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- EMDB-8770: Negative stain of influenza B virus recombinant neuraminidase -

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Basic information

Entry
Database: EMDB / ID: EMD-8770
TitleNegative stain of influenza B virus recombinant neuraminidase
Map dataInfluenza B virus neuraminidase
Sample
  • Complex: Influenza B neuraminidase
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / exo-alpha-sialidase / carbohydrate metabolic process / host cell plasma membrane / virion membrane / membrane / metal ion binding
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza B virus (B/Malaysia/2506/2004)
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsPodolsky K / Subramaniam S
CitationJournal: Nat Microbiol / Year: 2017
Title: Broadly protective murine monoclonal antibodies against influenza B virus target highly conserved neuraminidase epitopes.
Authors: Teddy John Wohlbold / Kira A Podolsky / Veronika Chromikova / Ericka Kirkpatrick / Veronica Falconieri / Philip Meade / Fatima Amanat / Jessica Tan / Benjamin R tenOever / Gene S Tan / ...Authors: Teddy John Wohlbold / Kira A Podolsky / Veronika Chromikova / Ericka Kirkpatrick / Veronica Falconieri / Philip Meade / Fatima Amanat / Jessica Tan / Benjamin R tenOever / Gene S Tan / Sriram Subramaniam / Peter Palese / Florian Krammer /
Abstract: A substantial proportion of influenza-related childhood deaths are due to infection with influenza B viruses, which co-circulate in the human population as two antigenically distinct lineages defined ...A substantial proportion of influenza-related childhood deaths are due to infection with influenza B viruses, which co-circulate in the human population as two antigenically distinct lineages defined by the immunodominant receptor binding protein, haemagglutinin. While broadly cross-reactive, protective monoclonal antibodies against the haemagglutinin of influenza B viruses have been described, none targeting the neuraminidase, the second most abundant viral glycoprotein, have been reported. Here, we analyse a panel of five murine anti-neuraminidase monoclonal antibodies that demonstrate broad binding, neuraminidase inhibition, in vitro antibody-dependent cell-mediated cytotoxicity and in vivo protection against influenza B viruses belonging to both haemagglutinin lineages and spanning over 70 years of antigenic drift. Electron microscopic analysis of two neuraminidase-antibody complexes shows that the conserved neuraminidase epitopes are located on the head of the molecule and that they are distinct from the enzymatic active site. In the mouse model, one therapeutic dose of antibody 1F2 was more protective than the current standard of treatment, oseltamivir, given twice daily for six days.
History
DepositionJun 15, 2017-
Header (metadata) releaseJul 19, 2017-
Map releaseJul 19, 2017-
UpdateNov 1, 2017-
Current statusNov 1, 2017Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.272
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.272
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8770.png

Downloads & links

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Map

FileDownload / File: emd_8770.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationInfluenza B virus neuraminidase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.8 Å/pix.
x 200 pix.
= 360. Å		1.8 Å/pix.
x 200 pix.
= 360. Å		1.8 Å/pix.
x 200 pix.
= 360. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.272 / Movie #1: 0.272
Minimum - Maximum-0.08471556 - 0.59615093
Average (Standard dev.)0.0033397425 (±0.030446896)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 360.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.81.81.8
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z360.000360.000360.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0850.5960.003

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Supplemental data

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Sample components

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Entire : Influenza B neuraminidase

EntireName: Influenza B neuraminidase
Components
  • Complex: Influenza B neuraminidase

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Supramolecule #1: Influenza B neuraminidase

SupramoleculeName: Influenza B neuraminidase / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Influenza B virus (B/Malaysia/2506/2004)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.3
StainingType: NEGATIVE / Material: Uranyl formate

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 100.0 e/Å2

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: RELION (ver. 1.4)
Details: The standard Fourier Shell Correlation-based measures for resolution are generally not very reliable for negative stain reconstructions because they tend to overestimate resolution and can ...Details: The standard Fourier Shell Correlation-based measures for resolution are generally not very reliable for negative stain reconstructions because they tend to overestimate resolution and can result in spurious values that depend on data size rather than quality, a feature that is also true for cryo-EM reconstructions (some of these issues are discussed in Subramaniam et al, Curr Opin Str. Biol 41: 194-202 (2016)). In negative stain reconstructions, we therefore use a comparison of the experimentally obtained maps with maps computed from the fitted coordinates over a range of resolutions and use this to estimate resolution conservatively. The computed maps at 20 A and 25 A are easily comparable to an experimentally obtained map, which is why we used 25 A as an estimate for resolution.
Number images used: 47592

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