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- EMDB-4421: Representative tomogram of immature M-PMV particles -

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Basic information

Database: EMDB / ID: 4421
TitleRepresentative tomogram of immature M-PMV particles
Map dataRepresentative tomogram of immature M-PMV particles for subtomogram averaging
SampleMason-Pfizer monkey virusSimian retrovirus:
SourceMason-Pfizer monkey 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: Oct 24, 2018 / Map release: Dec 5, 2018 / Last update: Dec 19, 2018

Structure visualization

  • 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


Fileemd_4421.map.gz (map file in CCP4 format, 5368000 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
780 pix
2.7 Å/pix.
= 2106. Å
1855 pix
2.7 Å/pix.
= 5008.5 Å
1855 pix
2.7 Å/pix.
= 5008.5 Å


Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Minimum - Maximum-1004.0 - 1004.0
Average (Standard dev.)4.9462495 (158.223890000000011)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 5008.5 Å / B: 5008.5 Å / C: 2106.0 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/z18551855780
origin x/y/z0.0000.0000.000
length x/y/z5008.5005008.5002106.000
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-1-1-1
D min/max/mean-1004.0001004.0004.946

Supplemental data

Sample components

Entire Mason-Pfizer monkey virus

EntireName: Mason-Pfizer monkey virus / Number of components: 1

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

Experimental details

Sample preparation

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

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
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

Image acquisition

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

Image processing

ProcessingMethod: electron tomography / Number of sections: 41
3D reconstructionSoftware: eTomo

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