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- EMDB-28515: Aleutian Mink Disease Virus VP2 -

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Basic information

Entry
Database: EMDB / ID: EMD-28515
TitleAleutian Mink Disease Virus VP2
Map data
Sample
  • Virus: Aleutian mink disease virus
    • Protein or peptide: Aleutian Mink Disease Virus (VP2-VLPs)
Biological speciesAleutian mink disease virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsMietzsch M / McKenna R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: Viruses / Year: 2022
Title: Capsid Structure of Aleutian Mink Disease Virus and Human Parvovirus 4: New Faces in the Parvovirus Family Portrait.
Authors: Renuk Lakshmanan / Mario Mietzsch / Alberto Jimenez Ybargollin / Paul Chipman / Xiaofeng Fu / Jianming Qiu / Maria Söderlund-Venermo / Robert McKenna /
Abstract: Parvoviruses are small, single-stranded DNA viruses with non-enveloped capsids. Determining the capsid structures provides a framework for annotating regions important to the viral life cycle. ...Parvoviruses are small, single-stranded DNA viruses with non-enveloped capsids. Determining the capsid structures provides a framework for annotating regions important to the viral life cycle. Aleutian mink disease virus (AMDV), a pathogen in minks, and human parvovirus 4 (PARV4), infecting humans, are parvoviruses belonging to the genera and , respectively. While Aleutian mink disease caused by AMDV is a major threat to mink farming, no clear clinical manifestations have been established following infection with PARV4 in humans. Here, the capsid structures of AMDV and PARV4 were determined via cryo-electron microscopy at 2.37 and 3.12 Å resolutions, respectively. Despite low amino acid sequence identities (10-30%) both viruses share the icosahedral nature of parvovirus capsids, with 60 viral proteins (VPs) assembling the capsid via two-, three-, and five-fold symmetry VP-related interactions, but display major structural variabilities in the surface loops when the capsid structures are superposed onto other parvoviruses. The capsid structures of AMDV and PARV4 will add to current knowledge of the structural platform for parvoviruses and permit future functional annotation of these viruses, which will help in understanding their infection mechanisms at a molecular level for the development of diagnostics and therapeutics.
History
DepositionOct 4, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateNov 9, 2022-
Current statusNov 9, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28515.png

Downloads & links

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Map

FileDownload / File: emd_28515.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)X (Row.)Y (Col.)
1.1 Å/pix.
x 420 pix.
= 459.9 Å		1.1 Å/pix.
x 420 pix.
= 459.9 Å		1.1 Å/pix.
x 420 pix.
= 459.9 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.095 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-10.254539 - 18.084341
Average (Standard dev.)-1.3219721e-09 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 459.90002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28515_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_28515_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Aleutian mink disease virus

EntireName: Aleutian mink disease virus
Components
  • Virus: Aleutian mink disease virus
    • Protein or peptide: Aleutian Mink Disease Virus (VP2-VLPs)

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Supramolecule #1: Aleutian mink disease virus

SupramoleculeName: Aleutian mink disease virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 28314 / Sci species name: Aleutian mink disease virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host systemOrganism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9
Virus shellShell ID: 1 / T number (triangulation number): 1

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Macromolecule #1: Aleutian Mink Disease Virus (VP2-VLPs)

MacromoleculeName: Aleutian Mink Disease Virus (VP2-VLPs) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Aleutian mink disease virus
SequenceString: MDSTEAEQMD TEQATNQTAE AGGGGGGGGG GGGGGGGVGN STGGFNNTTE FKVINNEVYI TCHATRMVHI NQADTDEYLI FNAGRTTDTK THQQKLNLEF FVYDDFHQQV MTPWYIVDSN AWGVWMSPKD FQQMKTLCSE ISLVTLEQEI DNVTIKTVTE TNQGNASTKQ ...String:
MDSTEAEQMD TEQATNQTAE AGGGGGGGGG GGGGGGGVGN STGGFNNTTE FKVINNEVYI TCHATRMVHI NQADTDEYLI FNAGRTTDTK THQQKLNLEF FVYDDFHQQV MTPWYIVDSN AWGVWMSPKD FQQMKTLCSE ISLVTLEQEI DNVTIKTVTE TNQGNASTKQ FNNDLTASLQ VALDTNNILP YTPAAPLGET LGFVPWRATK PTQYRYYHPC YIYNRYPNIQ KVATETLTWD AVQDDYLSVD EQYFNFITIE NNIPINILRT GDNFHTGLYE FNSKPCKLTL SYQSTRCLGL PPLCKPKTDT THKVTSKENG ADLIYIQGQD NTRLGHFWGE ERGKKNAEMN RIRPYNIGYQ YPEWIIPAGL QGSYFAGGPR QWSDTTKGAG THSQHLQQNF STRYIYDRNH GGDNEVDLLD GIPIHERSNY YSDNEIEQHT AKQPKLRTPP IHHSKIDSWE EEGWPAASGT HFEDEVIYLD YFNFSGEQEL NFPHEVLDDA AQMKKLLNSY QPTVAQDNVG PVYPWGQIWD KKPHMDHKPS MNNNAPFVCK NNPPGQLFVK LTENLTDTFN YDENPDRIKT YGYFTWRGKL VLKGKLSQVT CWNPVKRELI GEPGVFTKDK YHKQIPNNKG NFEIGLQYGR STIKYIY

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Average electron dose: 59.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cisTEM
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8015
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: ANGULAR RECONSTITUTION

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