+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0291 | ||||||||||||||||||||||||||||||
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Title | Immature MLV capsid hexamer structure in intact virus particles | ||||||||||||||||||||||||||||||
Map data | None | ||||||||||||||||||||||||||||||
Sample |
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Keywords | MLV / capsid / hexamer / VIRAL PROTEIN | ||||||||||||||||||||||||||||||
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 | ||||||||||||||||||||||||||||||
Biological species | Murine leukemia virus | ||||||||||||||||||||||||||||||
Method | subtomogram averaging / cryo EM / Resolution: 6.6 Å | ||||||||||||||||||||||||||||||
Authors | Qu K / Glass B | ||||||||||||||||||||||||||||||
Funding support | Germany, United Kingdom, Czech Republic, 9 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0291.map.gz | 25.1 MB | EMDB map data format | |
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Header (meta data) | emd-0291-v30.xml emd-0291.xml | 15.9 KB 15.9 KB | Display Display | EMDB header |
Images | emd_0291.png | 448.5 KB | ||
Filedesc metadata | emd-0291.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0291 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0291 | HTTPS FTP |
-Validation report
Summary document | emd_0291_validation.pdf.gz | 287.6 KB | Display | EMDB validaton report |
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Full document | emd_0291_full_validation.pdf.gz | 286.7 KB | Display | |
Data in XML | emd_0291_validation.xml.gz | 5.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0291 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0291 | HTTPS FTP |
-Related structure data
Related structure data | 6hwwMC 0290C 0292C 0293C 4419C 4421C 4422C 6gzaC 6hwiC 6hwxC 6hwyC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0291.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Murine leukemia virus
Entire | Name: Murine leukemia virus |
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Components |
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-Supramolecule #1: Murine leukemia virus
Supramolecule | Name: 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 |
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-Macromolecule #1: Putative gag polyprotein
Macromolecule | Name: Putative gag polyprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Murine leukemia virus |
Molecular weight | Theoretical: 25.418297 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: SSSDLYNWKN NNPSFSEDPG KLTALIESVL TTHQPTWDDC QQLLGTLLTG EEKQRVLLEA RKAVRGNDGR PTQLPNEVDA AFPLERPDW DYTTQRGRNH LVLYRQLLLA GMQNAGRSPT NLAKVKGITQ GPNESPSAFL ERLKEAYRRY TPYDPEDPGQ E TNVSMSFI ...String: SSSDLYNWKN NNPSFSEDPG KLTALIESVL TTHQPTWDDC QQLLGTLLTG EEKQRVLLEA RKAVRGNDGR PTQLPNEVDA AFPLERPDW DYTTQRGRNH LVLYRQLLLA GMQNAGRSPT NLAKVKGITQ GPNESPSAFL ERLKEAYRRY TPYDPEDPGQ E TNVSMSFI WQSAPDIGRK LERLEDLKSK TLGDLVREAE KIFNKRETPE EREERIRRET EEK UniProtKB: Putative gag polyprotein |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6 |
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Grid | Model: C-flat-2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK II |
Details | Purified virus solution was inactivated and diluted 1:1 with PBS containing 10 nm colloidal gold. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-6 / Number grids imaged: 1 / Average exposure time: 0.6 sec. / Average electron dose: 2.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: AV3, TOM) / Number subtomograms used: 23141 | ||||||
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Extraction | Number tomograms: 20 / Number images used: 23141 Software:
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Final angle assignment | Type: OTHER / Software: (Name: AV3, TOM) / Details: Subtomogram Averaging. |
-Atomic model buiding 1
Initial model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT | ||||||
Output model | PDB-6hww: |