+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2415 | |||||||||
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Title | Helical reconstruction of HMPV matrix protein-lipid filaments | |||||||||
Map data | Helical reconstruction of human metapneumovirus matrix protein M bound to DOPC | |||||||||
Sample |
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Keywords | human metapneumovirus / HMPV / matrix | |||||||||
Function / homology | Function and homology information virion assembly / viral envelope / host cell plasma membrane / identical protein binding / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Human metapneumovirus / synthetic construct (others) | |||||||||
Method | helical reconstruction / negative staining / Resolution: 28.0 Å | |||||||||
Authors | Leyrat C / Renner M / Harlos K / Huiskonen JT / Grimes JM | |||||||||
Citation | Journal: Structure / Year: 2014 Title: Structure and self-assembly of the calcium binding matrix protein of human metapneumovirus. Authors: Cedric Leyrat / Max Renner / Karl Harlos / Juha T Huiskonen / Jonathan M Grimes / Abstract: The matrix protein (M) of paramyxoviruses plays a key role in determining virion morphology by directing viral assembly and budding. Here, we report the crystal structure of the human metapneumovirus ...The matrix protein (M) of paramyxoviruses plays a key role in determining virion morphology by directing viral assembly and budding. Here, we report the crystal structure of the human metapneumovirus M at 2.8 Å resolution in its native dimeric state. The structure reveals the presence of a high-affinity Ca²⁺ binding site. Molecular dynamics simulations (MDS) predict a secondary lower-affinity site that correlates well with data from fluorescence-based thermal shift assays. By combining small-angle X-ray scattering with MDS and ensemble analysis, we captured the structure and dynamics of M in solution. Our analysis reveals a large positively charged patch on the protein surface that is involved in membrane interaction. Structural analysis of DOPC-induced polymerization of M into helical filaments using electron microscopy leads to a model of M self-assembly. The conservation of the Ca²⁺ binding sites suggests a role for calcium in the replication and morphogenesis of pneumoviruses. | |||||||||
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_2415.map.gz | 55.6 MB | EMDB map data format | |
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Header (meta data) | emd-2415-v30.xml emd-2415.xml | 10.6 KB 10.6 KB | Display Display | EMDB header |
Images | emd_2415.tif | 148.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2415 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2415 | HTTPS FTP |
-Validation report
Summary document | emd_2415_validation.pdf.gz | 221.6 KB | Display | EMDB validaton report |
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Full document | emd_2415_full_validation.pdf.gz | 220.7 KB | Display | |
Data in XML | emd_2415_validation.xml.gz | 6.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2415 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2415 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2415.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Helical reconstruction of human metapneumovirus matrix protein M bound to DOPC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.1 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 : Human metapneumovirus matrix protein M bound to DOPC
Entire | Name: Human metapneumovirus matrix protein M bound to DOPC |
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Components |
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-Supramolecule #1000: Human metapneumovirus matrix protein M bound to DOPC
Supramolecule | Name: Human metapneumovirus matrix protein M bound to DOPC / type: sample / ID: 1000 / Oligomeric state: helical / Number unique components: 2 |
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-Macromolecule #1: human metapneumovirus matrix protein
Macromolecule | Name: human metapneumovirus matrix protein / type: protein_or_peptide / ID: 1 Details: matrix protein was mixed with DOPC at a final concentration of 0.4 mM Oligomeric state: dimer / Recombinant expression: Yes |
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Source (natural) | Organism: Human metapneumovirus / Strain: NL1-00 / synonym: Human metapneumovirus |
Molecular weight | Theoretical: 55 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: BL21 Rosetta2 / Recombinant plasmid: pOPINS3C |
Sequence | UniProtKB: Matrix protein / GO: virion assembly, viral envelope / InterPro: Pneumovirus matrix protein |
-Macromolecule #2: 1,2-Dioleoyl-sn-glycero-3-phosphocholine
Macromolecule | Name: 1,2-Dioleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 2 / Name.synonym: DOPC / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: synthetic construct (others) |
Chemical component information | ChemComp-PCW: |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 0.2 mg/mL |
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Buffer | pH: 7.5 / Details: 20 mM Tris, 650 mM NaCl, 1M NDSB-201 |
Staining | Type: NEGATIVE Details: Grids with adsorbed protein-lipid mixtures floated on 2% w/v uranyl acetate for 30 seconds |
Grid | Details: 300 mesh copper grid with formvar carbon film |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Average: 295 K |
Date | Jul 16, 2013 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 1 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 48387 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 0.82 µm / Nominal defocus min: 0.72 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Details | The reconstruction was calculated using Burnham-Brandeis Helical Package |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 5.16 Å Applied symmetry - Helical parameters - Δ&Phi: 56.5 ° Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: OTHER / Software - Name: Burnham-Brandeis, Helical, Package / Details: Final map was filtered to 28 angstrom resolution |
CTF correction | Details: Each micrograph |