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- EMDB-19842: Vitellogenin from the honey bee hemolymph -

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Basic information

Entry
Database: EMDB / ID: EMD-19842
TitleVitellogenin from the honey bee hemolymph
Map data
Sample
  • Complex: Vitellogenin bound to native lipids and metals
    • Protein or peptide: Vitellogenin
  • Ligand: [(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate
KeywordsYolk / LLTP / vWD / CTCK / LIPID BINDING PROTEIN
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
Biological speciesApis cerana (Asiatic honeybee)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsMontserrat-Canals M / Schnelle K / Moeller A / Cunha E / Luecke H
Funding support Norway, Germany, 5 items
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: Nat Commun / Year: 2025
Title: Cryo-EM structure of native honey bee vitellogenin.
Authors: Mateu Montserrat-Canals / Kilian Schnelle / Vilde Leipart / Øyvind Halskau / Gro V Amdam / Arne Moeller / Eva S Cunha / Hartmut Luecke /
Abstract: Vitellogenin (Vg) is the main yolk precursor lipoprotein in almost all egg-laying animals. In addition, along its evolutionary history, Vg has developed a range of new functions in different taxa. In ...Vitellogenin (Vg) is the main yolk precursor lipoprotein in almost all egg-laying animals. In addition, along its evolutionary history, Vg has developed a range of new functions in different taxa. In the honey bee, Vg has functions related to immunity, antioxidant protection, social behavior and longevity. However, the molecular mechanisms underlying Vg functionalities are still poorly understood. Here, we report the cryo-EM structure of full-length honey bee Vg, one-step purified directly from hemolymph. The structure provides structural insights into the overall domain architecture, including the lipid binding cavity and the previously uncharacterized von Willebrand factor type D domain. A domain of unknown function has been identified as a C-terminal cystine knot domain based on structural homology. Information about post-translational modifications, cleavage products, metal and lipid binding allow an improved understanding of the mechanisms underlying the range of Vg functionalities. The findings have numerous implications for the structure-function relationship of vitellogenins of other species as well as members of the same protein superfamily, which share the same structural elements.
History
DepositionMar 13, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19842.png

Downloads & links

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Map

FileDownload / File: emd_19842.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 270.848 Å		0.85 Å/pix.
x 320 pix.
= 270.848 Å		0.85 Å/pix.
x 320 pix.
= 270.848 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8464 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0199683 - 1.9460194
Average (Standard dev.)0.0013309709 (±0.024555419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 270.84802 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19842_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19842_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Vitellogenin bound to native lipids and metals

EntireName: Vitellogenin bound to native lipids and metals
Components
  • Complex: Vitellogenin bound to native lipids and metals
    • Protein or peptide: Vitellogenin
  • Ligand: [(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate

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Supramolecule #1: Vitellogenin bound to native lipids and metals

SupramoleculeName: Vitellogenin bound to native lipids and metals / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Apis cerana (Asiatic honeybee) / Tissue: Hemolymph
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: Vitellogenin

MacromoleculeName: Vitellogenin / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Apis cerana (Asiatic honeybee) / Tissue: Hemolymph
Molecular weightTheoretical: 201.305797 KDa
SequenceString: MLLLLTLLLF AGTVAADFQH NWQVGNEYTY LVRSRTLTSL GDLSDVHTGI LIKALLTVQA KDSNVLAAKV WNGQYARVQQ SMPDGWETE ISDQMLELRD LPISGKPFQI RMKHGLIRDL IVDRDVPTWE VNILKSIVGQ LQVDTQGENA VKVNSVQVPT D DEPYASFK ...String:
MLLLLTLLLF AGTVAADFQH NWQVGNEYTY LVRSRTLTSL GDLSDVHTGI LIKALLTVQA KDSNVLAAKV WNGQYARVQQ SMPDGWETE ISDQMLELRD LPISGKPFQI RMKHGLIRDL IVDRDVPTWE VNILKSIVGQ LQVDTQGENA VKVNSVQVPT D DEPYASFK AMEDSVGGKC EVLYDIAPLS DFVIHRSPEL VPMPTLKGDG RHMEVIKIKN FDNCDQRINY HFGMTDNSRL EP GTNKNGK FFSRSSTSRI VISESLKHFT IQSSVTTSKM MVSPRLYDRQ NGLVLSRMNL TLAKMEKTSK PLPMVDNPES TGN LVYIYN NPFSDVEERR VSKTAMNSNQ IVSDNSLSSS EEKLKQDILN LRTDISSSSS SISSSEENDF WQPKPTLEDA PQNS LLPNF VGYKGKHIGK SGKVDVINAA KELIFQIANE LEDASNIPVH ATLEKFMILC NLMRTMNRKQ ISELESNMQI SPNEL KPND KSQVIKQNTW TVFRDAITQT GTGPAFLTIK EWIERGTTKS MEAANIMSKL PKTVRTPTDS YIRSFFELLQ NPKVSN EQF LNTAATLSFC EMIHNAQVNK RSIHNNYPVH TFGRLTSKHD NSLYDEYIPF LERELRKAHQ EKDSPRIQTY IMALGMI GE PKILSVFEPY LEGKQQMTVF QRTLMVGSLG KLTETNPKLA RSVLYKIYLN TMESHEVRCT AVFLLMKTNP PLSMLQRM A EFTKLDTNRQ VNSAVKSTIQ SLMKLKSPEW KDLAKKARSV NHLLTHHEYD YELSRGYIDE KILENQNIIT HMILNYVGS EDSVIPRILY LTWYSSNGDI KVPSTKVLAM ISSVKSFMEL SLRSVKDRET IISAAEKIAE ELKIVPEELV PLEGNLMINN KYALKFFPF DKHILDKLPT LISNYIEAVK EGKFMNVNML DTYESVHSFP TETGLPFVYT FNVIKLTKTS GTVQAQINPD F AFIVNSNL RLTFSKNVQG RVGFVTPFEH RHFISGIDSN LHVYAPLKIS LDVNTPKGNM QWKIWPMKGE EKSRLFHYSV VP FVSNHDI LNLRPLSMEK GTRPMIPDDN TSLALPKNEG PFRLNVETAK TNEEMWELID TEKLTDRLPY PWTMDNERYV KVD MYMNLE GEQKDPVIFS TSFDSKVMTR PDTDSENWTP KMMAVEPTDK QANSKTRRQE MMREAGRGIE SAKSYVVDVR VHVP GESES ETVLTLAWSE SNVESKGRLL GFWRVEMPRS NADYEVCIGS QIMVSPETLL SYDEKMDQKP KMDFNVDIRY GKNCG KGER IDMNGKLRQS PRLKELVGAT SIIKDCVEDM KRGNKILRTC QKAVVLSMLL DEVDISMEVP SDALIALYSQ GLFSLS EID NLDVSLDVSN PKNAGKKKID VRAKLNEYLD KADVIVNTPI MDAHFKDVKL SDFGFSTEDI LDTADEDLLI NNVFYED ET SCMLDKTRAQ TFDGKDYPLR LGPCWHAVMT TYPRINPDNH NEKLHIPKDK SVSVLSRENE AGQKEVKVLL GSDKIKFV P GTTSQPEVFV NGEKIVVSRN KAYQKVEENE IIFEIYKMGD RFIGLTSDKF DVSLALDGER VMLKASEDYR YSVRGLCGN FDHDSTNDFV GPKNCLFRKP EHFVASYALI SNQCEGDSLN VAKSLQDHDC IRQERTQQRN VISDSESGRL DTEMSTWGYH HNVNKHCTI HRTQVKETDD KICFTMRPVV SCASGCTAVE TKSKPYKFHC MEKNEAAMKL KKRIEKGANP DLSQKPVSTT E ELTVPFVC KA

UniProtKB: Vitellogenin

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Macromolecule #3: [(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]o...

MacromoleculeName: [(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate
type: ligand / ID: 3 / Number of copies: 1 / Formula: 43Y
Molecular weightTheoretical: 370.356 Da
Chemical component information

ChemComp-43Y:
[(2R)-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-2-propanoyloxy-propyl] propanoate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.2 mg/mL
BufferpH: 7.6 / Component:
ConcentrationName
0.5 MTris-HCl
0.2 MNaCl
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 62.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 840000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER
Output model

PDB-9enr:
Vitellogenin from the honey bee hemolymph

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