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- EMDB-28514: The capsid structure of Aleutian Mink Disease Virus -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-28514
TitleThe capsid structure of Aleutian Mink Disease Virus
Map data
Sample
  • Virus: Aleutian mink disease virus
    • Protein or peptide: Capsid protein VP1
KeywordsParvovirus / Capsid / AMDV / cryo-EM / Amdoparvovirus / Pathogen / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host membrane / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP1/VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesAleutian mink disease virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.37 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-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28514.png

Downloads & links

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Map

FileDownload / File: emd_28514.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.95 Å/pix.
x 500 pix.
= 474.5 Å		0.95 Å/pix.
x 500 pix.
= 474.5 Å		0.95 Å/pix.
x 500 pix.
= 474.5 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.949 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-8.772738 - 19.36195
Average (Standard dev.)-0.000000001008923 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-250-250-250
Dimensions500500500
Spacing500500500
CellA=B=C: 474.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28514_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_28514_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: Capsid protein VP1

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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
Virus shellShell ID: 1 / T number (triangulation number): 1

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Aleutian mink disease virus
Molecular weightTheoretical: 73.595305 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDSTEAEQMD TEQATNQTAE AGGGGGGGGG GGGGGGGVGN STGGFNNTTE FKVINNEVYI TCHATRMVHI NQADTDEYLI FNAGRTTDT KTHQQKLNLE FFVYDDFHQQ VMTPWYIVDS NAWGVWMSPK DFQQMKTLCS EISLVTLEQE IDNVTIKTVT E TNQGNAST ...String:
MDSTEAEQMD TEQATNQTAE AGGGGGGGGG GGGGGGGVGN STGGFNNTTE FKVINNEVYI TCHATRMVHI NQADTDEYLI FNAGRTTDT KTHQQKLNLE FFVYDDFHQQ VMTPWYIVDS NAWGVWMSPK DFQQMKTLCS EISLVTLEQE IDNVTIKTVT E TNQGNAST KQFNNDLTAS LQVALDTNNI LPYTPAAPLG ETLGFVPWRA TKPTQYRYYH PCYIYNRYPN IQKVATETLT WD AVQDDYL SVDEQYFNFI TIENNIPINI LRTGDNFHTG LYEFNSKPCK LTLSYQSTRC LGLPPLCKPK TDTTHKVTSK ENG ADLIYI QGQDNTRLGH FWGEERGKKN AEMNRIRPYN IGYQYPEWII PAGLQGSYFA GGPRQWSDTT KGAGTHSQHL QQNF STRYI YDRNHGGDNE VDLLDGIPIH ERSNYYSDNE IEQHTAKQPK LRTPPIHHSK IDSWEEEGWP AASGTHFEDE VIYLD YFNF SGEQELNFPH EVLDDAAQMK KLLNSYQPTV AQDNVGPVYP WGQIWDKKPH MDHKPSMNNN APFVCKNNPP GQLFVK LTE NLTDTFNYDE NPDRIKTYGY FTWRGKLVLK GKLSQVTCWN PVKRELIGEP GVFTKDKYHK QIPNNKGNFE IGLQYGR ST IKYIY

UniProtKB: Capsid protein VP1

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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 APOLLO (4k x 4k) / 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 / Type: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 93393
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: ANGULAR RECONSTITUTION

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