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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: 0290
TitleImmature M-PMV capsid hexamer structure in intact virus particles
Map data
SampleMason-Pfizer monkey virusSimian retrovirus:
virus / Gag-Pro-Pol polyprotein
Function / homologyReverse transcriptase thumb / dUTPase-like / Ribonuclease H domain / Integrase, N-terminal zinc-binding domain / Beta-retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / Retroviral matrix protein / Ribonuclease H-like superfamily / Integrase-like, N-terminal ...Reverse transcriptase thumb / dUTPase-like / Ribonuclease H domain / Integrase, N-terminal zinc-binding domain / Beta-retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / Retroviral matrix protein / Ribonuclease H-like superfamily / Integrase-like, N-terminal / Retropepsins / Aspartic peptidase domain superfamily / dUTPase, trimeric / Aspartic peptidase, active site / Retropepsin-like catalytic domain / dUTPase-like superfamily / Ribonuclease H superfamily / Integrase, C-terminal domain superfamily, retroviral / Zinc finger, CCHC-type superfamily / Beta-retroviral matrix superfamily / RNase H / Retroviral aspartyl protease / Reverse transcriptase (RNA-dependent DNA polymerase) / Integrase DNA binding domain / gag gene protein p24 (core nucleocapsid protein) / Peptidase A2A, retrovirus, catalytic / Zinc finger, CCHC-type / dUTPase / Reverse transcriptase thumb domain / Integrase DNA binding domain profile. / Integrase catalytic domain profile. / RNase H domain profile. / Reverse transcriptase (RT) catalytic domain profile. / Zinc finger integrase-type profile. / Aspartyl protease, retroviral-type family profile. / G-patch domain profile. / Zinc finger CCHC-type profile. / Integrase, catalytic core / Eukaryotic and viral aspartyl proteases active site. / Integrase Zinc binding domain / Retroviral GAG p10 protein / G-patch domain / G-patch domain / Reverse transcriptase domain / Retroviral nucleocapsid protein Gag / Integrase, C-terminal, retroviral / Integrase core domain / dUTP diphosphatase / dUTP diphosphatase activity / structural constituent of virion / Aspartic endopeptidases / calf thymus ribonuclease H / RNA-directed DNA polymerase / DNA integration / viral genome integration into host DNA / Nucleotidyltransferases / RNA-directed DNA polymerase activity / establishment of integrated proviral latency / RNA-DNA hybrid ribonuclease activity / viral entry into host cell / viral nucleocapsid / DNA recombination / Acting on Ester Bonds / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / aspartic-type endopeptidase activity / RNA binding / DNA binding / zinc ion binding / Gag-Pro-Pol polyprotein
Function and homology information
SourceMason-Pfizer monkey virus
Methodsubtomogram averaging / cryo EM / 7.2 Å resolution
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.
Validation ReportPDB-ID: 6hwi

SummaryFull reportAbout validation report
DateDeposition: Oct 12, 2018 / Header (metadata) release: Oct 24, 2018 / Map release: Dec 5, 2018 / Last update: Dec 19, 2018

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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 models: PDB-6hwi
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0290.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.35 Å/pix.
= 259.2 Å
192 pix
1.35 Å/pix.
= 259.2 Å
192 pix
1.35 Å/pix.
= 259.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.118 (by author), 0.118 (movie #1):
Minimum - Maximum-0.1224526 - 0.23652455
Average (Standard dev.)0.0036157074 (0.03370667)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin0.00.00.0
Limit191.0191.0191.0
Spacing192192192
CellA=B=C: 259.2 Å
α=β=γ: 90.0 deg.

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 / Number of components: 2

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Component #1: virus, Mason-Pfizer monkey virus

VirusName: Mason-Pfizer monkey virusSimian retrovirus / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Mason-Pfizer monkey virus
Source (engineered)Expression System: Homo sapiens (human) / Vector: pSHRM15 D26N / Cell of expression system: HEK 293T

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Component #2: protein, Gag-Pro-Pol polyprotein

ProteinName: Gag-Pro-Pol polyprotein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 21.817359 kDa
SourceSpecies: Mason-Pfizer monkey virus
Source (engineered)Expression System: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 6
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 288 K / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000.0 - 4500.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionSampling size: 5 microns
Details: Dose fluctuation was caused by the ring collapse of FEG during data collection.

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C6 (6 fold cyclic) / Number of subtomograms: 17109
3D reconstructionSoftware: AV3, TOM / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: Subtomogram Averaging.

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Output model

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