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- PDB-6n4v: CryoEM structure of Leviviridae PP7 WT coat protein dimer capsid ... -

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Basic information

Entry
Database: PDB / ID: 6n4v
TitleCryoEM structure of Leviviridae PP7 WT coat protein dimer capsid (PP7PP7-WT)
ComponentsCoat protein
KeywordsVIRUS LIKE PARTICLE / T4 / icosahedral / PP7 / biotechnology / vaccine / drug delivery
Function / homologyBacteriophage PP7, coat / Phage PP7 coat protein / Bacteriophage RNA-type, capsid / T=3 icosahedral viral capsid / regulation of translation / RNA binding / identical protein binding / Capsid protein
Function and homology information
Biological speciesPseudomonas phage PP7 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsLiangjun, Z. / Kopylov, M. / Potter, C.S. / Carragher, B. / Finn, M.G.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM103310 United States
CitationJournal: ACS Nano / Year: 2019
Title: Engineering the PP7 Virus Capsid as a Peptide Display Platform.
Authors: Liangjun Zhao / Mykhailo Kopylov / Clinton S Potter / Bridget Carragher / M G Finn /
Abstract: As self-assembling polyvalent nanoscale structures that can tolerate substantial genetic and chemical modification, virus-like particles are useful in a variety of fields. Here we describe the ...As self-assembling polyvalent nanoscale structures that can tolerate substantial genetic and chemical modification, virus-like particles are useful in a variety of fields. Here we describe the genetic modification and structural characterization of the Leviviridae PP7 capsid protein as a platform for the presentation of functional polypeptides. This particle was shown to tolerate the display of sequences from 1 kDa (a cell penetrating peptide) to 14 kDa (the Fc-binding double Z-domain) on its exterior surface as C-terminal genetic fusions to the coat protein. In addition, a dimeric construct allowed the presentation of exogenous loops between capsid monomers and the simultaneous presentation of two different peptides at different positions on the icosahedral structure. The PP7 particle is thereby significantly more tolerant of these types of polypeptide additions than Qβ and MS2, the other Leviviridae-derived VLPs in common use.
History
DepositionNov 20, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

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Assembly

Deposited unit
Af: Coat protein
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


Theoretical massNumber of molelcules
Total (without water)3,377,281120
Polymers3,377,281120
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
Coat protein


Mass: 28144.008 Da / Num. of mol.: 120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage PP7 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q38062

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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: Pseudomonas phage PP7 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Pseudomonas phage PP7 (virus)
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Nominal defocus min: 2 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 35 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2Leginonimage acquisition
4CTFFIND4CTF correction
10cryoSPARC0.6.5initial Euler assignment
11cryoSPARC0.6.5final Euler assignment
12RELION3classification
13cryoSPARC0.6.53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33224 / Num. of class averages: 5 / Symmetry type: POINT

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