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- EMDB-22885: Structure of the HeV F glycoprotein in complex with the 1F5 neutr... -

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Basic information

Entry
Database: EMDB / ID: EMD-22885
TitleStructure of the HeV F glycoprotein in complex with the 1F5 neutralizing antibody
Map data
SampleHeV F glycoprotein in complex with the 1F5 neutralizing antibody Fab fragment:
Fusion glycoprotein F0 / 1F5 Fab light chain / 1F5 heavy chain / ligand
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / integral component of membrane / plasma membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesHendra henipavirus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsDang HV / Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Veesler D
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)DP1AI158186 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120553 United States
CitationJournal: Nat Struct Mol Biol / Year: 2021
Title: Broadly neutralizing antibody cocktails targeting Nipah virus and Hendra virus fusion glycoproteins.
Authors: Ha V Dang / Robert W Cross / Viktoriya Borisevich / Zachary A Bornholdt / Brandyn R West / Yee-Peng Chan / Chad E Mire / Sofia Cheliout Da Silva / Antony S Dimitrov / Lianying Yan / Moushimi ...Authors: Ha V Dang / Robert W Cross / Viktoriya Borisevich / Zachary A Bornholdt / Brandyn R West / Yee-Peng Chan / Chad E Mire / Sofia Cheliout Da Silva / Antony S Dimitrov / Lianying Yan / Moushimi Amaya / Chanakha K Navaratnarajah / Larry Zeitlin / Thomas W Geisbert / Christopher C Broder / David Veesler /
Abstract: Hendra virus (HeV) and Nipah virus (NiV) are henipaviruses (HNVs) causing respiratory illness and severe encephalitis in humans, with fatality rates of 50-100%. There are no licensed therapeutics or ...Hendra virus (HeV) and Nipah virus (NiV) are henipaviruses (HNVs) causing respiratory illness and severe encephalitis in humans, with fatality rates of 50-100%. There are no licensed therapeutics or vaccines to protect humans. HeV and NiV use a receptor-binding glycoprotein (G) and a fusion glycoprotein (F) to enter host cells. HNV F and G are the main targets of the humoral immune response, and the presence of neutralizing antibodies is a correlate of protection against NiV and HeV in experimentally infected animals. We describe here two cross-reactive F-specific antibodies, 1F5 and 12B2, that neutralize NiV and HeV through inhibition of membrane fusion. Cryo-electron microscopy structures reveal that 1F5 and 12B2 recognize distinct prefusion-specific, conserved quaternary epitopes and lock F in its prefusion conformation. We provide proof-of-concept for using antibody cocktails for neutralizing NiV and HeV and define a roadmap for developing effective countermeasures against these highly pathogenic viruses.
History
DepositionOct 23, 2020-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ki6
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ki6
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_22885.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 352 pix.
= 369.6 Å
1.05 Å/pix.
x 352 pix.
= 369.6 Å
1.05 Å/pix.
x 352 pix.
= 369.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-4.5928073 - 6.278195
Average (Standard dev.)0.0036393902 (±0.11448228)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 369.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z369.600369.600369.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-4.5936.2780.004

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Supplemental data

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Additional map: Unsharpened map

Fileemd_22885_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map A

Fileemd_22885_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map B

Fileemd_22885_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire HeV F glycoprotein in complex with the 1F5 neutralizing antibody ...

EntireName: HeV F glycoprotein in complex with the 1F5 neutralizing antibody Fab fragment
Number of components: 5

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Component #1: protein, HeV F glycoprotein in complex with the 1F5 neutralizing ...

ProteinName: HeV F glycoprotein in complex with the 1F5 neutralizing antibody Fab fragment
Recombinant expression: No
SourceSpecies: Hendra henipavirus
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Fusion glycoprotein F0

ProteinName: Fusion glycoprotein F0 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 59.631574 kDa
SourceSpecies: Hendra henipavirus
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, 1F5 Fab light chain

ProteinName: 1F5 Fab light chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 23.362713 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Mus musculus (house mouse)

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Component #4: protein, 1F5 heavy chain

ProteinName: 1F5 heavy chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 49.291246 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Mus musculus (house mouse)

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Component #5: ligand, 2-acetamido-2-deoxy-beta-D-glucopyranose

LigandName: 2-acetamido-2-deoxy-beta-D-glucopyranose / Number of Copies: 6 / 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 solutionpH: 8
VitrificationCryogen 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: 70 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 34415
3D reconstructionSoftware: cryoSPARC / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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