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- EMDB-20541: CryoEM map of NA-80 Fab in complex with N9 Shangahi2 -

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Basic information

Entry
Database: EMDB / ID: EMD-20541
TitleCryoEM map of NA-80 Fab in complex with N9 Shangahi2
Map data
SampleNA-80 Fab in complex with N9 Shanghai2:
N9 Shanghai2 / NA-80 Fab / Neuraminidase / (NA-80 fragment antibody ...) x 2 / ligand
Function / homology
Function and homology information


exo-alpha-(2->3)-sialidase activity / exo-alpha-sialidase / exo-alpha-(2->6)-sialidase activity / exo-alpha-(2->8)-sialidase activity / viral budding from plasma membrane / carbohydrate metabolic process / host cell plasma membrane / virion membrane / integral component of membrane / metal ion binding
Glycoside hydrolase, family 34 / Sialidase, Influenza viruses A/B / Sialidase superfamily
Neuraminidase
Biological speciesInfluenza A virus (A/environment/Shanghai/S1439/2013(H7N9)) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsWard AB / Turner HL / Zhu X
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN 272201400024C United States
CitationJournal: Cell Host Microbe / Year: 2019
Title: Structural Basis of Protection against H7N9 Influenza Virus by Human Anti-N9 Neuraminidase Antibodies.
Authors: Xueyong Zhu / Hannah L Turner / Shanshan Lang / Ryan McBride / Sandhya Bangaru / Iuliia M Gilchuk / Wenli Yu / James C Paulson / James E Crowe / Andrew B Ward / Ian A Wilson /
Abstract: Influenza virus neuraminidase (NA) is a major target for small-molecule antiviral drugs. Antibodies targeting the NA surface antigen could also inhibit virus entry and egress to provide host ...Influenza virus neuraminidase (NA) is a major target for small-molecule antiviral drugs. Antibodies targeting the NA surface antigen could also inhibit virus entry and egress to provide host protection. However, our understanding of the nature and range of target epitopes is limited because of a lack of human antibody structures with influenza neuraminidase. Here, we describe crystal and cryogenic electron microscopy (cryo-EM) structures of NAs from human-infecting avian H7N9 viruses in complex with five human anti-N9 antibodies, systematically defining several antigenic sites and antibody epitope footprints. These antibodies either fully or partially block the NA active site or bind to epitopes distant from the active site while still showing neuraminidase inhibition. The inhibition of antibodies to NAs was further analyzed by glycan array and solution-based NA activity assays. Together, these structural studies provide insights into protection by anti-NA antibodies and templates for the development of NA-based influenza virus vaccines and therapeutics.
Validation ReportPDB-ID: 6pzz

SummaryFull reportAbout validation report
History
DepositionAug 1, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseDec 4, 2019-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.641
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.641
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6pzz
  • Surface level: 0.641
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20541.png

Downloads & links

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Map

FileDownload / File: emd_20541.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 288 pix.
= 296.64 Å		1.03 Å/pix.
x 288 pix.
= 296.64 Å		1.03 Å/pix.
x 288 pix.
= 296.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.641 / Movie #1: 0.641
Minimum - Maximum-0.9973722 - 1.9546124
Average (Standard dev.)0.0006580916 (±0.09035891)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 296.63998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z296.640296.640296.640
α/β/γ90.00090.00090.000
start NX/NY/NZ111-94150
NX/NY/NZ111123111
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.9971.9550.001

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Supplemental data

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Segmentation: #1

Fileemd_20541_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of CryoEM map of NA-80 Fab in complex with N9 Shanghai

Fileemd_20541_half_map_1.map
AnnotationHalf map A of CryoEM map of NA-80 Fab in complex with N9 Shanghai
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of CryoEM map of NA-80 Fab in complex with N9 Shanghai

Fileemd_20541_half_map_2.map
AnnotationHalf map B of CryoEM map of NA-80 Fab in complex with N9 Shanghai
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire NA-80 Fab in complex with N9 Shanghai2

EntireName: NA-80 Fab in complex with N9 Shanghai2 / Number of components: 7

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Component #1: protein, NA-80 Fab in complex with N9 Shanghai2

ProteinName: NA-80 Fab in complex with N9 Shanghai2 / Recombinant expression: No

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Component #2: protein, N9 Shanghai2

ProteinName: N9 Shanghai2 / Recombinant expression: No
SourceSpecies: Influenza A virus (A/environment/Shanghai/S1439/2013(H7N9))
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: protein, NA-80 Fab

ProteinName: NA-80 Fab / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Cricetinae gen. sp. (mammal)

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Component #4: protein, Neuraminidase

ProteinName: Neuraminidase / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 48.214508 kDa
SourceSpecies: Influenza A virus (A/environment/Shanghai/S1439/2013(H7N9))
Strain: A/environment/Shanghai/S1439/2013(H7N9)
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #5: protein, NA-80 fragment antibody light chain

ProteinName: NA-80 fragment antibody light chain / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 23.229693 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Cricetinae gen. sp. (mammal)

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Component #6: protein, NA-80 fragment antibody heavy chain

ProteinName: NA-80 fragment antibody heavy chain / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 23.84967 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Cricetinae gen. sp. (mammal)

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Component #7: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.88 mg/mL / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 800.0 - 2000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C4 (4 fold cyclic) / Number of projections: 11240
3D reconstructionSoftware: cryoSPARC / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Input PDB model: 5L14

5l14

Output model

6pzz

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