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- PDB-6hwi: Immature M-PMV capsid hexamer structure in intact virus particles -

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Basic information

Entry
Database: PDB / ID: 6hwi
TitleImmature M-PMV capsid hexamer structure in intact virus particles
ComponentsGag-Pro-Pol polyprotein
KeywordsVIRAL PROTEIN / M-PMV / capsid / hexamer
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / ribonuclease H / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / structural constituent of virion / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / viral translational frameshifting / symbiont entry into host cell / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / dUTPase-like / dUTPase ...Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / : / gag protein p24 N-terminal domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Gag-Pro polyprotein / Gag-Pro-Pol polyprotein
Similarity search - Component
Biological speciesMason-Pfizer monkey virus
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 7.2 Å
AuthorsQu, K. / Glass, B. / Dolezal, M. / Schur, F.K.M. / Rein, A. / Rumlova, M. / Ruml, T. / Kraeusslich, H.G. / Briggs, J.A.G.
Funding support Germany, United Kingdom, Czech Republic, 9items
OrganizationGrant numberCountry
German Research FoundationBR 3635/2-1 Germany
German Research FoundationKR 906/7-1 Germany
German Research FoundationKR 906/8-1 Germany
European Research CouncilERC-CoG-648432 Germany
Medical Research Council (United Kingdom)MC_UP_1201/16 United Kingdom
Czech Science Foundation17-25602S Czech Republic
Ministry of Education (Czech Republic)LO1302 Czech Republic
Ministry of Education (Czech Republic)LO1304 Czech Republic
Ministry of Education (Czech Republic)LO1601 Czech Republic
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Structure and architecture of immature and mature murine leukemia virus capsids.
Authors: Kun Qu / Bärbel Glass / Michal Doležal / Florian K M Schur / Brice Murciano / Alan Rein / Michaela Rumlová / Tomáš Ruml / Hans-Georg Kräusslich / John A G Briggs /
Abstract: Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as ...Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein-protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry.
History
DepositionOct 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation

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Assembly

Deposited unit
A: Gag-Pro-Pol polyprotein
B: Gag-Pro-Pol polyprotein
C: Gag-Pro-Pol polyprotein


Theoretical massNumber of molelcules
Total (without water)65,4523
Polymers65,4523
Non-polymers00
Water00
1
A: Gag-Pro-Pol polyprotein
B: Gag-Pro-Pol polyprotein
C: Gag-Pro-Pol polyprotein
x 6


Theoretical massNumber of molelcules
Total (without water)392,71218
Polymers392,71218
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
build point asymmetric unit5

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Components

#1: Protein Gag-Pro-Pol polyprotein / Pr180


Mass: 21817.359 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mason-Pfizer monkey virus / Gene: gag-pro-pol / Production host: Homo sapiens (human) / References: UniProt: P07572, UniProt: P07570*PLUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Mason-Pfizer monkey virus / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mason-Pfizer monkey virus
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK 293T / Plasmid: pSHRM15 D26N
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Purified virus solution was inactivated and diluted 1:1 with PBS containing 10 nm colloidal gold.
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 288 K

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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 magnification: 105000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 0.6 sec. / Electron dose: 2 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1
Details: Dose fluctuation was caused by the ring collapse of FEG during data collection.
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV
Image scansSampling size: 5 µm / Width: 3710 / Height: 3838 / Movie frames/image: 6 / Used frames/image: 1-6

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Processing

EM software
IDNameCategoryDetails
1AmiraFPMvolume selectionVolume selection
2MATLABvolume selectionVolume extraction
3SerialEMimage acquisitionDose-symmetric tilt-scheme
5MATLABCTF correctionCTF determination
6IMODCTF correctionPhase flipping only
9Cootmodel fitting
10UCSF Chimeramodel fitting
12PHENIXmodel refinement
14AV3final Euler assignment
15TOMfinal Euler assignment
17AV33D reconstruction
18TOM3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17109 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 34 / Num. of volumes extracted: 17109
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL

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