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- EMDB-0290: Immature M-PMV capsid hexamer structure in intact virus particles -

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Basic information

Entry
Database: EMDB / ID: EMD-0290
TitleImmature M-PMV capsid hexamer structure in intact virus particles
Map dataNone
Sample
  • Virus: Mason-Pfizer monkey virus
    • Protein or peptide: Gag-Pro-Pol polyprotein
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / viral process / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency ...dUTP diphosphatase / dUTP diphosphatase activity / nucleotide metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / viral process / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / structural constituent of virion / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / proteolysis / DNA binding / RNA binding / zinc ion binding
Similarity search - Function
GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / G-patch domain / G-patch domain profile. / G-patch domain / glycine rich nucleic binding domain / dUTPase-like / dUTPase ...GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / 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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain 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
Methodsubtomogram averaging / cryo EM / Resolution: 7.2 Å
AuthorsQu K / Glass B / Dolezal M / Schur FKM / Rein A / Rumlova M / Ruml T / Kraeusslich HG / Briggs JAG
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, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseDec 5, 2018-
UpdateDec 19, 2018-
Current statusDec 19, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.118
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.118
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6hwi
  • Surface level: 0.118
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6hwi
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0290.png

Downloads & links

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Map

FileDownload / File: emd_0290.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.118 / Movie #1: 0.118
Minimum - Maximum-0.1224526 - 0.23652455
Average (Standard dev.)0.0036157074 (±0.03370667)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 259.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z259.200259.200259.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.1220.2370.004

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Supplemental data

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Sample components

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Entire : Mason-Pfizer monkey virus

EntireName: Mason-Pfizer monkey virus
Components
  • Virus: Mason-Pfizer monkey virus
    • Protein or peptide: Gag-Pro-Pol polyprotein

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Supramolecule #1: Mason-Pfizer monkey virus

SupramoleculeName: Mason-Pfizer monkey virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11855 / Sci species name: Mason-Pfizer monkey virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host systemOrganism: Homo sapiens (human) / Recombinant cell: HEK 293T / Recombinant plasmid: pSHRM15 D26N

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Macromolecule #1: Gag-Pro-Pol polyprotein

MacromoleculeName: Gag-Pro-Pol polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mason-Pfizer monkey virus
Molecular weightTheoretical: 21.817359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GFDFAVIKEL KTAASQYGAT APYTLAIVES VADNWLTPTD WNTLVRAVLS GGDHLLWKSE FFENCRDTAK RNQQAGNGWD FDMLTGSGN YSSTDAQMQY DPGLFAQIQA AATKAWRKLP VKGDPGASLT GVKQGPDEPF ADFVHRLITT AGRIFGSAEA G VDYVKQLA ...String:
GFDFAVIKEL KTAASQYGAT APYTLAIVES VADNWLTPTD WNTLVRAVLS GGDHLLWKSE FFENCRDTAK RNQQAGNGWD FDMLTGSGN YSSTDAQMQY DPGLFAQIQA AATKAWRKLP VKGDPGASLT GVKQGPDEPF ADFVHRLITT AGRIFGSAEA G VDYVKQLA YENANPACQA AIRPYRKKTD LTGYIRLCSD IG

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 6
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK II
DetailsPurified virus solution was inactivated and diluted 1:1 with PBS containing 10 nm colloidal gold.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-6 / Number grids imaged: 1 / Average exposure time: 0.6 sec. / Average electron dose: 2.0 e/Å2
Details: Dose fluctuation was caused by the ring collapse of FEG during data collection.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 34 / Number images used: 17109
Software:
Namedetails
AmiraFPMVolume selection
MATLABVolume extraction
CTF correctionSoftware:
Namedetails
MATLABCTF determination
IMODPhase flipping only
Final angle assignmentType: OTHER / Software: (Name: AV3, TOM) / Details: Subtomogram Averaging.
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: AV3, TOM) / Number subtomograms used: 17109

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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