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- PDB-9hat: pT=3 virus-like particle of ssRNA phage Beihai26 coat protein -

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Basic information

Entry
Database: PDB / ID: 9hat
TitlepT=3 virus-like particle of ssRNA phage Beihai26 coat protein
ComponentsCapsid protein
KeywordsVIRUS LIKE PARTICLE / ssRNA phage / coat protein
Function / homologyBacteriophage RNA-type, capsid / Capsid protein
Function and homology information
Biological speciesLeviviridae sp. (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsKalnins, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: To Be Published
Title: pT=3 virus like particle of ssRNA phage Beihai26
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: Capsid protein
AC: Capsid protein
AD: Capsid protein
AE: Capsid protein
AG: Capsid protein
AH: Capsid protein
AI: Capsid protein
AK: Capsid protein
AL: Capsid protein
AM: Capsid protein
AO: Capsid protein
AP: Capsid protein
AQ: Capsid protein
AS: Capsid protein
AT: Capsid protein
AU: Capsid protein
AW: Capsid protein
AX: Capsid protein
AY: Capsid protein
BA: Capsid protein
BB: Capsid protein
BC: Capsid protein
BE: Capsid protein
BF: Capsid protein
BG: Capsid protein
BI: Capsid protein
BJ: Capsid protein
BK: Capsid protein
BM: Capsid protein
BN: Capsid protein
BO: Capsid protein
BQ: Capsid protein
BR: Capsid protein
BS: Capsid protein
BU: Capsid protein
BV: Capsid protein
BW: Capsid protein
BY: Capsid protein
BZ: Capsid protein
CA: Capsid protein
CC: Capsid protein
CD: Capsid protein
CE: Capsid protein
CG: Capsid protein
CH: Capsid protein
CI: Capsid protein
CK: Capsid protein
CL: Capsid protein
CM: Capsid protein
CO: Capsid protein
CP: Capsid protein
CQ: Capsid protein
CS: Capsid protein
CT: Capsid protein
CU: Capsid protein
CW: Capsid protein
CX: Capsid protein
CY: Capsid protein
DA: Capsid protein
DB: Capsid protein
DC: Capsid protein
DE: Capsid protein
DF: Capsid protein
DG: Capsid protein
DI: Capsid protein
DJ: Capsid protein
DK: Capsid protein
DM: Capsid protein
DN: Capsid protein
DO: Capsid protein
DQ: Capsid protein
DR: Capsid protein
DS: Capsid protein
DU: Capsid protein
DV: Capsid protein
DW: Capsid protein
DY: Capsid protein
DZ: Capsid protein
EA: Capsid protein
EC: Capsid protein
ED: Capsid protein
EE: Capsid protein
EG: Capsid protein
EH: Capsid protein
EI: Capsid protein
EK: Capsid protein
EL: Capsid protein
EM: Capsid protein
EO: Capsid protein
EP: Capsid protein
EQ: Capsid protein
ES: Capsid protein
ET: Capsid protein
EU: Capsid protein
EW: Capsid protein
EX: Capsid protein
EY: Capsid protein
FA: Capsid protein
FB: Capsid protein
FC: Capsid protein
FE: Capsid protein
FF: Capsid protein
FG: Capsid protein
FI: Capsid protein
FJ: Capsid protein
FK: Capsid protein
FM: Capsid protein
FN: Capsid protein
FO: Capsid protein
FQ: Capsid protein
FR: Capsid protein
FS: Capsid protein
FU: Capsid protein
FV: Capsid protein
FW: Capsid protein
FY: Capsid protein
FZ: Capsid protein
GA: Capsid protein
GC: Capsid protein
GD: Capsid protein
GE: Capsid protein
GG: Capsid protein
GH: Capsid protein
GI: Capsid protein
GK: Capsid protein
GL: Capsid protein
GM: Capsid protein
GO: Capsid protein
GP: Capsid protein
GQ: Capsid protein
GS: Capsid protein
GT: Capsid protein
GU: Capsid protein
GW: Capsid protein
GX: Capsid protein
GY: Capsid protein
HA: Capsid protein
HB: Capsid protein
HC: Capsid protein
HE: Capsid protein
HF: Capsid protein
HG: Capsid protein
HI: Capsid protein
HJ: Capsid protein
HK: Capsid protein
HM: Capsid protein
HN: Capsid protein
HO: Capsid protein
HQ: Capsid protein
HR: Capsid protein
HS: Capsid protein
HU: Capsid protein
HV: Capsid protein
HW: Capsid protein
HY: Capsid protein
HZ: Capsid protein
IA: Capsid protein
IC: Capsid protein
ID: Capsid protein
IE: Capsid protein
IG: Capsid protein
IH: Capsid protein
II: Capsid protein
IK: Capsid protein
IL: Capsid protein
IM: Capsid protein
IO: Capsid protein
IP: Capsid protein
IQ: Capsid protein
IS: Capsid protein
IT: Capsid protein
IU: Capsid protein
IW: Capsid protein
IX: Capsid protein
IY: Capsid protein
JA: Capsid protein
JB: Capsid protein
JC: Capsid protein
JE: Capsid protein
JF: Capsid protein


Theoretical massNumber of molelcules
Total (without water)2,321,346180
Polymers2,321,346180
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 ...
Capsid protein


Mass: 12896.364 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) / References: UniProt: A0A1L3KIJ1
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 Beihai26 / 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 (max): 70 K
Image recordingAverage exposure time: 4 sec. / Electron dose: 1.6 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2714
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: 28843
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28843 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 110.094 / 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: 14.87 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0056165420
ELECTRON MICROSCOPYf_angle_d0.6497226080
ELECTRON MICROSCOPYf_chiral_restr0.044428080
ELECTRON MICROSCOPYf_plane_restr0.005629520
ELECTRON MICROSCOPYf_dihedral_angle_d6.16724120

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