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- PDB-7pe2: Cryo-EM structure of BMV-derived VLP expressed in E. coli (eVLP) -

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Basic information

Entry
Database: PDB / ID: 7pe2
TitleCryo-EM structure of BMV-derived VLP expressed in E. coli (eVLP)
ComponentsCoat protein
KeywordsVIRUS LIKE PARTICLE / BMV / brome mosaic virus / capsid proteins
Function / homologyBromovirus coat protein / Bromovirus coat protein / viral capsid / structural molecule activity / Coat protein
Function and homology information
Biological speciesBrome mosaic virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRuszkowski, M. / Strugala, A. / Indyka, P. / Urbanowicz, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nanoscale / Year: 2022
Title: Cryo-EM reconstructions of BMV-derived virus-like particles reveal assembly defects in the icosahedral lattice structure.
Authors: Milosz Ruszkowski / Aleksander Strugala / Paulina Indyka / Guillaume Tresset / Marek Figlerowicz / Anna Urbanowicz /
Abstract: The increasing interest in virus-like particles (VLPs) has been reflected by the growing number of studies on their assembly and application. However, the formation of complete VLPs is a complex ...The increasing interest in virus-like particles (VLPs) has been reflected by the growing number of studies on their assembly and application. However, the formation of complete VLPs is a complex phenomenon, making it difficult to rationally design VLPs with desired features . In this paper, we describe VLPs assembled from the recombinant capsid protein of brome mosaic virus (BMV). The analysis of VLPs was performed by Cryo-EM reconstructions and allowed us to visualize a few classes of VLPs, giving insight into the VLP self-assembly process. Apart from the mature icosahedral VLP practically identical with native virions, we describe putative VLP intermediates displaying non-icosahedral arrangements of capsomers, proposed to occur before the final disorder-order transition stage of icosahedral VLP assembly. Some of the described VLP classes show a lack of protein shell continuity, possibly resulting from too strong interaction with the cargo (in this case tRNA) with the capsid protein. We believe that our results are a useful prerequisite for the rational design of VLPs in the future and lead the way to the effective production of modified VLPs.
History
DepositionAug 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Coat protein
B: Coat protein
C: Coat protein
D: Coat protein
E: Coat protein
F: Coat protein
G: Coat protein
H: Coat protein
I: Coat protein
J: Coat protein
K: Coat protein
L: Coat protein
M: Coat protein
N: Coat protein
O: Coat protein
P: Coat protein
Q: Coat protein
R: Coat protein
S: Coat protein
T: Coat protein
V: Coat protein
W: Coat protein
X: Coat protein
Y: Coat protein
Z: Coat protein
AA: Coat protein
BA: Coat protein
CA: Coat protein
DA: Coat protein
EA: Coat protein
FA: Coat protein
GA: Coat protein
HA: Coat protein
IA: Coat protein
JA: Coat protein
KA: Coat protein
LA: Coat protein
MA: Coat protein
NA: Coat protein
OA: Coat protein
PA: Coat protein
QA: Coat protein
RA: Coat protein
SA: Coat protein
TA: Coat protein
UA: Coat protein
VA: Coat protein
WA: Coat protein
XA: Coat protein
YA: Coat protein
ZA: Coat protein
AB: Coat protein
BB: Coat protein
CB: Coat protein
DB: Coat protein
EB: Coat protein
FB: Coat protein
GB: Coat protein
HB: Coat protein
IB: Coat protein
JB: Coat protein
KB: Coat protein
LB: Coat protein
MB: Coat protein
NB: Coat protein
OB: Coat protein
PB: Coat protein
QB: Coat protein
RB: Coat protein
SB: Coat protein
TB: Coat protein
UB: Coat protein
VB: Coat protein
WB: Coat protein
XB: Coat protein
YB: Coat protein
ZB: Coat protein
AC: Coat protein
BC: Coat protein
CC: Coat protein
DC: Coat protein
EC: Coat protein
FC: Coat protein
GC: Coat protein
HC: Coat protein
IC: Coat protein
JC: Coat protein
KC: Coat protein
LC: Coat protein
MC: Coat protein
NC: Coat protein
OC: Coat protein
PC: Coat protein
QC: Coat protein
RC: Coat protein
SC: Coat protein
TC: Coat protein
UC: Coat protein
VC: Coat protein
WC: Coat protein
XC: Coat protein
YC: Coat protein
ZC: Coat protein
AD: Coat protein
BD: Coat protein
CD: Coat protein
DD: Coat protein
ED: Coat protein
FD: Coat protein
GD: Coat protein
HD: Coat protein
ID: Coat protein
JD: Coat protein
KD: Coat protein
LD: Coat protein
MD: Coat protein
ND: Coat protein
OD: Coat protein
PD: Coat protein
QD: Coat protein
RD: Coat protein
SD: Coat protein
TD: Coat protein
UD: Coat protein
VD: Coat protein
WD: Coat protein
XD: Coat protein
YD: Coat protein
ZD: Coat protein
AE: Coat protein
BE: Coat protein
CE: Coat protein
DE: Coat protein
EE: Coat protein
FE: Coat protein
GE: Coat protein
HE: Coat protein
IE: Coat protein
JE: Coat protein
KE: Coat protein
LE: Coat protein
ME: Coat protein
NE: Coat protein
OE: Coat protein
PE: Coat protein
QE: Coat protein
RE: Coat protein
SE: Coat protein
TE: Coat protein
UE: Coat protein
VE: Coat protein
WE: Coat protein
XE: Coat protein
YE: Coat protein
ZE: Coat protein
AF: Coat protein
BF: Coat protein
CF: Coat protein
DF: Coat protein
EF: Coat protein
FF: Coat protein
GF: Coat protein
HF: Coat protein
IF: Coat protein
JF: Coat protein
KF: Coat protein
LF: Coat protein
MF: Coat protein
NF: Coat protein
OF: Coat protein
PF: Coat protein
QF: Coat protein
RF: Coat protein
SF: Coat protein
TF: Coat protein
UF: Coat protein
VF: Coat protein
WF: Coat protein
XF: Coat protein
YF: Coat protein


Theoretical massNumber of molelcules
Total (without water)3,702,365180
Polymers3,702,365180
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area756760 Å2
ΔGint-4448 kcal/mol
Surface area1121670 Å2
MethodPISA

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Components

#1: Protein ...
Coat protein


Mass: 20568.693 Da / Num. of mol.: 180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brome mosaic virus / Production host: Escherichia coli (E. coli) / References: UniProt: Q9QCJ1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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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: Brome mosaic virus / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Brome mosaic virus
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 4.8
Details: 25 mM NaOAc pH 4.8, 5 mM MgCl2, 25 mM NaCl, 10 mM KCl
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 105000 X / Calibrated defocus min: 900 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12569

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9RELION3.1initial Euler assignment
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 260759
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11521 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6VOC

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