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- PDB-9har: pT=3 virus-like particle of ssRNA phage ESE017 coat protein -

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Basic information

Entry
Database: PDB / ID: 9har
TitlepT=3 virus-like particle of ssRNA phage ESE017 coat protein
ComponentsCoat protein
KeywordsVIRUS LIKE PARTICLE / ssRNA phage / coat protein
Function / homologyviral capsid / Coat protein
Function and homology information
Biological speciesssRNA phage ESE017 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsKalnins, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: To Be Published
Title: pT=3 particle of ssRNA phage ESE017 coat protein
Authors: Kalnins, G.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams /
Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
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
AB: Coat protein
AC: Coat protein
AD: Coat protein
AE: Coat protein
AF: Coat protein
AG: Coat protein
AH: Coat protein
AI: Coat protein
AJ: Coat protein
AK: Coat protein
AL: Coat protein
AM: Coat protein
AN: Coat protein
AO: Coat protein
AP: Coat protein
AQ: Coat protein
AR: Coat protein
AS: Coat protein
AT: Coat protein
AU: Coat protein
AV: Coat protein
AW: Coat protein
AX: Coat protein
AY: Coat protein
AZ: Coat protein
BA: Coat protein
BB: Coat protein
BC: Coat protein
BD: Coat protein
BE: Coat protein
BF: Coat protein
BG: Coat protein
BH: Coat protein
BI: Coat protein
BJ: Coat protein
BK: Coat protein
BL: Coat protein
BM: Coat protein
BN: Coat protein
BO: Coat protein
BP: Coat protein
BQ: Coat protein
BR: Coat protein
BS: Coat protein
BT: Coat protein
BU: Coat protein
BV: Coat protein
BW: Coat protein
BX: Coat protein
BY: Coat protein
BZ: Coat protein
CA: Coat protein
CB: Coat protein
CC: Coat protein
CD: Coat protein
CE: Coat protein
CF: Coat protein
CG: Coat protein
CH: Coat protein
CI: Coat protein
CJ: Coat protein
CK: Coat protein
CL: Coat protein
CM: Coat protein
CN: Coat protein
CO: Coat protein
CP: Coat protein
CQ: Coat protein
CR: Coat protein
CS: Coat protein
CT: Coat protein
CU: Coat protein
CV: Coat protein
CW: Coat protein
CX: Coat protein
CY: Coat protein
CZ: Coat protein
DA: Coat protein
DB: Coat protein
DC: Coat protein
DD: Coat protein
DE: Coat protein
DF: Coat protein
DG: Coat protein
DH: Coat protein
DI: Coat protein
DJ: Coat protein
DK: Coat protein
DL: Coat protein
DM: Coat protein
DN: Coat protein
DO: Coat protein
DP: Coat protein
DQ: Coat protein
DR: Coat protein
DS: Coat protein
DT: Coat protein
DU: Coat protein
DV: Coat protein
DW: Coat protein
DX: Coat protein
DY: Coat protein
DZ: Coat protein
EA: Coat protein
EB: Coat protein
EC: Coat protein
ED: Coat protein
EE: Coat protein
EF: Coat protein
EG: Coat protein
EH: Coat protein
EI: Coat protein
EJ: Coat protein
EK: Coat protein
EL: Coat protein
EM: Coat protein
EN: Coat protein
EO: Coat protein
EP: Coat protein
EQ: Coat protein
ER: Coat protein
ES: Coat protein
ET: Coat protein
EU: Coat protein
EV: Coat protein
EW: Coat protein
EX: Coat protein
EY: Coat protein
EZ: Coat protein
FA: Coat protein
FB: Coat protein
FC: Coat protein
FD: Coat protein
FE: Coat protein
FF: Coat protein
FG: Coat protein
FH: Coat protein
FI: Coat protein
FJ: Coat protein
FK: Coat protein
FL: Coat protein
FM: Coat protein
FN: Coat protein
FO: Coat protein
FP: Coat protein
FQ: Coat protein
FR: Coat protein
FS: Coat protein
FT: Coat protein
FU: Coat protein
FV: Coat protein
FW: Coat protein
FX: Coat protein
FY: Coat protein
FZ: Coat protein
GA: Coat protein
GB: Coat protein
GC: Coat protein
GD: Coat protein
GE: Coat protein
GF: Coat protein
GG: Coat protein
GH: Coat protein
GI: Coat protein
GJ: Coat protein
GK: Coat protein
GL: Coat protein
GM: Coat protein
GN: Coat protein
GO: Coat protein
GP: Coat protein
GQ: Coat protein
GR: Coat protein
GS: Coat protein
GT: Coat protein
GU: Coat protein
GV: Coat protein
GW: Coat protein
GX: Coat protein


Theoretical massNumber of molelcules
Total (without water)2,503,355180
Polymers2,503,355180
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


Mass: 13907.525 Da / Num. of mol.: 180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ssRNA phage ESE017 (virus) / Gene: ESE017_2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8S5KXW9
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: pT=3 virus like particle of ssRNA phage ESE017 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: ssRNA phage ESE017 (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 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 magnification: 165000 X / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen 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: 2850
Image scansWidth: 3838 / Height: 3710 / Movie frames/image: 57 / Used frames/image: 1-57

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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: 15154
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15154 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 94.15 / 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: 34.6 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0044178200
ELECTRON MICROSCOPYf_angle_d0.6585242640
ELECTRON MICROSCOPYf_chiral_restr0.045830240
ELECTRON MICROSCOPYf_plane_restr0.005531320
ELECTRON MICROSCOPYf_dihedral_angle_d5.622125020

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