Research Foundation (DFG)SFB 944 Germany
German Research Foundation (DFG)SFB 1557 Germany
German Research Foundation (DFG)INST190/196-1 FUGG Germany
CitationJournal: To Be Published
Title: Cryo-EM structure determination of native honey bee vitellogenin
Authors: Montserrat-Canals, M. / Schnelle, K. / Leipart, V. / Halskau, O. / Amdam, G. / Moeller, A. / Cunha, E. / Luecke, H.
History
DepositionMar 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Mar 26, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 26, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vitellogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,5873
Polymers201,3061
Non-polymers1,2812
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint12 kcal/mol
Surface area73600 Å2
MethodPISA

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Components

#1: Protein Vitellogenin


Mass: 201305.797 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Apis cerana (Asiatic honeybee) / Tissue: Hemolymph / References: UniProt: Q868N5
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-43Y / [(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate / 1,2-dipropionyl-sn-glycero-3-phosphocholine


Mass: 370.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H29NO8P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Vitellogenin bound to native lipids and metals / Type: COMPLEX / Entity ID: #1 / Source: NATURAL
Molecular weightValue: 0.18 MDa / Experimental value: YES
Source (natural)Organism: Apis cerana (Asiatic honeybee) / Tissue: Hemolymph
Buffer solutionpH: 7.6
Buffer component
IDConc.NameBuffer-ID
10.5 MTris-HCl1
20.2 MNaCl1
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 62.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.1particle selection
4cryoSPARC4.1CTF correction
10cryoSPARC4.2initial Euler assignment
11cryoSPARC4.2final Euler assignment
13cryoSPARC4.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 840000 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER
RefinementHighest resolution: 3.2 Å / Cross valid method: NONE
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312362
ELECTRON MICROSCOPYf_angle_d0.56716739
ELECTRON MICROSCOPYf_dihedral_angle_d4.5141716
ELECTRON MICROSCOPYf_chiral_restr0.0451913
ELECTRON MICROSCOPYf_plane_restr0.0052152

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