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

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Basic information

Entry
Database: PDB / ID: 6wh3
TitleCapsid structure of Penaeus monodon metallodensovirus at pH 8.2
ComponentsPenaeus monodon metallodensovirus major capsid protein
KeywordsVIRUS LIKE PARTICLE / parvovirus / densovirus / Penaeus monodon / crustacean / pathogen / Parvovirinae / metallodensovirus / shrimp / prawn / capsid
Biological speciesPenaeus monodon metallodensovirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsPenzes, J.J. / Pham, H.T. / Chipman, P. / Bhattacharya, N. / McKenna, R. / Agbandje-McKenna, M. / Tijssen, P.
Funding support Canada, United States, 5items
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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionApr 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Derived calculations / Category: citation / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.2Aug 19, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 2, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Assembly

Deposited unit
A: Penaeus monodon metallodensovirus major capsid protein
B: Penaeus monodon metallodensovirus major capsid protein
C: Penaeus monodon metallodensovirus major capsid protein
D: Penaeus monodon metallodensovirus major capsid protein
E: Penaeus monodon metallodensovirus major capsid protein
F: Penaeus monodon metallodensovirus major capsid protein
G: Penaeus monodon metallodensovirus major capsid protein
H: Penaeus monodon metallodensovirus major capsid protein
I: Penaeus monodon metallodensovirus major capsid protein
J: Penaeus monodon metallodensovirus major capsid protein
K: Penaeus monodon metallodensovirus major capsid protein
L: Penaeus monodon metallodensovirus major capsid protein
M: Penaeus monodon metallodensovirus major capsid protein
N: Penaeus monodon metallodensovirus major capsid protein
O: Penaeus monodon metallodensovirus major capsid protein
P: Penaeus monodon metallodensovirus major capsid protein
Q: Penaeus monodon metallodensovirus major capsid protein
R: Penaeus monodon metallodensovirus major capsid protein
S: Penaeus monodon metallodensovirus major capsid protein
T: Penaeus monodon metallodensovirus major capsid protein
U: Penaeus monodon metallodensovirus major capsid protein
V: Penaeus monodon metallodensovirus major capsid protein
W: Penaeus monodon metallodensovirus major capsid protein
X: Penaeus monodon metallodensovirus major capsid protein
Y: Penaeus monodon metallodensovirus major capsid protein
Z: Penaeus monodon metallodensovirus major capsid protein
8: Penaeus monodon metallodensovirus major capsid protein
7: Penaeus monodon metallodensovirus major capsid protein
6: Penaeus monodon metallodensovirus major capsid protein
5: Penaeus monodon metallodensovirus major capsid protein
4: Penaeus monodon metallodensovirus major capsid protein
3: Penaeus monodon metallodensovirus major capsid protein
a: Penaeus monodon metallodensovirus major capsid protein
b: Penaeus monodon metallodensovirus major capsid protein
c: Penaeus monodon metallodensovirus major capsid protein
d: Penaeus monodon metallodensovirus major capsid protein
e: Penaeus monodon metallodensovirus major capsid protein
f: Penaeus monodon metallodensovirus major capsid protein
g: Penaeus monodon metallodensovirus major capsid protein
h: Penaeus monodon metallodensovirus major capsid protein
i: Penaeus monodon metallodensovirus major capsid protein
j: Penaeus monodon metallodensovirus major capsid protein
k: Penaeus monodon metallodensovirus major capsid protein
l: Penaeus monodon metallodensovirus major capsid protein
m: Penaeus monodon metallodensovirus major capsid protein
n: Penaeus monodon metallodensovirus major capsid protein
o: Penaeus monodon metallodensovirus major capsid protein
p: Penaeus monodon metallodensovirus major capsid protein
q: Penaeus monodon metallodensovirus major capsid protein
r: Penaeus monodon metallodensovirus major capsid protein
s: Penaeus monodon metallodensovirus major capsid protein
t: Penaeus monodon metallodensovirus major capsid protein
u: Penaeus monodon metallodensovirus major capsid protein
v: Penaeus monodon metallodensovirus major capsid protein
w: Penaeus monodon metallodensovirus major capsid protein
x: Penaeus monodon metallodensovirus major capsid protein
y: Penaeus monodon metallodensovirus major capsid protein
z: Penaeus monodon metallodensovirus major capsid protein
1: Penaeus monodon metallodensovirus major capsid protein
2: Penaeus monodon metallodensovirus major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,470,260120
Polymers2,467,85560
Non-polymers2,40560
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area526110 Å2
ΔGint-2916 kcal/mol
Surface area505120 Å2

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Components

#1: Protein ...
Penaeus monodon metallodensovirus major capsid protein


Mass: 41130.918 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus monodon metallodensovirus / Gene: ORF4 / Plasmid: pFastBac1-HM / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
#2: Chemical...
ChemComp-CA / CALCIUM ION / Calcium


Mass: 40.078 Da / Num. of mol.: 60 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Penaeus monodon metallodensovirus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Penaeus monodon metallodensovirus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf9 / Plasmid: pFastBac1-HM
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Penaeus monodon
Virus shellTriangulation number (T number): 1
Buffer solutionpH: 8.2
Details: 20 mM HEPES, 20 mM MES, 20 mM sodium acetate, 0.15 M NaCl, 3.7 mM CaCl2
Buffer componentName: Universal buffer
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 75 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10-2155_2155: / Classification: refinement
EM software
IDNameVersionCategory
7Auto3DEM4.05.2model fitting
12Auto3DEM4.05.23D reconstruction
13Auto3DEM4.05.2model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.96 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Num. of particles: 12873 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.011162420
ELECTRON MICROSCOPYf_angle_d1.063221040
ELECTRON MICROSCOPYf_dihedral_angle_d6.483163080
ELECTRON MICROSCOPYf_chiral_restr0.06624120
ELECTRON MICROSCOPYf_plane_restr0.00628620

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