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- EMDB-22884: Structure of the NiV F glycoprotein in complex with the 12B2 neut... -

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Basic information

Entry
Database: EMDB / ID: EMD-22884
TitleStructure of the NiV F glycoprotein in complex with the 12B2 neutralizing antibody
Map dataSharpened map
Sample
  • Complex: NiV F glycoprotein in complex with the 12B2 neutralizing antibody Fab fragment
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: 12B2 Fab light chain
    • Protein or peptide: 12B2 heavy chain
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesNipah virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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: 0.9
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ki4
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ki4
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22884.png

Downloads & links

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Map

FileDownload / File: emd_22884.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.9 / Movie #1: 0.9
Minimum - Maximum-3.2331254 - 5.06676
Average (Standard dev.)0.0034426998 (±0.087210074)
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-3.2335.0670.003

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Supplemental data

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Additional map: Unsharpened map

Fileemd_22884_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_22884_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_22884_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NiV F glycoprotein in complex with the 12B2 neutralizing antibody...

EntireName: NiV F glycoprotein in complex with the 12B2 neutralizing antibody Fab fragment
Components
  • Complex: NiV F glycoprotein in complex with the 12B2 neutralizing antibody Fab fragment
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: 12B2 Fab light chain
    • Protein or peptide: 12B2 heavy chain

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Supramolecule #1: NiV F glycoprotein in complex with the 12B2 neutralizing antibody...

SupramoleculeName: NiV F glycoprotein in complex with the 12B2 neutralizing antibody Fab fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Nipah virus
Recombinant expressionOrganism: Homo sapiens (human)
Recombinant expressionOrganism: Mus musculus (house mouse)

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Nipah virus
Molecular weightTheoretical: 60.028074 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVVILDKRCY CNLLILILMI SECSVGILHY EKLSKIGLVK GVTRKYKIKS NPLTKDIVIK MIPNVSNMSQ CTGSVMENYK TRLNGILTP IKGALEIYKN NTHDLVGDVR LAGVIMAGVA IGIATAAQIT AGVALYEAMK NADNINKLKS SIESTNEAVV K LQETAEKT ...String:
MVVILDKRCY CNLLILILMI SECSVGILHY EKLSKIGLVK GVTRKYKIKS NPLTKDIVIK MIPNVSNMSQ CTGSVMENYK TRLNGILTP IKGALEIYKN NTHDLVGDVR LAGVIMAGVA IGIATAAQIT AGVALYEAMK NADNINKLKS SIESTNEAVV K LQETAEKT VYVLTALQDY INTNLVPTID KISCKQTELS LDLALSKYLS DLLFVFGPNL QDPVSNSMTI QAISQAFGGN YE TLLRTLG YATEDFDDLL ESDSITGQII YVDLSSYYII VRVYFPILTE IQQAYIQELL PVSFNNDDSE WISIVPNFIL VRN TLISNI EIGFCLITKR SVICNQDYAT PMTNNMRECL TGSTEKCPRE LVVSSHVPRF ALSNGVLFAN CISVTCQCQT TGRA ISQSG EQTLLMIDNT TCPTAVLGNV IISLGKYLGS VNYNSEGIAI GPPVFTDKVD ISSQISSMNQ SLQQSKDYIK EAQRL LDTV NPSMKQIEDK IEEILSKIYH IENEIARIKK LIGEAPGGIE GRKLKETAAA KFERQHMDS

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Macromolecule #2: 12B2 Fab light chain

MacromoleculeName: 12B2 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.657051 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DIQMTQSPAS LSASVGETVT ITCRASENIY SYLAWYQHKQ GKSPQLLVYN AKSLAEGVPS RFSGSGSGTQ FSLKINSLQP EDFGSYYCQ HHYGTPWTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIQMTQSPAS LSASVGETVT ITCRASENIY SYLAWYQHKQ GKSPQLLVYN AKSLAEGVPS RFSGSGSGTQ FSLKINSLQP EDFGSYYCQ HHYGTPWTFG GGTKLEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

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Macromolecule #3: 12B2 heavy chain

MacromoleculeName: 12B2 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 48.630758 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: QVQLKESGPG LVAPSQSLSI TCTVSGFSLA SYGVHWVRQP PGKGLEWLGV IWTGGSTNYN SALMSRLSIN RDNSKSQVFL KLNSLQTDD TAIYYCARDR GYGYGGFAYW GQGTLVTVSA AKTTPPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSLSSG ...String:
QVQLKESGPG LVAPSQSLSI TCTVSGFSLA SYGVHWVRQP PGKGLEWLGV IWTGGSTNYN SALMSRLSIN RDNSKSQVFL KLNSLQTDD TAIYYCARDR GYGYGGFAYW GQGTLVTVSA AKTTPPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSLSSG VHTFPAVLQS DLYTLSSSVT VPSSTWPSET VTCNVAHPAS STKVDKKIVP RDCGCKPCIC TVPEVSSVFI FP PKPKDVL TITLTPKVTC VVVDISKDDP EVQFSWFVDD VEVHTAQTQP REEQFNSTFR SVSELPIMHQ DWLNGKEFKC RVN SAAFPA PIEKTISKTK GRPKAPQVYT IPPPKEQMAK DKVSLTCMIT DFFPEDITVE WQWNGQPAEN YKNTQPIMDT DGSY FVYSK LNVQKSNWEA GNTFTCSVLH EGLHNHHTEK SLSHSPGK

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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: 8
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 70.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: cryoSPARC ab initio
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 28776

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