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- EMDB-26660: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 -
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Open data
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Basic information
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Title | Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 | |||||||||
![]() | Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 | |||||||||
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![]() | Henipavirus / Nipah virus / NiV / F / fusion / prefusion / preF / pre-F / neutralizing antibody / Fab / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
![]() | Byrne PO / McLellan JS | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for antibody recognition of vulnerable epitopes on Nipah virus F protein. Authors: Patrick O Byrne / Brian E Fisher / David R Ambrozak / Elizabeth G Blade / Yaroslav Tsybovsky / Barney S Graham / Jason S McLellan / Rebecca J Loomis / ![]() ![]() Abstract: Nipah virus (NiV) is a pathogenic paramyxovirus that causes fatal encephalitis in humans. Two envelope glycoproteins, the attachment protein (G/RBP) and fusion protein (F), facilitate entry into host ...Nipah virus (NiV) is a pathogenic paramyxovirus that causes fatal encephalitis in humans. Two envelope glycoproteins, the attachment protein (G/RBP) and fusion protein (F), facilitate entry into host cells. Due to its vital role, NiV F presents an attractive target for developing vaccines and therapeutics. Several neutralization-sensitive epitopes on the NiV F apex have been described, however the antigenicity of most of the F protein's surface remains uncharacterized. Here, we immunize mice with prefusion-stabilized NiV F and isolate ten monoclonal antibodies that neutralize pseudotyped virus. Cryo-electron microscopy reveals eight neutralization-sensitive epitopes on NiV F, four of which have not previously been described. Novel sites span the lateral and basal faces of NiV F, expanding the known library of vulnerable epitopes. Seven of ten antibodies bind the Hendra virus (HeV) F protein. Multiple sequence alignment suggests that some of these newly identified neutralizing antibodies may also bind F proteins across the Henipavirus genus. This work identifies new epitopes as targets for therapeutics, provides a molecular basis for NiV neutralization, and lays a foundation for development of new cross-reactive antibodies targeting Henipavirus F proteins. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 290.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.4 KB 18.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.2 KB | Display | ![]() |
Images | ![]() | 51 KB | ||
Masks | ![]() | 307.5 MB | ![]() | |
Filedesc metadata | ![]() | 5.9 KB | ||
Others | ![]() ![]() ![]() | 154.2 MB 285.8 MB 285.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7upbMC ![]() 7uopC ![]() 7up9C ![]() 7upaC ![]() 7updC ![]() 7upkC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.94 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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-Additional map: Additional map 1
File | emd_26660_additional_1.map | ||||||||||||
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Annotation | Additional map 1 | ||||||||||||
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-Half map: Half Map 1
File | emd_26660_half_map_1.map | ||||||||||||
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Annotation | Half Map 1 | ||||||||||||
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-Half map: Half Map 2
File | emd_26660_half_map_2.map | ||||||||||||
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Annotation | Half Map 2 | ||||||||||||
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Sample components
-Entire : Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1
Entire | Name: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 |
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Components |
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-Supramolecule #1: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1
Supramolecule | Name: Prefusion-stabilized Nipah virus fusion protein complexed with Fab 1H1 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Fusion glycoprotein F0
Macromolecule | Name: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 52.295176 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MVVILDKRCY CNLLILILMI SECSVGILHY EKLSKIGLVK GVTRKYKIKS NPLTKDIVIK MIPNVSNMSQ CTGSVMENYK TRLNGILTP IKGALEIYKN NTHDCVGDVR LAGVCMAGVA IGIATAAQIT AGVALYEAMK NADNINKLKS SIESTNEAVV K LQETAEKT ...String: MVVILDKRCY CNLLILILMI SECSVGILHY EKLSKIGLVK GVTRKYKIKS NPLTKDIVIK MIPNVSNMSQ CTGSVMENYK TRLNGILTP IKGALEIYKN NTHDCVGDVR LAGVCMAGVA IGIATAAQIT AGVALYEAMK NADNINKLKS SIESTNEAVV K LQETAEKT VYVFTALQDY INTNLVPTID KIPCKQTELS LDLALSKYLS DLLFVFGPNL QDPVSNSMTI QAISQAFGGN YE TLLRTLG YATEDFDDLL ESDSITGQII YVDLSSYYII VRVYFPILTE IQQAYIQELL PVSFNNDNSE WISIVPNFIL VRN TLISNI EIGFCLITKR SVICNQDYAT PMTNNMRECL TGSTEKCPRE LVVSSHVPRF ALSNGVLFAN CISVTCQCQT TGRA ISQSG EQTLLMIDNT TCPTAVLGNV IISLGKYLGS VNYNSEGIAI GPPVFTDKVD ISSQISSMNQ SLQQSKDYIK UniProtKB: Fusion glycoprotein F0 |
-Macromolecule #2: Fab 1H1 heavy chain
Macromolecule | Name: Fab 1H1 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 13.185511 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: VQLQQSGAEL MRPGASMKIS CKATGYTFSS YWIDWVKQRP GHGLEWIGEI LPGSGDTNYN ENFKGKAAFT ADTSSNTAYM QLTSLTSED SAVFYCARGG RYHGQGFFDY WGQGTTLTVS S |
-Macromolecule #3: Fab 1H1 light chain
Macromolecule | Name: Fab 1H1 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.681091 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: IQMTQSPASL SASVGETVTI TCRPSENVHI YLAWYQQKQG KSPQLLVYNA KTLADGVPSR FSGSASGTQF SLKINSLQPE DFGSYYCQH FWSIPYTFGG GTKLEIK |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |