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

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Basic information

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


host cytoskeleton / microtubule-dependent intracellular transport of viral material towards nucleus / viral release from host cell / host cell / viral nucleocapsid / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / DNA binding / RNA binding / cytoplasm
Similarity search - Function
Gag polyprotein / : / : / Spumavirus gag protein, N-terminal / Spumavirus Gag polyprotein, conserved central domain / Spumavirus Gag polyprotein, C-terminal
Similarity search - Domain/homology
Biological speciesEastern chimpanzee simian foamy virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsCalcraft, T. / Nans, A. / Rosenthal, P.B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick Institute United Kingdom
CitationJournal: Cell / Year: 2024
Title: Integrated cryoEM structure of a spumaretrovirus reveals cross-kingdom evolutionary relationships and the molecular basis for assembly and virus entry.
Authors: Thomas Calcraft / Nicole Stanke-Scheffler / Andrea Nans / Dirk Lindemann / Ian A Taylor / Peter B Rosenthal /
Abstract: Foamy viruses (FVs) are an ancient lineage of retroviruses, with an evolutionary history spanning over 450 million years. Vector systems based on Prototype Foamy Virus (PFV) are promising candidates ...Foamy viruses (FVs) are an ancient lineage of retroviruses, with an evolutionary history spanning over 450 million years. Vector systems based on Prototype Foamy Virus (PFV) are promising candidates for gene and oncolytic therapies. Structural studies of PFV contribute to the understanding of the mechanisms of FV replication, cell entry and infection, and retroviral evolution. Here we combine cryoEM and cryoET to determine high-resolution in situ structures of the PFV icosahedral capsid (CA) and envelope glycoprotein (Env), including its type III transmembrane anchor and membrane-proximal external region (MPER), and show how they are organized in an integrated structure of assembled PFV particles. The atomic models reveal an ancient retroviral capsid architecture and an unexpected relationship between Env and other class 1 fusion proteins of the Mononegavirales. Our results represent the de novo structure determination of an assembled retrovirus particle.
History
DepositionMay 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Jul 24, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _em_admin.last_update
Revision 1.3Aug 7, 2024Group: Data collection / Database references / Category: em_admin / pdbx_database_related / Item: _em_admin.last_update
Revision 1.4Aug 21, 2024Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gag polyprotein
B: Gag polyprotein
C: Gag polyprotein
D: Gag polyprotein
E: Gag polyprotein


Theoretical massNumber of molelcules
Total (without water)353,4675
Polymers353,4675
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.309017, -0.951057), (0.951057, 0.309017), (1)283.7445, -44.94076
3given(-0.809017, -0.587785), (0.587785, -0.809017), (1)414.16741, 211.02888
4given(-0.809017, 0.587785), (-0.587785, -0.809017), (1)211.02888, 414.16742
5given(0.309017, 0.951057), (-0.951057, 0.309017), (1)-44.94076, 283.74449

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Components

#1: Protein
Gag polyprotein


Mass: 70693.414 Da / Num. of mol.: 5
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
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97872 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: RECIPROCAL
RefinementResolution: 3.4→3.4 Å / Cor.coef. Fo:Fc: 0.865 / SU B: 11.932 / SU ML: 0.195 / ESU R: 0.199
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.31658 --
obs0.31658 43838 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 129.622 Å2
Refinement stepCycle: 1 / Total: 1335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0130.0111361
ELECTRON MICROSCOPYr_bond_other_d00.0161263
ELECTRON MICROSCOPYr_angle_refined_deg1.4981.6381856
ELECTRON MICROSCOPYr_angle_other_deg0.7491.542938
ELECTRON MICROSCOPYr_dihedral_angle_1_deg3.2875173
ELECTRON MICROSCOPYr_dihedral_angle_2_deg0.3271012
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.3810220
ELECTRON MICROSCOPYr_dihedral_angle_4_deg
ELECTRON MICROSCOPYr_chiral_restr0.0730.2217
ELECTRON MICROSCOPYr_gen_planes_refined0.0040.021570
ELECTRON MICROSCOPYr_gen_planes_other0.0030.02254
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_it19.49712.053695
ELECTRON MICROSCOPYr_mcbond_other19.41212.055695
ELECTRON MICROSCOPYr_mcangle_it24.10618.193867
ELECTRON MICROSCOPYr_mcangle_other24.09718.21868
ELECTRON MICROSCOPYr_scbond_it28.06314.294666
ELECTRON MICROSCOPYr_scbond_other28.04214.309667
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other36.70620.709990
ELECTRON MICROSCOPYr_long_range_B_refined37.2391458
ELECTRON MICROSCOPYr_long_range_B_other37.2261459
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.38→3.468 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork2.166 3265 -
obs--100 %

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