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- EMDB-9143: CryoEM map of cleaved H7 Netherlands in complex with H7.5 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-9143
TitleCryoEM map of cleaved H7 Netherlands in complex with H7.5 Fab
Map dataCryoEM map of cleaved H7 Netherlands in complex with H7.5 Fab
Sample
  • Complex: CryoEM map of cleaved H7 Netherlands in complex with H7.5 Fab
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.2 Å
AuthorsWard AB / Turner HL / Pallesen J
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 31, 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: 0.0334
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0334
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9143.png

Downloads & links

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Map

FileDownload / File: emd_9143.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of cleaved H7 Netherlands in complex with H7.5 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 256 pix.
= 294.4 Å		1.15 Å/pix.
x 256 pix.
= 294.4 Å		1.15 Å/pix.
x 256 pix.
= 294.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0334 / Movie #1: 0.0334
Minimum - Maximum-0.006960726 - 0.06858502
Average (Standard dev.)0.0007548503 (±0.0053966884)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 294.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z294.400294.400294.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0070.0690.001

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Supplemental data

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Sample components

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Entire : CryoEM map of cleaved H7 Netherlands in complex with H7.5 Fab

EntireName: CryoEM map of cleaved H7 Netherlands in complex with H7.5 Fab
Components
  • Complex: CryoEM map of cleaved H7 Netherlands in complex with H7.5 Fab

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Supramolecule #1: CryoEM map of cleaved H7 Netherlands in complex with H7.5 Fab

SupramoleculeName: CryoEM map of cleaved H7 Netherlands 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

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: EMDB MAP / Details: Our map of H7 HA0 was low-pass filtered to 40A.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 25146
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 1.4)

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