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- EMDB-38899: Ebola virus glycoprotein in complex with a broadly neutralizing a... -

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Basic information

Entry
Database: EMDB / ID: EMD-38899
TitleEbola virus glycoprotein in complex with a broadly neutralizing antibody 2G1
Map data
Sample
  • Complex: Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1
    • Complex: Ebola virus glycoprotein
      • Protein or peptide: Virion spike glycoprotein
      • Protein or peptide: SGP
    • Complex: 2G1 Fab
      • Protein or peptide: 2G1 VH
      • Protein or peptide: 2G1 VL
KeywordsANTIVIRAL PROTEIN
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / fusion of virus membrane with host endosome membrane / viral envelope / host cell plasma membrane / virion membrane / extracellular region / membrane
Similarity search - Function
: / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2
Similarity search - Domain/homology
SGP / Envelope glycoprotein
Similarity search - Component
Biological speciesHenipavirus nipahense / Ebola virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsFan PF / Yu CM / Chen W
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82204260 China
CitationJournal: Emerg Microbes Infect / Year: 2024
Title: A pan-orthoebolavirus neutralizing antibody encoded by mRNA effectively prevents virus infection.
Authors: Pengfei Fan / Bingjie Sun / Zixuan Liu / Ting Fang / Yi Ren / Xiaofan Zhao / Zhenwei Song / Yilong Yang / Jianmin Li / Changming Yu / Wei Chen /
Abstract: is a genus of hazardous pathogens that has caused over 30 outbreaks. However, currently approved therapies are limited in scope, as they are only effective against the Ebola virus and lack cross- ... is a genus of hazardous pathogens that has caused over 30 outbreaks. However, currently approved therapies are limited in scope, as they are only effective against the Ebola virus and lack cross-protection against other orthoebolaviruses. Here, we demonstrate that a previously isolated human-derived antibody, 2G1, can recognize the glycoprotein (GP) of every orthoebolavirus species. The cryo-electron microscopy structure of 2G1 Fab in complex with the GPΔMucin trimer reveals that 2G1 binds a quaternary pocket formed by three subunits from two GP protomers. 2G1 recognizes highly conserved epitopes among filoviruses and achieves neutralization by blocking GP proteolysis. We designed an efficient mRNA module capable of producing test antibodies at expression levels exceeding 1500 ng/mL in vitro. The lipid nanoparticle (LNP)-encapsulated mRNA-2G1 exhibited potent neutralizing activities against the HIV-pseudotyped Ebola and Sudan viruses that were 19.8 and 12.5 times that of IgG format, respectively. In mice, the antibodies encoded by the mRNA-2G1-LNP peaked within 24 h, effectively blocking the invasion of pseudoviruses with no apparent liver toxicity. This study suggests that the 2G1 antibody and its mRNA formulation represent promising candidate interventions for orthoebolavirus disease, and it provides an efficient mRNA framework applicable to antibody-based therapies.
History
DepositionJan 29, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38899.png

Downloads & links

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Map

FileDownload / File: emd_38899.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å		1.1 Å/pix.
x 384 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.6701415 - 1.4473783
Average (Standard dev.)-0.00017585265 (±0.023662347)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38899_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38899_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Ebola virus glycoprotein in complex with a broadly neutralizing a...

EntireName: Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1
Components
  • Complex: Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1
    • Complex: Ebola virus glycoprotein
      • Protein or peptide: Virion spike glycoprotein
      • Protein or peptide: SGP
    • Complex: 2G1 Fab
      • Protein or peptide: 2G1 VH
      • Protein or peptide: 2G1 VL

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Supramolecule #1: Ebola virus glycoprotein in complex with a broadly neutralizing a...

SupramoleculeName: Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Henipavirus nipahense

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Supramolecule #2: Ebola virus glycoprotein

SupramoleculeName: Ebola virus glycoprotein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Ebola virus

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Supramolecule #3: 2G1 Fab

SupramoleculeName: 2G1 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 2G1 VH

MacromoleculeName: 2G1 VH / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.535075 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGG LVKRGGSLRL SCVVSGYTFG GYSMHWVRQA PGKGLEWVSG ISSSSYYKYY ADSVKGRFTI SRDNAKNSLY LQMNSLRAE DTAVYYCARD MGYCSGGSCP NFDFWGQGTT VTVSS

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Macromolecule #2: 2G1 VL

MacromoleculeName: 2G1 VL / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.342541 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IQMTQSPSSL SASVGDRVTI TCRTSQSISN YLNWYQQIPG KAPKLLISTA SNLHSGVSSR FSGSGSGTHF TLTISSLQPE DFATYYCQQ SYSTPSFGQG TKVEIK

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Macromolecule #3: Virion spike glycoprotein

MacromoleculeName: Virion spike glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
Molecular weightTheoretical: 10.883393 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VIVNAQPKCN PNLHYWTTQD EGAAIGLAWI PYFGPAAEGI YTEGLMHNQD GLICGLRQLA NETTQALQLF LRATTELRTF SILNRKAID FLLQRWAA

UniProtKB: Envelope glycoprotein

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Macromolecule #4: SGP

MacromoleculeName: SGP / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
Molecular weightTheoretical: 16.984287 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SIPLGVIHNS TLQVSDVDKL VCRDKLSSTN QLRSVGLNLE GNGVATDVPS VTKRWGFRSG VPPKVVNYEA GEWAENCYNL EIKKPDGSE CLPAAPDGIR GFPRCRYVHK VSGTGPCAGD FAFHKEGAFF LYDRLASTVI YRGTTFAEGV VAFLILAA

UniProtKB: SGP

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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

Concentration1.0 mg/mL
BufferpH: 7.4 / Details: 137 mM NaCl, 2.7mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number real images: 8926 / 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: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7kej

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 326558
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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