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- EMDB-71328: Structure of EBOV glycoprotein in complex with Nanosota-EB1 and EB2 -

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Basic information

Entry
Database: EMDB / ID: EMD-71328
TitleStructure of EBOV glycoprotein in complex with Nanosota-EB1 and EB2
Map dataunsharpened map of EBOV glycoprotein in complex Nanosota-EB1 and EB2
Sample
  • Complex: EBOV glycoprotein in complex with Nanosota-EB1 and EB2
    • Complex: EBOV glycoprotein
      • Protein or peptide: Envelope glycoprotein
    • Complex: Nanosota-EB1 and EB2
      • Protein or peptide: Nanosota-EB1
      • Protein or peptide: Nanosota-EB2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / 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 / entry receptor-mediated virion attachment to host cell / host cell cytoplasm / 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, extracellular domain / Filoviruses glycoprotein / 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: 2.92 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: A Highly Potent and Broadly Accessible Bispecific Nanobody for the Treatment of Ebola Virus Infections
Authors: Bu F / Ye G / Li F
History
DepositionJun 20, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71328.png

Downloads & links

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Map

FileDownload / File: emd_71328.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map of EBOV glycoprotein in complex Nanosota-EB1 and EB2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 450 pix.
= 398.4 Å		0.89 Å/pix.
x 450 pix.
= 398.4 Å		0.89 Å/pix.
x 450 pix.
= 398.4 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: 0.05
Minimum - Maximum-0.2188908 - 0.5256514
Average (Standard dev.)0.00026660503 (±0.00884791)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 398.39984 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened map of EBOV glycoprotein in complex Nanosota-EB1 and EB2

Fileemd_71328_additional_1.map
Annotationsharpened map of EBOV glycoprotein in complex Nanosota-EB1 and 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 glycoprotein in complex Nanosota-EB1 and EB2

Fileemd_71328_half_map_1.map
Annotationhalf map_A of EBOV glycoprotein in complex Nanosota-EB1 and 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 glycoprotein in complex Nanosota-EB1 and EB2

Fileemd_71328_half_map_2.map
Annotationhalf map_B of EBOV glycoprotein in complex Nanosota-EB1 and 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 glycoprotein in complex with Nanosota-EB1 and EB2

EntireName: EBOV glycoprotein in complex with Nanosota-EB1 and EB2
Components
  • Complex: EBOV glycoprotein in complex with Nanosota-EB1 and EB2
    • Complex: EBOV glycoprotein
      • Protein or peptide: Envelope glycoprotein
    • Complex: Nanosota-EB1 and EB2
      • Protein or peptide: Nanosota-EB1
      • Protein or peptide: Nanosota-EB2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: EBOV glycoprotein in complex with Nanosota-EB1 and EB2

SupramoleculeName: EBOV glycoprotein in complex with Nanosota-EB1 and EB2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: EBOV glycoprotein

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

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Supramolecule #3: Nanosota-EB1 and EB2

SupramoleculeName: Nanosota-EB1 and EB2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Vicugna pacos (alpaca)

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Macromolecule #1: Envelope glycoprotein

MacromoleculeName: Envelope glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
Molecular weightTheoretical: 56.53466 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 GRRTRREAIV NAQPKCNPNL HYWTTQDEGA AIGLAWIPYF GPAAEGIYIE GLMHNQDGLI CGLR QLANE TTQALQLFLR ATTELRTFSI LNRKAIDFLL QRWGGTCHIL GPDCCIEPHD WTKNITDKID QIIHDFVDGS GYIPE APRD GQAYVRKDGE WVLLSTFLGH HHHHH

UniProtKB: Envelope glycoprotein, Envelope glycoprotein

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Macromolecule #2: Nanosota-EB1

MacromoleculeName: Nanosota-EB1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 15.592182 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG QVQAGGSLRL SCAASGSTSV IYAMGWYRQA PGKQRELVAA ITRGVGSTNY ADSVKGRFTI SRDNAKNTMY LQMNSLKPE DTAVYYCNAR LLVAPPPYEY DYWGQGTQVT VSSGGQHHHH HHGAYPYDVP DYAS

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Macromolecule #3: Nanosota-EB2

MacromoleculeName: Nanosota-EB2 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Vicugna pacos (alpaca)
Molecular weightTheoretical: 15.590982 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VQLQESGGGV VQAGGSLRLS CSASGRTFSN YAMAWFRQAP GKDREFAAGI NYNGERTAYA DSVKGRFTIS RDDAKNTVYL QMNSLKPED TAVYSCAARP WSIANLAYTY DSWGQGTQVT VSSGGQHHHH HHGAYPYDVP DYAS

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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

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

9bsu

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 62575
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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