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- EMDB-2415: Helical reconstruction of HMPV matrix protein-lipid filaments -

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Basic information

Entry
Database: EMDB / ID: EMD-2415
TitleHelical reconstruction of HMPV matrix protein-lipid filaments
Map dataHelical reconstruction of human metapneumovirus matrix protein M bound to DOPC
Sample
  • Sample: Human metapneumovirus matrix protein M bound to DOPC
  • Protein or peptide: human metapneumovirus matrix protein
  • Ligand: 1,2-Dioleoyl-sn-glycero-3-phosphocholine
Keywordshuman metapneumovirus / HMPV / matrix
Function / homology
Function and homology information


virion assembly / structural constituent of virion / host cell cytoplasm / viral envelope / host cell nucleus / host cell plasma membrane / metal ion binding / identical protein binding
Similarity search - Function
Pneumovirus matrix protein / Pneumovirus matrix protein / Pneumovirus matrix, N-terminal / : / Pneumovirus matrix protein N-terminal domain / Pneumovirus matrix protein C-terminal domain
Similarity search - Domain/homology
Biological speciesHuman metapneumovirus / synthetic construct (others)
Methodhelical reconstruction / negative staining / Resolution: 28.0 Å
AuthorsLeyrat C / Renner M / Harlos K / Huiskonen JT / Grimes JM
CitationJournal: 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
DepositionJul 16, 2013-
Header (metadata) releaseAug 14, 2013-
Map releaseDec 18, 2013-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2415.tif

Downloads & links

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Map

FileDownload / File: emd_2415.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical reconstruction of human metapneumovirus matrix protein M bound to DOPC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.1 Å/pix.
x 256 pix.
= 793.6 Å		3.1 Å/pix.
x 256 pix.
= 793.6 Å		3.1 Å/pix.
x 256 pix.
= 793.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-6.34101105 - 10.958843229999999
Average (Standard dev.)0.02637818 (±1.23229754)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 793.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.13.13.1
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z793.600793.600793.600
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-6.34110.9590.026

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Supplemental data

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Sample components

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Entire : Human metapneumovirus matrix protein M bound to DOPC

EntireName: Human metapneumovirus matrix protein M bound to DOPC
Components
  • Sample: Human metapneumovirus matrix protein M bound to DOPC
  • Protein or peptide: human metapneumovirus matrix protein
  • Ligand: 1,2-Dioleoyl-sn-glycero-3-phosphocholine

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Supramolecule #1000: Human metapneumovirus matrix protein M bound to DOPC

SupramoleculeName: 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

MacromoleculeName: 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
Source (natural)Organism: Human metapneumovirus / Strain: NL1-00 / synonym: Human metapneumovirus
Molecular weightTheoretical: 55 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21 Rosetta2 / Recombinant plasmid: pOPINS3C
SequenceUniProtKB: Matrix protein / GO: virion assembly, viral envelope / InterPro: Pneumovirus matrix protein

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Macromolecule #2: 1,2-Dioleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1,2-Dioleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 2 / Name.synonym: DOPC / Recombinant expression: No / Database: NCBI
Source (natural)Organism: synthetic construct (others)
Chemical component information

ChemComp-PCW:
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / DOPC, phospholipid*YM

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Experimental details

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Structure determination

Methodnegative staining
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5 / Details: 20 mM Tris, 650 mM NaCl, 1M NDSB-201
StainingType: NEGATIVE
Details: Grids with adsorbed protein-lipid mixtures floated on 2% w/v uranyl acetate for 30 seconds
GridDetails: 300 mesh copper grid with formvar carbon film
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureAverage: 295 K
DateJul 16, 2013
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 1 / Bits/pixel: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated 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 stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

DetailsThe reconstruction was calculated using Burnham-Brandeis Helical Package
Final reconstructionApplied 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 correctionDetails: Each micrograph

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