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- EMDB-21668: Capsid structure of Penaeus monodon metallodensovirus following E... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21668 | ||||||||||||||||||
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Title | Capsid structure of Penaeus monodon metallodensovirus following EDTA treatment | ||||||||||||||||||
![]() | Capsid structure of Penaeus monodon metallodensovirus, EDTA-treated | ||||||||||||||||||
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![]() | parvovirus / densovirus / Penaeus monodon / crustacean / pathogen / Parvovirinae / metallodensovirus / shrimp / prawn / capsid / VIRUS LIKE PARTICLE | ||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.78 Å | ||||||||||||||||||
![]() | Penzes JJ / Pham HT | ||||||||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Molecular biology and structure of a novel penaeid shrimp densovirus elucidate convergent parvoviral host capsid evolution. Authors: Judit J Pénzes / Hanh T Pham / Paul Chipman / Nilakshee Bhattacharya / Robert McKenna / Mavis Agbandje-McKenna / Peter Tijssen / ![]() ![]() Abstract: The giant tiger prawn () is a decapod crustacean widely reared for human consumption. Currently, viruses of two distinct lineages of parvoviruses (PVs, family ; subfamily ) infect penaeid shrimp. ...The giant tiger prawn () is a decapod crustacean widely reared for human consumption. Currently, viruses of two distinct lineages of parvoviruses (PVs, family ; subfamily ) infect penaeid shrimp. Here, a PV was isolated and cloned from Vietnamese specimens, designated metallodensovirus (PmMDV). This is the first member of a third divergent lineage shown to infect penaeid decapods. PmMDV has a transcription strategy unique among invertebrate PVs, using extensive alternative splicing and incorporating transcription elements characteristic of vertebrate-infecting PVs. The PmMDV proteins have no significant sequence similarity with other PVs, except for an SF3 helicase domain in its nonstructural protein. Its capsid structure, determined by cryoelectron microscopy to 3-Å resolution, has a similar surface morphology to densovirus, despite the lack of significant capsid viral protein (VP) sequence similarity. Unlike other PVs, PmMDV folds its VP without incorporating a βA strand and displayed unique multimer interactions, including the incorporation of a Ca cation, attaching the N termini under the icosahedral fivefold symmetry axis, and forming a basket-like pentamer helix bundle. While the PmMDV VP sequence lacks a canonical phospholipase A2 domain, the structure of an EDTA-treated capsid, determined to 2.8-Å resolution, suggests an alternative membrane-penetrating cation-dependent mechanism in its N-terminal region. PmMDV is an observed example of convergent evolution among invertebrate PVs with respect to host-driven capsid structure and unique as a PV showing a cation-sensitive/dependent basket structure for an alternative endosomal egress. | ||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 78.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.1 KB 12.1 KB | Display Display | ![]() |
Images | ![]() | 99.9 KB | ||
Filedesc metadata | ![]() | 5.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 453 KB | Display | ![]() |
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Full document | ![]() | 452.5 KB | Display | |
Data in XML | ![]() | 7.5 KB | Display | |
Data in CIF | ![]() | 8.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wh7MC ![]() 6wh3C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Capsid structure of Penaeus monodon metallodensovirus, EDTA-treated | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.059 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Penaeus monodon metallodensovirus
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Penaeus monodon metallodensovirus
Supramolecule | Name: Penaeus monodon metallodensovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2672571 / Sci species name: Penaeus monodon metallodensovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / T number (triangulation number): 1 |
-Macromolecule #1: Penaeus monodon metallodensovirus major capsid protein
Macromolecule | Name: Penaeus monodon metallodensovirus major capsid protein type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 41.130918 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSDEVSSSTD VVSRKRRRHD EGGKALEDIA VHGASEGDGS APGGSVWQTT DYIALSMVVY RTAIKLRNFV NIRGLTPTEM IVIPWNVMR FYCEYNTGTY GLSGNVHHKN YSMLLACKAH RPTKVGYTLS NLILTSDELV STGGTLGTTT TFNTSPYMIH S IDDQQCLS ...String: MSDEVSSSTD VVSRKRRRHD EGGKALEDIA VHGASEGDGS APGGSVWQTT DYIALSMVVY RTAIKLRNFV NIRGLTPTEM IVIPWNVMR FYCEYNTGTY GLSGNVHHKN YSMLLACKAH RPTKVGYTLS NLILTSDELV STGGTLGTTT TFNTSPYMIH S IDDQQCLS KVYPKTDTVW PVSSMRELDY VASTVSGDNA IIPSTIFNKN RYWKQGDDAL HFSHDLDLGF WFGSDYGNAY VP QNNDSMN AVGTIPTSKH INVRGVNNRG MAGHYLSFPP IRTNDGQFKL NAQFTLETEI EFEFRLWEQG VQGINSVHTN LNP ANDSLW IQSYGSLVSI TESKINNIQF GPTCPRVDAR NKGGKMSMLF DHH |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8.2 Component - Name: Universal buffer, supplemented with 100 mM EDTA Details: 20 mM HEPES, 20 mM MES, 20 mM sodium acetate, 0.15 M NaCl, 3.7 mM CaCl2, 100 mM EDTA |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER / Details: Ab initio model prediction |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Software - Name: Auto3DEM (ver. 4.05.2) / Number images used: 30977 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |