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- EMDB-9144: Negative Stain EM map of uncleaved H7 New York in complex with H7... -

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Basic information

Entry
Database: EMDB / ID: EMD-9144
TitleNegative Stain EM map of uncleaved H7 New York in complex with H7.5 Fab
Map dataNegative stain EM map of uncleaved H7 New York in complex with H7.5 Fab
Sample
  • Complex: Negative stain EM map of uncleaved H7 New York in complex with H7.5 Fab
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsWard AB / Turner HL
CitationJournal: PLoS Biol / Year: 2019
Title: Potent anti-influenza H7 human monoclonal antibody induces separation of hemagglutinin receptor-binding head domains.
Authors: Hannah L Turner / Jesper Pallesen / Shanshan Lang / Sandhya Bangaru / Sarah Urata / Sheng Li / Christopher A Cottrell / Charles A Bowman / James E Crowe / Ian A Wilson / Andrew B Ward /
Abstract: Seasonal influenza virus infections can cause significant morbidity and mortality, but the threat from the emergence of a new pandemic influenza strain might have potentially even more devastating ...Seasonal influenza virus infections can cause significant morbidity and mortality, but the threat from the emergence of a new pandemic influenza strain might have potentially even more devastating consequences. As such, there is intense interest in isolating and characterizing potent neutralizing antibodies that target the hemagglutinin (HA) viral surface glycoprotein. Here, we use cryo-electron microscopy (cryoEM) to decipher the mechanism of action of a potent HA head-directed monoclonal antibody (mAb) bound to an influenza H7 HA. The epitope of the antibody is not solvent accessible in the compact, prefusion conformation that typifies all HA structures to date. Instead, the antibody binds between HA head protomers to an epitope that must be partly or transiently exposed in the prefusion conformation. The "breathing" of the HA protomers is implied by the exposure of this epitope, which is consistent with metastability of class I fusion proteins. This structure likely therefore represents an early structural intermediate in the viral fusion process. Understanding the extent of transient exposure of conserved neutralizing epitopes also may lead to new opportunities to combat influenza that have not been appreciated previously.
History
DepositionSep 27, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseFeb 20, 2019-
UpdateFeb 20, 2019-
Current statusFeb 20, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 56
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 56
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9144.png

Downloads & links

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Map

FileDownload / File: emd_9144.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of uncleaved H7 New York in complex with H7.5 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 128 pix.
= 262.4 Å		2.05 Å/pix.
x 128 pix.
= 262.4 Å		2.05 Å/pix.
x 128 pix.
= 262.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 56.0 / Movie #1: 56
Minimum - Maximum-99.481949999999998 - 177.110520000000008
Average (Standard dev.)1.4373949 (±15.325771)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z262.400262.400262.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-99.482177.1111.437

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Supplemental data

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Sample components

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Entire : Negative stain EM map of uncleaved H7 New York in complex with H7...

EntireName: Negative stain EM map of uncleaved H7 New York in complex with H7.5 Fab
Components
  • Complex: Negative stain EM map of uncleaved H7 New York in complex with H7.5 Fab

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Supramolecule #1: Negative stain EM map of uncleaved H7 New York in complex with H7...

SupramoleculeName: Negative stain EM map of uncleaved H7 New York in complex with H7.5 Fab
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F

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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: 7.4
StainingType: NEGATIVE / Material: Uranyl Formate
GridPretreatment - Type: GLOW DISCHARGE / Details: unspecified

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Detector mode: COUNTING / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPARX / Number images used: 17851
Initial angle assignmentType: OTHER / Software - Name: EMAN2 (ver. 1.4)
Final angle assignmentType: OTHER

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