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- EMDB-44747: A broadly-neutralizing antibody against Ebolavirus glycoprotein t... -

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Basic information

Entry
Database: EMDB / ID: EMD-44747
TitleA broadly-neutralizing antibody against Ebolavirus glycoprotein that can potentiate the breadth and neutralization potency of other anti-glycoprotein antibodies
Map data
Sample
  • Complex: Zaire Ebola Glycoprotein dTM (GP1 and GP2 including MLD) complexed with 11883 and 11886
    • Complex: Zaire ebolavirus glycoprotein containing MLD
      • Protein or peptide: Virion spike glycoprotein GP1
      • Protein or peptide: Virion spike glycoprotein GP2
    • Complex: 11883 Fab heavy and light chains
      • Protein or peptide: 11883 heavy chain
      • Protein or peptide: 11883 light chain
    • Complex: 11886 Fab heavy and light chains
      • Protein or peptide: 11886 heavy chain
      • Protein or peptide: 11886 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsEbola / IgG / neutralization / complex / glycoprotein / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / lipid binding / 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
Envelope glycoprotein / Envelope glycoprotein
Similarity search - Component
Biological speciesEbola virus / Oryctolagus cuniculus (rabbit) / Ebolavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsDonnellan FR / Rayaprolu V / Rijal P / O'Dowd V / Parvate A / Callaway H / Hariharan C / Parekh D / Hui S / Shaffer K ...Donnellan FR / Rayaprolu V / Rijal P / O'Dowd V / Parvate A / Callaway H / Hariharan C / Parekh D / Hui S / Shaffer K / Hastie K / Shimanski L / Muller-Krauter H / Stecker T / Balaram A / Halfmann P / Saphire EO / Lightwood DJ / Townsend AR / Draper SJ
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N01796X/1 United Kingdom
CitationJournal: To Be Published
Title: A broadly-neutralizing antibody against Ebolavirus glycoprotein that can potentiate the breadth and neutralization potency of other anti-glycoprotein antibodies
Authors: Donnellan FR / Rayaprolu V / Rijal P / O'Dowd V / Parvate A / Callaway H / Hariharan C / Parekh D / Hui S / Shaffer K / Hastie K / Shimanski L / Muller-Krauter H / Stecker T / Balaram A / ...Authors: Donnellan FR / Rayaprolu V / Rijal P / O'Dowd V / Parvate A / Callaway H / Hariharan C / Parekh D / Hui S / Shaffer K / Hastie K / Shimanski L / Muller-Krauter H / Stecker T / Balaram A / Halfmann P / Saphire EO / Lightwood DJ / Townsend AR / Draper SJ
History
DepositionMay 5, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44747.png

Downloads & links

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Map

FileDownload / File: emd_44747.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 512 pix.
= 340.787 Å		0.67 Å/pix.
x 512 pix.
= 340.787 Å		0.67 Å/pix.
x 512 pix.
= 340.787 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.6656 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055
Minimum - Maximum-0.17135307 - 0.35193503
Average (Standard dev.)0.000084950516 (±0.009169778)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 340.7872 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_44747_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44747_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Zaire Ebola Glycoprotein dTM (GP1 and GP2 including MLD) complexe...

EntireName: Zaire Ebola Glycoprotein dTM (GP1 and GP2 including MLD) complexed with 11883 and 11886
Components
  • Complex: Zaire Ebola Glycoprotein dTM (GP1 and GP2 including MLD) complexed with 11883 and 11886
    • Complex: Zaire ebolavirus glycoprotein containing MLD
      • Protein or peptide: Virion spike glycoprotein GP1
      • Protein or peptide: Virion spike glycoprotein GP2
    • Complex: 11883 Fab heavy and light chains
      • Protein or peptide: 11883 heavy chain
      • Protein or peptide: 11883 light chain
    • Complex: 11886 Fab heavy and light chains
      • Protein or peptide: 11886 heavy chain
      • Protein or peptide: 11886 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Zaire Ebola Glycoprotein dTM (GP1 and GP2 including MLD) complexe...

SupramoleculeName: Zaire Ebola Glycoprotein dTM (GP1 and GP2 including MLD) complexed with 11883 and 11886
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Molecular weightTheoretical: 450 KDa

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Supramolecule #2: Zaire ebolavirus glycoprotein containing MLD

SupramoleculeName: Zaire ebolavirus glycoprotein containing MLD / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Ebola virus
Molecular weightTheoretical: 180 KDa

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Supramolecule #3: 11883 Fab heavy and light chains

SupramoleculeName: 11883 Fab heavy and light chains / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 100 KDa

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Supramolecule #4: 11886 Fab heavy and light chains

SupramoleculeName: 11886 Fab heavy and light chains / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 100 KDa

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Macromolecule #1: 11883 heavy chain

MacromoleculeName: 11883 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Organ: Spleen / Cell: Splenocytes
Molecular weightTheoretical: 15.837846 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SFEATMETGL RWLLLVAVLK GVQCQEQLVE SGGGLVQPEG SLTLTCTASG FSFSSNCWRC WVRQAPGKGL EWIACVCAGR SGGTTYYAS WAKGRFTISK TSSPTVTLQM TSLTAADTAT YFCARAGYDD YGDASFFNLW GPGTLVTVS

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Macromolecule #2: 11883 light chain

MacromoleculeName: 11883 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 14.97094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
SFEATMNMRA PTQLLGLLLL WLPGARCAVV LTQTASPVST PVGGTVTIKC QASQNIYSNL AWYQQKPGQP PKLLIYSAST LASGVPSRF KGSGSGTEYT LTISDLECAD AATYYCQRYY YLSGSADNTF GGGTEVVVKR T

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Macromolecule #3: 11886 heavy chain

MacromoleculeName: 11886 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 15.854976 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RSFEATMETG LRWLLLVAVL KGVQCQSVEE SGGRLVTPGT PLTLTCIVSG FSLSNYYMSW VRQVPGKGLE WIGVIGWSGT SSYASWAKG RFTISKTAST TVDLKITSPT TEDTATYFCA RVLYIGGGFN YYDAFDPWGP GTLVTVS

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Macromolecule #4: 11886 light chain

MacromoleculeName: 11886 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 15.134112 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
RSFEATMNMR APTQLLGLLL LWLPGARCDV VMTQTPASVS EPVGGTVTIK CQASQSIGSN LAWYQQKPGQ PPKLLIYAAS TLASGVPSR FKGSGSGTEF TLTISDLECA DAATYYCQCT YYDSSYVYNN FGGGTEVVVK RT

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Macromolecule #5: Virion spike glycoprotein GP1

MacromoleculeName: Virion spike glycoprotein GP1 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebolavirus
Molecular weightTheoretical: 31.256092 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: RSIPLGVIHN STLQVSDVDK LVCRDKLSST NQLRSVGLNL EGNGVATDVP SATKRWGFRS GVPPKVVNYE AGEWAENCYN LEIKKPDGS ECLPAAPDGI RGFPRCRYVH KVSGTGPCAG DFAFHKEGAF FLYDRLASTV IYRGTTFAEG VVAFLILPQA K KDFFSSHP ...String:
RSIPLGVIHN STLQVSDVDK LVCRDKLSST NQLRSVGLNL EGNGVATDVP SATKRWGFRS GVPPKVVNYE AGEWAENCYN LEIKKPDGS ECLPAAPDGI RGFPRCRYVH KVSGTGPCAG DFAFHKEGAF FLYDRLASTV IYRGTTFAEG VVAFLILPQA K KDFFSSHP LREPVNATED PSSGYYSTTI RYQATGFGTN ETEYLFEVDN LTYVQLESRF TPQFLLQLNE TIYTSGKRSN TT GKLIWKV NPEIDTTIGE WAFWETKKNL TRKIRSEELS FT

UniProtKB: Envelope glycoprotein

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Macromolecule #6: Virion spike glycoprotein GP2

MacromoleculeName: Virion spike glycoprotein GP2 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebolavirus
Molecular weightTheoretical: 15.206248 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString:
AIVNAQPKCN PNLHYWTTQD EGAAIGLAWI PYFGPAAEGI YTEGLMHNQD GLICGLRQLA NETTQALQLF LRATTELRTF SILNRKAID FLLQRWGGTC HILGPDCCIE PHDWTKNITD KIDQIIHDFV DKTLPD

UniProtKB: Envelope glycoprotein

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 9 / 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

Concentration1.9 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mMTris
150.0 mMsodium chlorideNaCl
20.0 uMLMNG
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 35 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
DetailsTotal dose of 50e/A2
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9552 / 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 / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7tn9

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 66500
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9bop:
A broadly-neutralizing antibody against Ebolavirus glycoprotein that can potentiate the breadth and neutralization potency of other anti-glycoprotein antibodies

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