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- PDB-8ozn: In situ cryoEM structure of the Prototype Foamy Virus capsid, hex... -

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Basic information

Entry
Database: PDB / ID: 8ozn
TitleIn situ cryoEM structure of the Prototype Foamy Virus capsid, hexamer 2 localised reconstruction
ComponentsGag polyprotein
KeywordsVIRAL PROTEIN / capsid / Gag / foamy virus / hexamer
Function / homology
Function and homology information


host cytoskeleton / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / viral capsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / nucleus / cytoplasm
Similarity search - Function
Gag polyprotein / Spumavirus gag protein, N-terminal
Similarity search - Domain/homology
Biological speciesEastern chimpanzee simian foamy virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCalcraft, T. / Nans, A. / Rosenthal, P.B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: To Be Published
Title: In situ cryoEM structures of PFV
Authors: Calcraft, T. / Lindemann, D. / Rosenthal, P.B.
History
DepositionMay 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Gag polyprotein
I: Gag polyprotein
J: Gag polyprotein
K: Gag polyprotein
L: Gag polyprotein
M: Gag polyprotein


Theoretical massNumber of molelcules
Total (without water)424,1606
Polymers424,1606
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Gag polyprotein


Mass: 70693.414 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eastern chimpanzee simian foamy virus / Gene: gag / Production host: Homo sapiens (human) / References: UniProt: A0A1Q1N9V7

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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: Eastern chimpanzee simian foamy virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Eastern chimpanzee simian foamy virus
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen 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 FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 48 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansWidth: 3838 / Height: 3710

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Processing

SoftwareName: REFMAC / Version: 5.8.0352 / Classification: refinement
EM software
IDNameCategory
1crYOLOparticle selection
2EPUimage acquisition
4GctfCTF correction
9REFMACmodel refinement
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 52141
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 340192 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
RefinementResolution: 3.5→3.5 Å / Cor.coef. Fo:Fc: 0.867 / SU B: 9.977 / SU ML: 0.154 / ESU R: 0.429
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.3079 --
obs0.3079 82448 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 142.312 Å2
Refinement stepCycle: 1 / Total: 8030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0150.0118186
ELECTRON MICROSCOPYr_bond_other_d00.0167592
ELECTRON MICROSCOPYr_angle_refined_deg1.9041.63811168
ELECTRON MICROSCOPYr_angle_other_deg0.9241.5417662
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.30351042
ELECTRON MICROSCOPYr_dihedral_angle_2_deg1.2461070
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.325101320
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0680.21312
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.029430
ELECTRON MICROSCOPYr_gen_planes_other0.0070.021522
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it24.92313.2414186
ELECTRON MICROSCOPYr_mcbond_other24.91913.2414186
ELECTRON MICROSCOPYr_mcangle_it30.77719.8855222
ELECTRON MICROSCOPYr_mcangle_other30.77519.8885223
ELECTRON MICROSCOPYr_scbond_it32.74615.94000
ELECTRON MICROSCOPYr_scbond_other32.74215.9034001
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other43.90822.995947
ELECTRON MICROSCOPYr_long_range_B_refined44.7928728
ELECTRON MICROSCOPYr_long_range_B_other44.7928729
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.49→3.581 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.687 6069 -
obs--100 %

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