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- EMDB-4422: Representative tomogram of immature MLV particles -

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Basic information

Entry
Database: EMDB / ID: 4422
TitleRepresentative tomogram of immature MLV particles
Map dataRepresentative tomogram of immature MLV particles for subtomogram averaging
SampleMurine leukemia virus:
virus
SourceMurine leukemia virus
Methodelectron tomography / cryo EM
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.
DateDeposition: Nov 14, 2018 / Header (metadata) release: Dec 5, 2018 / Map release: Dec 5, 2018 / Last update: Dec 5, 2018

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

Downloads & links

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Map

Fileemd_4422.map.gz (map file in CCP4 format, 5574461 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
810 pix
2.7 Å/pix.
= 2187. Å
1855 pix
2.7 Å/pix.
= 5008.5 Å
1855 pix
2.7 Å/pix.
= 5008.5 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Density
Minimum - Maximum-1127.0 - 1224.0
Average (Standard dev.)6.217764 (186.0428)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions18551855810
Origin-1.0-1.0-1.0
Limit1853.01853.0808.0
Spacing18551855810
CellA: 5008.5 Å / B: 5008.5 Å / C: 2187.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z2.72.72.7
M x/y/z18551855810
origin x/y/z0.0000.0000.000
length x/y/z5008.5005008.5002187.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS-1-1-1
NC/NR/NS18551855810
D min/max/mean-1127.0001224.0006.218

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Supplemental data

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Sample components

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Entire Murine leukemia virus

EntireName: Murine leukemia virus / Number of components: 1

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Component #1: virus, Murine leukemia virus

VirusName: Murine leukemia virus / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Murine leukemia virus
Source (engineered)Expression System: Homo sapiens (human) / Vector: M2204 / Cell of expression system: HEK 293T

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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: 2.5 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

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Image processing

ProcessingMethod: electron tomography / Number of sections: 40
3D reconstructionSoftware: eTomo

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