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- EMDB-23562: Negative stain EM map of 1E01 Fab in complex with N2 Singapore16 -

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Basic information

Entry
Database: EMDB / ID: EMD-23562
TitleNegative stain EM map of 1E01 Fab in complex with N2 Singapore16
Map dataNegative stain EM map of 1E01 Fab in complex with N2 Singapore16
Sample
  • Complex: 1E01 antibody-Neuraminidase N2 Singapore16 complex
    • Complex: 1E01 antibody
    • Complex: Neuraminidase N2 Singapore16
Function / homology
Function and homology information


: / : / : / exo-alpha-sialidase / carbohydrate metabolic process / host cell plasma membrane / virion membrane / metal ion binding / membrane
Similarity search - Function
Glycoside hydrolase, family 34 / Neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesInfluenza A virus / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 14.9 Å
AuthorsTurner HL / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: Nat Commun / Year: 2022
Title: Antibodies targeting the neuraminidase active site inhibit influenza H3N2 viruses with an S245N glycosylation site.
Authors: Daniel Stadlbauer / Meagan McMahon / Hannah L Turner / Xueyong Zhu / Hongquan Wan / Juan Manuel Carreño / George O'Dell / Shirin Strohmeier / Zain Khalil / Marta Luksza / Harm van Bakel / ...Authors: Daniel Stadlbauer / Meagan McMahon / Hannah L Turner / Xueyong Zhu / Hongquan Wan / Juan Manuel Carreño / George O'Dell / Shirin Strohmeier / Zain Khalil / Marta Luksza / Harm van Bakel / Viviana Simon / Ali H Ellebedy / Ian A Wilson / Andrew B Ward / Florian Krammer /
Abstract: Contemporary influenza A H3N2 viruses circulating since 2016 have acquired a glycosylation site in the neuraminidase in close proximity to the enzymatic active site. Here, we investigate if this ...Contemporary influenza A H3N2 viruses circulating since 2016 have acquired a glycosylation site in the neuraminidase in close proximity to the enzymatic active site. Here, we investigate if this S245N glycosylation site, as a result of antigenic evolution, can impact binding and function of human monoclonal antibodies that target the conserved active site. While we find that a reduction in the inhibitory ability of neuraminidase active site binders is measurable, this class of broadly reactive monoclonal antibodies maintains protective efficacy in vivo.
History
DepositionMar 2, 2021-
Header (metadata) releaseMar 9, 2022-
Map releaseMar 9, 2022-
UpdateJan 11, 2023-
Current statusJan 11, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0152
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0152
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23562.png

Downloads & links

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Map

FileDownload / File: emd_23562.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of 1E01 Fab in complex with N2 Singapore16
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 160 pix.
= 283.2 Å		1.77 Å/pix.
x 160 pix.
= 283.2 Å		1.77 Å/pix.
x 160 pix.
= 283.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0152 / Movie #1: 0.0152
Minimum - Maximum-0.03598675 - 0.070487246
Average (Standard dev.)0.00015243658 (±0.005923321)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 283.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.771.771.77
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z283.200283.200283.200
α/β/γ90.00090.00090.000
start NX/NY/NZ161360275
NX/NY/NZ300237246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0360.0700.000

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Supplemental data

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Sample components

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Entire : 1E01 antibody-Neuraminidase N2 Singapore16 complex

EntireName: 1E01 antibody-Neuraminidase N2 Singapore16 complex
Components
  • Complex: 1E01 antibody-Neuraminidase N2 Singapore16 complex
    • Complex: 1E01 antibody
    • Complex: Neuraminidase N2 Singapore16

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Supramolecule #1: 1E01 antibody-Neuraminidase N2 Singapore16 complex

SupramoleculeName: 1E01 antibody-Neuraminidase N2 Singapore16 complex / type: complex / ID: 1 / Parent: 0

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Supramolecule #3: 1E01 antibody

SupramoleculeName: 1E01 antibody / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Influenza A virus

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Supramolecule #2: Neuraminidase N2 Singapore16

SupramoleculeName: Neuraminidase N2 Singapore16 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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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
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec.

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 14.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 40555
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0) / Details: bayesian polishing
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 3.0) / Details: bayesian poilishing
Final 3D classificationSoftware - Name: RELION (ver. 3.0)

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