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- EMDB-22113: Honey bee vitellogenin -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-22113
TitleHoney bee vitellogenin
Map dataVitellogenin (Vg) protein from honey bees
Sample
  • Organelle or cellular component: purified honey bee vitellogenin
    • Other: vitellogenin
Function / homology
Function and homology information


lipid transporter activity / nutrient reservoir 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. / Lipoprotein N-terminal Domain ...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 mellifera (honey bee)
Methodsingle particle reconstruction / negative staining / Resolution: 27.0 Å
AuthorsSalmela H / Harwood G / Herrero-Galan E / Amdam G
Funding support1 items
OrganizationGrant numberCountry
Research Council of Norway#262137
CitationJournal: Apidologie / Year: 2022
Title: Nuclear translocation of vitellogenin in the honey bee ().
Authors: Heli Salmela / Gyan P Harwood / Daniel Münch / Christine G Elsik / Elías Herrero-Galán / Maria K Vartiainen / Gro V Amdam /
Abstract: Vitellogenin (Vg) is a conserved protein used by nearly all oviparous animals to produce eggs. It is also pleiotropic and performs functions in oxidative stress resistance, immunity, and, in honey ...Vitellogenin (Vg) is a conserved protein used by nearly all oviparous animals to produce eggs. It is also pleiotropic and performs functions in oxidative stress resistance, immunity, and, in honey bees, behavioral development of the worker caste. It has remained enigmatic how Vg affects multiple traits. Here, we asked whether Vg enters the nucleus and acts via DNA-binding. We used cell fractionation, immunohistology, and cell culture to show that a structural subunit of honey bee Vg translocates into cell nuclei. We then demonstrated Vg-DNA binding theoretically and empirically with prediction software and chromatin immunoprecipitation with sequencing (ChIP-seq), finding binding sites at genes influencing immunity and behavior. Finally, we investigated the immunological and enzymatic conditions affecting Vg cleavage and nuclear translocation and constructed a 3D structural model. Our data are the first to show Vg in the nucleus and suggest a new fundamental regulatory role for this ubiquitous protein.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13592-022-00914-9.
History
DepositionJun 3, 2020-
Header (metadata) releaseJun 9, 2021-
Map releaseJun 9, 2021-
UpdateApr 6, 2022-
Current statusApr 6, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22113.png

Downloads & links

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Map

FileDownload / File: emd_22113.map.gz / Format: CCP4 / Size: 489.3 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVitellogenin (Vg) protein from honey bees
Voxel sizeX=Y=Z: 4.66 Å
Density
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.07230113 - 0.17134126
Average (Standard dev.)0.0008707952 (±0.018463848)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions505050
Spacing505050
CellA=B=C: 233.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.664.664.66
M x/y/z505050
origin x/y/z0.0000.0000.000
length x/y/z233.000233.000233.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS505050
D min/max/mean-0.0720.1710.001

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Supplemental data

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Sample components

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Entire : purified honey bee vitellogenin

EntireName: purified honey bee vitellogenin
Components
  • Organelle or cellular component: purified honey bee vitellogenin
    • Other: vitellogenin

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Supramolecule #1: purified honey bee vitellogenin

SupramoleculeName: purified honey bee vitellogenin / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Apis mellifera (honey bee)

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Macromolecule #1: vitellogenin

MacromoleculeName: vitellogenin / type: other / ID: 1 / Classification: other
Source (natural)Organism: Apis mellifera (honey bee)
SequenceString: MLLLLTLLLF AGTVAADFQH NWQVGNEYTY LVRSRTLTSL GDLSDVHTGI LIKALLTVQA KDSNVLAAK VWNGQYARVQ QSMPDGWETE ISDQMLELRD LPISGKPFQI RMKHGLIRDL I VDRDVPTW EVNILKSIVG QLQVDTQGEN AVKVNSVQVP TDDEPYASFK ...String:
MLLLLTLLLF AGTVAADFQH NWQVGNEYTY LVRSRTLTSL GDLSDVHTGI LIKALLTVQA KDSNVLAAK VWNGQYARVQ QSMPDGWETE ISDQMLELRD LPISGKPFQI RMKHGLIRDL I VDRDVPTW EVNILKSIVG QLQVDTQGEN AVKVNSVQVP TDDEPYASFK AMEDSVGGKC EV LYDIAPL SDFVIHRSPE LVPMPTLKGD GRHMEVIKIK NFDNCDQRIN YHFGMTDNSR LEP GTNKNG KFFSRSSTSR IVISESLKHF TIQSSVTTSK MMVSPRLYDR QNGLVLSRMN LTLA KMEKT SKPLPMVDNP ESTGNLVYIY NNPFSDVEER RVSKTAMNSN QIVSDNSLSS SEEKL KQDI LNLRTDISSS SSSISSSEEN DFWQPKPTLE DAPQNSLLPN FVGYKGKHIG KSGKVD VIN AAKELIFQIA NELEDASNIP VHATLEKFMI LCNLMRTMNR KQISELESNM QISPNEL KP NDKSQVIKQN TWTVFRDAIT QTGTGPAFLT IKEWIERGTT KSMEAANIMS KLPKTVRT P TDSYIRSFFE LLQNPKVSNE QFLNTAATLS FCEMIHNAQV NKRSIHNNYP VHTFGRLTS KHDNSLYDEY IPFLERELRK AHQEKDSPRI QTYIMALGMI GEPKILSVFE PYLEGKQQMT VFQRTLMVG SLGKLTETNP KLARSVLYKI YLNTMESHEV RCTAVFLLMK TNPPLSMLQR M AEFTKLDT NRQVNSAVKS TIQSLMKLKS PEWKDLAKKA RSVNHLLTHH EYDYELSRGY ID EKILENQ NIITHMILNY VGSEDSVIPR ILYLTWYSSN GDIKVPSTKV LAMISSVKSF MEL SLRSVK DRETIISAAE KIAEELKIVP EELVPLEGNL MINNKYALKF FPFDKHILDK LPTL ISNYI EAVKEGKFMN VNMLDTYESV HSFPTETGLP FVYTFNVIKL TKTSGTVQAQ INPDF AFIV NSNLRLTFSK NVQGRVGFVT PFEHRHFISG IDSNLHVYAP LKISLDVNTP KGNMQW KIW PMKGEEKSRL FHYSVVPFVS NHDILNLRPL SMEKGTRPMI PDDNTSLALP KNEGPFR LN VETAKTNEEM WELIDTEKLT DRLPYPWTMD NERYVKVDMY MNLEGEQKDP VIFSTSFD S KVMTRPDTDS ENWTPKMMAV EPTDKQANSK TRRQEMMREA GRGIESAKSY VVDVRVHVP GESESETVLT LAWSESNVES KGRLLGFWRV EMPRSNADYE VCIGSQIMVS PETLLSYDEK MDQKPKMDF NVDIRYGKNC GKGERIDMNG KLRQSPRLKE LVGATSIIKD CVEDMKRGNK I LRTCQKAV VLSMLLDEVD ISMEVPSDAL IALYSQGLFS LSEIDNLDVS LDVSNPKNAG KK KIDVRAK LNEYLDKADV IVNTPIMDAH FKDVKLSDFG FSTEDILDTA DEDLLINNVF YED ETSCML DKTRAQTFDG KDYPLRLGPC WHAVMTTYPR INPDNHNEKL HIPKDKSVSV LSRE NEAGQ KEVKVLLGSD KIKFVPGTTS QPEVFVNGEK IVVSRNKAYQ KVEENEIIFE IYKMG DRFI GLTSDKFDVS LALDGERVML KASEDYRYSV RGLCGNFDHD STNDFVGPKN CLFRKP EHF VASYALISNQ CEGDSLNVAK SLQDHDCIRQ ERTQQRNVIS DSESGRLDTE MSTWGYH HN VNKHCTIHRT QVKETDDKIC FTMRPVVSCA SGCTAVETKS KPYKFHCMEK NEAAMKLK K RIEKGANPDL SQKPVSTTEE LTVPFVCKA

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.1 mg/mL
BufferpH: 7.5 / Component - Concentration: 150.0 mM / Component - Formula: NaClSodium chloride / Component - Name: sodium chloride / Details: 20 mM Tris
StainingType: NEGATIVE / Material: Uranyl Acetate
Details: Aliquotes of pure Vg (1.1 mg/ml in 20 mM Tris, 150 mM NaCl, pH 7.5) were applied to carbon-coated copper grids (30 s) and stained with 2% uranyl acetate
GridMaterial: COPPER / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeJEOL 1230
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 25.0 e/Å2

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Image processing

CTF correctionSoftware - Name: Xmipp
Final reconstructionResolution.type: BY AUTHOR / Resolution: 27.0 Å / Software - Name: EMAN / Number images used: 15000
FSC plot (resolution estimation)

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