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- EMDB-0292: Mature MLV capsid hexamer structure in intact virus particles -

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Basic information

Entry
Database: EMDB / ID: EMD-0292
TitleMature MLV capsid hexamer structure in intact virus particles
Map dataNone
Sample
  • Virus: Murine leukemia virus
    • Protein or peptide: Putative gag polyproteinGroup-specific antigen
Function / homology
Function and homology information


virion assembly / viral budding via host ESCRT complex / host multivesicular body / viral nucleocapsid / structural constituent of virion / nucleic acid binding / host cell plasma membrane / RNA binding / zinc ion binding / membrane
Similarity search - Function
Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger ...Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Putative gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesMurine leukemia 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 15, 2018-
Header (metadata) releaseNov 28, 2018-
Map releaseDec 5, 2018-
UpdateApr 3, 2019-
Current statusApr 3, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0919
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0919
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6hwx
  • Surface level: 0.0919
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6hwx
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0292.png

Downloads & links

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Map

FileDownload / File: emd_0292.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: 0.0919 / Movie #1: 0.0919
Minimum - Maximum-0.13294029 - 0.28723255
Average (Standard dev.)0.00076356734 (±0.026249535)
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-0.1330.2870.001

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Supplemental data

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Sample components

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Entire : Murine leukemia virus

EntireName: Murine leukemia virus
Components
  • Virus: Murine leukemia virus
    • Protein or peptide: Putative gag polyproteinGroup-specific antigen

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Supramolecule #1: Murine leukemia virus

SupramoleculeName: Murine leukemia virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 11786 / Sci species name: Murine leukemia virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host systemOrganism: Homo sapiens (human) / Recombinant cell: HEK 293T / Recombinant plasmid: M2204

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Macromolecule #1: Putative gag polyprotein

MacromoleculeName: Putative gag polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Murine leukemia virus
Molecular weightTheoretical: 27.165305 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PLRMGGNGQL QYWPFSSSDL YNWKNNNPSF SEDPGKLTAL IESVLTTHQP TWDDCQQLLG TLLTGEEKQR VLLEARKAVR GNDGRPTQL PNEVDAAFPL ERPDWDYTTQ RGRNHLVLYR QLLLAGMQNA GRSPTNLAKV KGITQGPNES PSAFLERLKE A YRRYTPYD ...String:
PLRMGGNGQL QYWPFSSSDL YNWKNNNPSF SEDPGKLTAL IESVLTTHQP TWDDCQQLLG TLLTGEEKQR VLLEARKAVR GNDGRPTQL PNEVDAAFPL ERPDWDYTTQ RGRNHLVLYR QLLLAGMQNA GRSPTNLAKV KGITQGPNES PSAFLERLKE A YRRYTPYD PEDPGQETNV SMSFIWQSAP DIGRKLERLE DLKSKTLGDL VREAEKIFNK RETPEEREER IRRETEEK

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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
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: 7.5 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: 2 / Average exposure time: 0.6 sec. / Average electron dose: 1.8 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: 65 / Number images used: 23397
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) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 7.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: AV3, TOM) / Number subtomograms used: 23397

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Atomic model buiding 1

Initial model
PDB IDChain

1u7k

chain_id: A, residue_range: 1-131

6gza

chain_id: A, residue_range: 1-87
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6hwx:
Mature MLV capsid hexamer structure in intact virus particles

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