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- EMDB-71566: Structure of EBOV GP, MWAC-3634, and Nanosota-EB2 ternary complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-71566
TitleStructure of EBOV GP, MWAC-3634, and Nanosota-EB2 ternary complex
Map dataunsharpened map of EBOV GP in complex with compound 3634
Sample
  • Complex: EBOV GP, MWAC-3634, and Nanosota-EB2 ternary complex
    • Complex: EBOV GP
      • Protein or peptide: Envelope glycoprotein GP1
      • Protein or peptide: Envelope glycoprotein GP2
    • Complex: Nanosota-EB2
      • Protein or peptide: Nanosota-EB2
  • Ligand: (3S,4R)-1-{(2P)-2-(6-chloroquinolin-4-yl)-1-[(1R)-1-(naphthalen-1-yl)ethyl]-1H-1,3-benzimidazole-6-carbonyl}-N-methyl-4-[3-(trifluoromethyl)phenyl]pyrrolidine-3-carboxamide
KeywordsEBOV / glycoprotein / inhibitor / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / symbiont entry into host cell / lipid binding / host cell plasma membrane / virion membrane / extracellular region / identical protein binding
Similarity search - Function
Filoviruses glycoprotein / : / Filoviruses glycoprotein, extracellular domain / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesEbola virus - Mayinga, Zaire, 1976 / Vicugna pacos (alpaca) / Ebola virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsBu F / Ye G / Li F
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI171954 United States
CitationJournal: To Be Published
Title: Structure of EBOV GP, MWAC-3634, and Nanosota-EB2 ternary complex
Authors: Bu F / Ye G / Li F
History
DepositionJul 2, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71566.png

Downloads & links

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Map

FileDownload / File: emd_71566.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map of EBOV GP in complex with compound 3634
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 300 pix.
= 265.6 Å		0.89 Å/pix.
x 300 pix.
= 265.6 Å		0.89 Å/pix.
x 300 pix.
= 265.6 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: 0.064
Minimum - Maximum-0.22468033 - 0.49132997
Average (Standard dev.)0.0003113816 (±0.013073078)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 265.5999 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map of EBOV GP in complex with compound 3634

Fileemd_71566_additional_1.map
Annotationsharpened map of EBOV GP in complex with compound 3634
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 in complex with compound 3634

Fileemd_71566_half_map_1.map
Annotationhalf map_A of EBOV GP in complex with compound 3634
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 in complex with compound 3634

Fileemd_71566_half_map_2.map
Annotationhalf map_B of EBOV GP in complex with compound 3634
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, MWAC-3634, and Nanosota-EB2 ternary complex

EntireName: EBOV GP, MWAC-3634, and Nanosota-EB2 ternary complex
Components
  • Complex: EBOV GP, MWAC-3634, and Nanosota-EB2 ternary complex
    • Complex: EBOV GP
      • Protein or peptide: Envelope glycoprotein GP1
      • Protein or peptide: Envelope glycoprotein GP2
    • Complex: Nanosota-EB2
      • Protein or peptide: Nanosota-EB2
  • Ligand: (3S,4R)-1-{(2P)-2-(6-chloroquinolin-4-yl)-1-[(1R)-1-(naphthalen-1-yl)ethyl]-1H-1,3-benzimidazole-6-carbonyl}-N-methyl-4-[3-(trifluoromethyl)phenyl]pyrrolidine-3-carboxamide

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Supramolecule #1: EBOV GP, MWAC-3634, and Nanosota-EB2 ternary complex

SupramoleculeName: EBOV GP, MWAC-3634, and Nanosota-EB2 ternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: EBOV GP

SupramoleculeName: EBOV GP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976

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Supramolecule #3: Nanosota-EB2

SupramoleculeName: Nanosota-EB2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Vicugna pacos (alpaca)

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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: 15.722139 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCVHSGRTFS NDAMAWFRQA PGKDREFAAG IDYNGGRTAY TDSVKGRFTI SRDNAKNTVY LQMNSLKPE DTAVYSCAAR PWSIANLAYT YDSWGQGTQV TVSSGGQHHH HHHGAYPYDV PDYAS

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Macromolecule #2: Envelope glycoprotein GP1

MacromoleculeName: Envelope glycoprotein GP1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus / Strain: Mayinga, Zaire, 1976
Molecular weightTheoretical: 37.6645 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SASSIPLGVI HNSTLQVSDV DKLVCRDKLS STNQLRSVGL NLEGNGVATD VPSATKRWGF RSGVPPKVV NYEAGEWAEN CYNLEIKKPD GSECLPAAPD GIRGFPRCRY VHKVSGTGPC AGDFAFHKEG AFFLYDRLAS T VIYRGTTF ...String:
MDAMKRGLCC VLLLCGAVFV SASSIPLGVI HNSTLQVSDV DKLVCRDKLS STNQLRSVGL NLEGNGVATD VPSATKRWGF RSGVPPKVV NYEAGEWAEN CYNLEIKKPD GSECLPAAPD GIRGFPRCRY VHKVSGTGPC AGDFAFHKEG AFFLYDRLAS T VIYRGTTF AEGVVAFLIL PQAKKDFFSS HPLREPVNAT EDPSSGYYST TIRYQATGFG TNETEYLFEV DNLTYVQLES RF TPQFLLQ LNETIYTSGK RSNTTGKLIW KVNPEIDTTI GEWAFWETKK NLTRKIRSEE LSFTVVSTHH QDTGEESASS GKL GLITNT IAGVAGLITG GRRTRR

UniProtKB: Envelope glycoprotein, Envelope glycoprotein

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Macromolecule #3: Envelope glycoprotein GP2

MacromoleculeName: Envelope glycoprotein GP2 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus / Strain: Mayinga, Zaire, 1976
Molecular weightTheoretical: 18.888287 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EAIVNAQPKC NPNLHYWTTQ DEGAAIGLAW IPYFGPAAEG IYIEGLMHNQ DGLICGLRQL ANETTQALQL FLRATTELRT FSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDF VDGSGYIPEA PRDGQAYVRK DGEWVLLSTF L GHHHHHH

UniProtKB: Envelope glycoprotein

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Macromolecule #7: (3S,4R)-1-{(2P)-2-(6-chloroquinolin-4-yl)-1-[(1R)-1-(naphthalen-1...

MacromoleculeName: (3S,4R)-1-{(2P)-2-(6-chloroquinolin-4-yl)-1-[(1R)-1-(naphthalen-1-yl)ethyl]-1H-1,3-benzimidazole-6-carbonyl}-N-methyl-4-[3-(trifluoromethyl)phenyl]pyrrolidine-3-carboxamide
type: ligand / ID: 7 / Number of copies: 3 / Formula: A1CIK
Molecular weightTheoretical: 732.192 Da

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 6106 / Average electron dose: 54.5 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9bsv

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 257283
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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