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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 dataSharpened map
Sample
  • Complex: HeV F glycoprotein in complex with the 1F5 neutralizing antibody Fab fragment
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: 1F5 Fab light chain
    • Protein or peptide: 1F5 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNipah virus / Hendra virus / henipavirus / neutralizing antibody / monoclonal antibody / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / 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 / 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-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing 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

emd_22885.png

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)
AnnotationSharpened map
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

Histogram

Histogram (log scale)
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

Histogram

Histogram (log scale)

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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

Histogram

Histogram (log scale)

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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

Histogram

Histogram (log scale)

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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
Components
  • Complex: HeV F glycoprotein in complex with the 1F5 neutralizing antibody Fab fragment
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: 1F5 Fab light chain
    • Protein or peptide: 1F5 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HeV F glycoprotein in complex with the 1F5 neutralizing antibody ...

SupramoleculeName: HeV F glycoprotein in complex with the 1F5 neutralizing antibody Fab fragment
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Hendra henipavirus

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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: Hendra henipavirus
Molecular weightTheoretical: 59.631574 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MATQEVRLKC LLCGIIVLVL SLEGLGILHY EKLSKIGLVK GITRKYKIKS NPLTKDIVIK MIPNVSNVSK CTGTVMENYK SRLTGILSP IKGAIELYNN NTHDLVGDVK LAGVVMAGIA IGIATAAQIT AGVALYEAMK NADNINKLKS SIESTNEAVV K LQETAEKT ...String:
MATQEVRLKC LLCGIIVLVL SLEGLGILHY EKLSKIGLVK GITRKYKIKS NPLTKDIVIK MIPNVSNVSK CTGTVMENYK SRLTGILSP IKGAIELYNN NTHDLVGDVK LAGVVMAGIA IGIATAAQIT AGVALYEAMK NADNINKLKS SIESTNEAVV K LQETAEKT VYVLTALQDY INTNLVPTID QISCKQTELA LDLALSKYLS DLLFVFGPNL QDPVSNSMTI QAISQAFGGN YE TLLRTLG YATEDFDDLL ESDSIAGQIV YVDLSSYYII VRVYFPILTE IQQAYVQELL PVSFNNDNSE WISIVPNFVL IRN TLISNI EVKYCLITKK SVICNQDYAT PMTASVRECL TGSTDKCPRE LVVSSHVPRF ALSGGVLFAN CISVTCQCQT TGRA ISQSG EQTLLMIDNT TCTTVVLGNI IISLGKYLGS INYNSESIAV GPPVYTDKVD ISSQISSMNQ SLQQSKDYIK EAQKI LDTV NPSMKQIEDK IEEILSKIYH IENEIARIKK LIGEAPGGIE GRKLKETAAA KFERQHMDS

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: 1F5 Fab light chain

MacromoleculeName: 1F5 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.362713 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: QIVLTQSPAI MSASLGEAIT LTCSASSSVS YMHWYQQKSG TSPKLLIYST SNLASGVPSR FSGSGSGTFY SLTISSVEAE DAADYYCHQ WYSYPWTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK ...String:
QIVLTQSPAI MSASLGEAIT LTCSASSSVS YMHWYQQKSG TSPKLLIYST SNLASGVPSR FSGSGSGTFY SLTISSVEAE DAADYYCHQ WYSYPWTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NRNEC

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Macromolecule #3: 1F5 heavy chain

MacromoleculeName: 1F5 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 49.291246 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DVQLQESGPG LVKPSQSLSL TCSVTGYSIT SDYYWNWIRQ FPGNKLEWMG YVTYDGSNNY NPSLKNRISI TRDSSKNQFF LKLNSVISE DTATYYCARF GSSYWAMDYW GQGTSLTVSS AKTTPPSVYP LAPGSAAQTN SMVTLGCLVK GYFPEPVTVT W NSGSLSSG ...String:
DVQLQESGPG LVKPSQSLSL TCSVTGYSIT SDYYWNWIRQ FPGNKLEWMG YVTYDGSNNY NPSLKNRISI TRDSSKNQFF LKLNSVISE DTATYYCARF GSSYWAMDYW GQGTSLTVSS 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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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Startup modelType of model: OTHER / Details: cryoSPARC ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 34415
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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