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- EMDB-21667: Capsid structure of Penaeus monodon metallodensovirus at pH 8.2 -

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Basic information

Entry
Database: EMDB / ID: EMD-21667
TitleCapsid structure of Penaeus monodon metallodensovirus at pH 8.2
Map dataCapsid structure of Penaeus monodon metallodensovirus at pH 8.2
Sample
  • Virus: Penaeus monodon metallodensovirus
    • Protein or peptide: Penaeus monodon metallodensovirus major capsid protein
  • Ligand: CALCIUM ION
Keywordsparvovirus / densovirus / Penaeus monodon / crustacean / pathogen / Parvovirinae / metallodensovirus / shrimp / prawn / capsid / VIRUS LIKE PARTICLE
Biological speciesPenaeus monodon metallodensovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsPenzes JJ / Pham HT
Funding support Canada, United States, 5 items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 OD018142-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 RR025080-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM109524 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM082946 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
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
DepositionApr 7, 2020-
Header (metadata) releaseApr 22, 2020-
Map releaseApr 22, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6wh3
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6wh3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21667.png

Downloads & links

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Map

FileDownload / File: emd_21667.map.gz / Format: CCP4 / Size: 246 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCapsid structure of Penaeus monodon metallodensovirus at pH 8.2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.04 Å/pix.
x 401 pix.
= 415.436 Å		1.04 Å/pix.
x 401 pix.
= 415.436 Å		1.04 Å/pix.
x 401 pix.
= 415.436 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.036 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 2
Minimum - Maximum-12.178599999999999 - 21.7774
Average (Standard dev.)-0.000000000007218 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-200-200-200
Dimensions401401401
Spacing401401401
CellA=B=C: 415.436 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0361.0361.036
M x/y/z401401401
origin x/y/z0.0000.0000.000
length x/y/z415.436415.436415.436
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S213
start NC/NR/NS-200-200-200
NC/NR/NS401401401
D min/max/mean-12.17921.777-0.000

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Supplemental data

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Sample components

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Entire : Penaeus monodon metallodensovirus

EntireName: Penaeus monodon metallodensovirus
Components
  • Virus: Penaeus monodon metallodensovirus
    • Protein or peptide: Penaeus monodon metallodensovirus major capsid protein
  • Ligand: CALCIUM ION

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Supramolecule #1: Penaeus monodon metallodensovirus

SupramoleculeName: Penaeus monodon metallodensovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 2672571 / Sci species name: Penaeus monodon metallodensovirus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Penaeus monodon (black tiger shrimp)
Virus shellShell ID: 1 / T number (triangulation number): 1

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Macromolecule #1: Penaeus monodon metallodensovirus major capsid protein

MacromoleculeName: Penaeus monodon metallodensovirus major capsid protein
type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Penaeus monodon metallodensovirus
Molecular weightTheoretical: 41.130918 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 60 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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: 8.2 / Component - Name: Universal buffer
Details: 20 mM HEPES, 20 mM MES, 20 mM sodium acetate, 0.15 M NaCl, 3.7 mM CaCl2
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 75.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Software - Name: Auto3DEM (ver. 4.05.2) / Number images used: 12873
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-6wh3:
Capsid structure of Penaeus monodon metallodensovirus at pH 8.2

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