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- EMDB-44873: EBOV GP/Nanosota-EB2 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-44873
TitleEBOV GP/Nanosota-EB2 complex
Map dataunsharpened map of EBOV GP/Nanosota-EB2
Sample
  • Complex: EBOV GP/Nanosota-EB2 complex
    • Complex: Nanosota-EB2
      • Protein or peptide: Nanosota-EB2
    • Complex: EBOV glycoprotein
      • Protein or peptide: Envelope glycoprotein
  • Ligand: alpha-D-mannopyranose
KeywordsEBOV glycoprotein / nanobody / VIRAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated killing of host cell / host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / fusion of virus membrane with host endosome membrane ...symbiont-mediated killing of host cell / host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / symbiont entry into host cell / host cell plasma membrane / virion membrane / extracellular region / identical protein binding
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesVicugna pacos (alpaca) / Ebola virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBu F / Ye G / Liu B / Li F
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI089728 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI110700 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI171954 United States
CitationJournal: PLoS Pathog / Year: 2024
Title: Discovery of Nanosota-EB1 and -EB2 as Novel Nanobody Inhibitors Against Ebola Virus Infection.
Authors: Fan Bu / Gang Ye / Kimberly Morsheimer / Alise Mendoza / Hailey Turner-Hubbard / Morgan Herbst / Benjamin Spiller / Brian E Wadzinski / Brett Eaton / Manu Anantpadma / Ge Yang / Bin Liu / ...Authors: Fan Bu / Gang Ye / Kimberly Morsheimer / Alise Mendoza / Hailey Turner-Hubbard / Morgan Herbst / Benjamin Spiller / Brian E Wadzinski / Brett Eaton / Manu Anantpadma / Ge Yang / Bin Liu / Robert Davey / Fang Li /
Abstract: The Ebola filovirus (EBOV) poses a serious threat to global health and national security. Nanobodies, a type of single-domain antibody, have demonstrated promising therapeutic potential. We ...The Ebola filovirus (EBOV) poses a serious threat to global health and national security. Nanobodies, a type of single-domain antibody, have demonstrated promising therapeutic potential. We identified two anti-EBOV nanobodies, Nanosota-EB1 and Nanosota-EB2, which specifically target the EBOV glycoprotein (GP). Cryo-EM and biochemical data revealed that Nanosota-EB1 binds to the glycan cap of GP1, preventing its protease cleavage, while Nanosota-EB2 binds to critical membrane-fusion elements in GP2, stabilizing it in the pre-fusion state. Nanosota-EB2 is a potent neutralizer of EBOV infection in vitro and offers excellent protection in a mouse model of EBOV challenge, while Nanosota-EB1 provides moderate neutralization and protection. Nanosota-EB1 and Nanosota-EB2 are the first nanobodies shown to inhibit authentic EBOV. Combined with our newly developed structure-guided in vitro evolution approach, they lay the foundation for nanobody-based therapies against EBOV and other viruses within the ebolavirus genus.
History
DepositionMay 13, 2024-
Header (metadata) releaseDec 18, 2024-
Map releaseDec 18, 2024-
UpdateJan 29, 2025-
Current statusJan 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44873.png

Downloads & links

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Map

FileDownload / File: emd_44873.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map of EBOV GP/Nanosota-EB2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 320 pix.
= 283.307 Å		0.89 Å/pix.
x 320 pix.
= 283.307 Å		0.89 Å/pix.
x 320 pix.
= 283.307 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88533 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.079
Minimum - Maximum-0.36039776 - 0.66762775
Average (Standard dev.)0.000036431797 (±0.015687631)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 283.30664 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map of EBOV GP/Nanosota-EB2

Fileemd_44873_additional_1.map
Annotationsharpened map of EBOV GP/Nanosota-EB2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A of EBOV GP/Nanosota-EB2

Fileemd_44873_half_map_1.map
Annotationhalf map_A of EBOV GP/Nanosota-EB2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B of EBOV GP/Nanosota-EB2

Fileemd_44873_half_map_2.map
Annotationhalf map_B of EBOV GP/Nanosota-EB2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : EBOV GP/Nanosota-EB2 complex

EntireName: EBOV GP/Nanosota-EB2 complex
Components
  • Complex: EBOV GP/Nanosota-EB2 complex
    • Complex: Nanosota-EB2
      • Protein or peptide: Nanosota-EB2
    • Complex: EBOV glycoprotein
      • Protein or peptide: Envelope glycoprotein
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: EBOV GP/Nanosota-EB2 complex

SupramoleculeName: EBOV GP/Nanosota-EB2 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Nanosota-EB2

SupramoleculeName: Nanosota-EB2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: Recombinant nanobody protein
Source (natural)Organism: Vicugna pacos (alpaca)

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Supramolecule #3: EBOV glycoprotein

SupramoleculeName: EBOV glycoprotein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Ebola virus

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Macromolecule #1: Nanosota-EB2

MacromoleculeName: Nanosota-EB2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 15.719111 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG VVQAGGSLRL SCSASGRTFS NYAMAWFRQA PGKDREFAAG INYNGERTAY ADSVKGRFTI SRDDAKNTVY LQMNSLKPE DTAVYSCAAR PWSIANLAYT YDSWGQGTQV TVSSGGQHHH HHHGAYPYDV PDYAS

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Macromolecule #2: Envelope glycoprotein

MacromoleculeName: Envelope glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
Molecular weightTheoretical: 77.812781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGVTGILQLP RDRFKRTSFF LWVIILFQRT FSIPLGVIHN STLQVSDVDK LVCRDKLSST NQLRSVGLNL EGNGVATDVP SATKRWGFR SGVPPKVVNY EAGEWAENCY NLEIKKPDGS ECLPAAPDGI RGFPRCRYVH KVSGTGPCAG DFAFHKEGAF F LYDRLAST ...String:
MGVTGILQLP RDRFKRTSFF LWVIILFQRT FSIPLGVIHN STLQVSDVDK LVCRDKLSST NQLRSVGLNL EGNGVATDVP SATKRWGFR SGVPPKVVNY EAGEWAENCY NLEIKKPDGS ECLPAAPDGI RGFPRCRYVH KVSGTGPCAG DFAFHKEGAF F LYDRLAST VIYRGTTFAE GVVAFLILPQ AKKDFFSSHP LREPVNATED PSSGYYSTTI RYQATGFGTN ETEYLFEVDN LT YVQLESR FTPQFLLQLN ETIYTSGKRS NTTGKLIWKV NPEIDTTIGE WAFWETKKNL TRKIRSEELS FTVVSNGAKN ISG QSPART SSDPGTNTTT EDHKIMASEN SSAMVQVHSQ GREAAVSHLT TLATISTSPQ SLTTKPGPDN STHNTPVYKL DISE ATQVE QHHRRTDNDS TASDTPSATT AAGPPKAENT NTSKSTDFLD PATTTSPQNH SETAGNNNTH HQDTGEESAS SGKLG LITN TIAGVAGLIT GGRRTRREAI VNAQPKCNPN LHYWTTQDEG AAIGLAWIPY FGPAAEGIYI EGLMHNQDGL ICGLRQ LAN ETTQALQLFL RATTELRTFS ILNRKAIDFL LQRWGGTCHI LGPDCCIEPH DWTKNITDKI DQIIHDFVDK TLPDQGD ND NWWTGWRQWI PAGIGVTGVI IAVIALFCIC KFVFGSGYIP EAPRDGQAYV RKDGEWVLLS TFLG

UniProtKB: Envelope glycoprotein

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Macromolecule #6: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 6 / Number of copies: 1 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 404158
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5jq7


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9bsv:
EBOV GP/Nanosota-EB2 complex

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