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- PDB-9has: pT=3 virus-like particle of ssRNA phage ESO003 coat protein -

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Basic information

Entry
Database: PDB / ID: 9has
TitlepT=3 virus-like particle of ssRNA phage ESO003 coat protein
Componentscoat protein of ssRNA phage ESO003
KeywordsVIRUS LIKE PARTICLE / ssRNA phage / coat protein
Biological speciesLeviviridae sp. (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsKalnins, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: pT=3 virus like particle of ssRNA phage ESO003
Authors: Kalnins, G.
History
DepositionNov 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: coat protein of ssRNA phage ESO003
AB: coat protein of ssRNA phage ESO003
AC: coat protein of ssRNA phage ESO003
AD: coat protein of ssRNA phage ESO003
AE: coat protein of ssRNA phage ESO003
AF: coat protein of ssRNA phage ESO003
AG: coat protein of ssRNA phage ESO003
AH: coat protein of ssRNA phage ESO003
AI: coat protein of ssRNA phage ESO003
AJ: coat protein of ssRNA phage ESO003
AK: coat protein of ssRNA phage ESO003
AL: coat protein of ssRNA phage ESO003
AM: coat protein of ssRNA phage ESO003
AN: coat protein of ssRNA phage ESO003
AO: coat protein of ssRNA phage ESO003
AP: coat protein of ssRNA phage ESO003
AQ: coat protein of ssRNA phage ESO003
AR: coat protein of ssRNA phage ESO003
AS: coat protein of ssRNA phage ESO003
AT: coat protein of ssRNA phage ESO003
AU: coat protein of ssRNA phage ESO003
AV: coat protein of ssRNA phage ESO003
AW: coat protein of ssRNA phage ESO003
AX: coat protein of ssRNA phage ESO003
AY: coat protein of ssRNA phage ESO003
AZ: coat protein of ssRNA phage ESO003
BA: coat protein of ssRNA phage ESO003
BB: coat protein of ssRNA phage ESO003
BC: coat protein of ssRNA phage ESO003
BD: coat protein of ssRNA phage ESO003
BE: coat protein of ssRNA phage ESO003
BF: coat protein of ssRNA phage ESO003
BG: coat protein of ssRNA phage ESO003
BH: coat protein of ssRNA phage ESO003
BI: coat protein of ssRNA phage ESO003
BJ: coat protein of ssRNA phage ESO003
BK: coat protein of ssRNA phage ESO003
BL: coat protein of ssRNA phage ESO003
BM: coat protein of ssRNA phage ESO003
BN: coat protein of ssRNA phage ESO003
BO: coat protein of ssRNA phage ESO003
BP: coat protein of ssRNA phage ESO003
BQ: coat protein of ssRNA phage ESO003
BR: coat protein of ssRNA phage ESO003
BS: coat protein of ssRNA phage ESO003
BT: coat protein of ssRNA phage ESO003
BU: coat protein of ssRNA phage ESO003
BV: coat protein of ssRNA phage ESO003
BW: coat protein of ssRNA phage ESO003
BX: coat protein of ssRNA phage ESO003
BY: coat protein of ssRNA phage ESO003
BZ: coat protein of ssRNA phage ESO003
CA: coat protein of ssRNA phage ESO003
CB: coat protein of ssRNA phage ESO003
CC: coat protein of ssRNA phage ESO003
CD: coat protein of ssRNA phage ESO003
CE: coat protein of ssRNA phage ESO003
CF: coat protein of ssRNA phage ESO003
CG: coat protein of ssRNA phage ESO003
CH: coat protein of ssRNA phage ESO003
CI: coat protein of ssRNA phage ESO003
CJ: coat protein of ssRNA phage ESO003
CK: coat protein of ssRNA phage ESO003
CL: coat protein of ssRNA phage ESO003
CM: coat protein of ssRNA phage ESO003
CN: coat protein of ssRNA phage ESO003
CO: coat protein of ssRNA phage ESO003
CP: coat protein of ssRNA phage ESO003
CQ: coat protein of ssRNA phage ESO003
CR: coat protein of ssRNA phage ESO003
CS: coat protein of ssRNA phage ESO003
CT: coat protein of ssRNA phage ESO003
CU: coat protein of ssRNA phage ESO003
CV: coat protein of ssRNA phage ESO003
CW: coat protein of ssRNA phage ESO003
CX: coat protein of ssRNA phage ESO003
CY: coat protein of ssRNA phage ESO003
CZ: coat protein of ssRNA phage ESO003
DA: coat protein of ssRNA phage ESO003
DB: coat protein of ssRNA phage ESO003
DC: coat protein of ssRNA phage ESO003
DD: coat protein of ssRNA phage ESO003
DE: coat protein of ssRNA phage ESO003
DF: coat protein of ssRNA phage ESO003
DG: coat protein of ssRNA phage ESO003
DH: coat protein of ssRNA phage ESO003
DI: coat protein of ssRNA phage ESO003
DJ: coat protein of ssRNA phage ESO003
DK: coat protein of ssRNA phage ESO003
DL: coat protein of ssRNA phage ESO003
DM: coat protein of ssRNA phage ESO003
DN: coat protein of ssRNA phage ESO003
DO: coat protein of ssRNA phage ESO003
DP: coat protein of ssRNA phage ESO003
DQ: coat protein of ssRNA phage ESO003
DR: coat protein of ssRNA phage ESO003
DS: coat protein of ssRNA phage ESO003
DT: coat protein of ssRNA phage ESO003
DU: coat protein of ssRNA phage ESO003
DV: coat protein of ssRNA phage ESO003
DW: coat protein of ssRNA phage ESO003
DX: coat protein of ssRNA phage ESO003
DY: coat protein of ssRNA phage ESO003
DZ: coat protein of ssRNA phage ESO003
EA: coat protein of ssRNA phage ESO003
EB: coat protein of ssRNA phage ESO003
EC: coat protein of ssRNA phage ESO003
ED: coat protein of ssRNA phage ESO003
EE: coat protein of ssRNA phage ESO003
EF: coat protein of ssRNA phage ESO003
EG: coat protein of ssRNA phage ESO003
EH: coat protein of ssRNA phage ESO003
EI: coat protein of ssRNA phage ESO003
EJ: coat protein of ssRNA phage ESO003
EK: coat protein of ssRNA phage ESO003
EL: coat protein of ssRNA phage ESO003
EM: coat protein of ssRNA phage ESO003
EN: coat protein of ssRNA phage ESO003
EO: coat protein of ssRNA phage ESO003
EP: coat protein of ssRNA phage ESO003
EQ: coat protein of ssRNA phage ESO003
ER: coat protein of ssRNA phage ESO003
ES: coat protein of ssRNA phage ESO003
ET: coat protein of ssRNA phage ESO003
EU: coat protein of ssRNA phage ESO003
EV: coat protein of ssRNA phage ESO003
EW: coat protein of ssRNA phage ESO003
EX: coat protein of ssRNA phage ESO003
EY: coat protein of ssRNA phage ESO003
EZ: coat protein of ssRNA phage ESO003
FA: coat protein of ssRNA phage ESO003
FB: coat protein of ssRNA phage ESO003
FC: coat protein of ssRNA phage ESO003
FD: coat protein of ssRNA phage ESO003
FE: coat protein of ssRNA phage ESO003
FF: coat protein of ssRNA phage ESO003
FG: coat protein of ssRNA phage ESO003
FH: coat protein of ssRNA phage ESO003
FI: coat protein of ssRNA phage ESO003
FJ: coat protein of ssRNA phage ESO003
FK: coat protein of ssRNA phage ESO003
FL: coat protein of ssRNA phage ESO003
FM: coat protein of ssRNA phage ESO003
FN: coat protein of ssRNA phage ESO003
FO: coat protein of ssRNA phage ESO003
FP: coat protein of ssRNA phage ESO003
FQ: coat protein of ssRNA phage ESO003
FR: coat protein of ssRNA phage ESO003
FS: coat protein of ssRNA phage ESO003
FT: coat protein of ssRNA phage ESO003
FU: coat protein of ssRNA phage ESO003
FV: coat protein of ssRNA phage ESO003
FW: coat protein of ssRNA phage ESO003
FX: coat protein of ssRNA phage ESO003
FY: coat protein of ssRNA phage ESO003
FZ: coat protein of ssRNA phage ESO003
GA: coat protein of ssRNA phage ESO003
GB: coat protein of ssRNA phage ESO003
GC: coat protein of ssRNA phage ESO003
GD: coat protein of ssRNA phage ESO003
GE: coat protein of ssRNA phage ESO003
GF: coat protein of ssRNA phage ESO003
GG: coat protein of ssRNA phage ESO003
GH: coat protein of ssRNA phage ESO003
GI: coat protein of ssRNA phage ESO003
GJ: coat protein of ssRNA phage ESO003
GK: coat protein of ssRNA phage ESO003
GL: coat protein of ssRNA phage ESO003
GM: coat protein of ssRNA phage ESO003
GN: coat protein of ssRNA phage ESO003
GO: coat protein of ssRNA phage ESO003
GP: coat protein of ssRNA phage ESO003
GQ: coat protein of ssRNA phage ESO003
GR: coat protein of ssRNA phage ESO003
GS: coat protein of ssRNA phage ESO003
GT: coat protein of ssRNA phage ESO003
GU: coat protein of ssRNA phage ESO003
GV: coat protein of ssRNA phage ESO003
GW: coat protein of ssRNA phage ESO003
GX: coat protein of ssRNA phage ESO003


Theoretical massNumber of molelcules
Total (without water)2,199,217180
Polymers2,199,217180
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
coat protein of ssRNA phage ESO003


Mass: 12217.873 Da / Num. of mol.: 180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leviviridae sp. (virus) / Production host: Escherichia coli BL21(DE3) (bacteria)
Has protein modificationN

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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: virus like particles of ssRNA phage ESO003 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Leviviridae sp. (virus)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 8 / Details: 20 mM Tris-HCl, pH 8.0
Buffer componentConc.: 20 mM / Name: Tris-HCl
SpecimenConc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil Active R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 70 K
Image recordingAverage exposure time: 4 sec. / Electron dose: 1.4 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1297
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 57

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Processing

EM software
IDNameCategory
1RELIONparticle selection
2SerialEMimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
9RELIONinitial Euler assignment
10RELIONfinal Euler assignment
11RELIONclassification
12RELION3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 11758
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1297 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 81.5005 / Protocol: AB INITIO MODEL / Space: REAL
Atomic model buildingSource name: AlphaFold / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 36.89 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0055156060
ELECTRON MICROSCOPYf_angle_d0.7207212040
ELECTRON MICROSCOPYf_chiral_restr0.047526640
ELECTRON MICROSCOPYf_plane_restr0.004926820
ELECTRON MICROSCOPYf_dihedral_angle_d7.430621780

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