+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-28515 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Aleutian Mink Disease Virus VP2 | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Biological species | Aleutian mink disease virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.18 Å | |||||||||
Authors | Mietzsch M / McKenna R | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_28515.map.gz | 262.2 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-28515-v30.xml emd-28515.xml | 13.8 KB 13.8 KB | Display Display | EMDB header |
Images | emd_28515.png | 74.1 KB | ||
Others | emd_28515_half_map_1.map.gz emd_28515_half_map_2.map.gz | 72.7 MB 72.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-28515 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-28515 | HTTPS FTP |
-Validation report
Summary document | emd_28515_validation.pdf.gz | 862.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_28515_full_validation.pdf.gz | 862.2 KB | Display | |
Data in XML | emd_28515_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | emd_28515_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28515 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-28515 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_28515.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.095 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #1
File | emd_28515_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_28515_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Aleutian mink disease virus
Entire | Name: Aleutian mink disease virus |
---|---|
Components |
|
-Supramolecule #1: Aleutian mink disease virus
Supramolecule | Name: 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 system | Organism: Spodoptera frugiperda (fall armyworm) / Recombinant cell: Sf9 |
Virus shell | Shell ID: 1 / T number (triangulation number): 1 |
-Macromolecule #1: Aleutian Mink Disease Virus (VP2-VLPs)
Macromolecule | Name: Aleutian Mink Disease Virus (VP2-VLPs) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Aleutian mink disease virus |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Average electron dose: 59.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
CTF correction | Software - Name: cisTEM |
---|---|
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 8015 |
Initial angle assignment | Type: COMMON LINE |
Final angle assignment | Type: ANGULAR RECONSTITUTION |