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- PDB-9bop: A broadly-neutralizing antibody against Ebolavirus glycoprotein t... -

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Basic information

Entry
Database: PDB / ID: 9bop
TitleA broadly-neutralizing antibody against Ebolavirus glycoprotein that can potentiate the breadth and neutralization potency of other anti-glycoprotein antibodies
Components
  • (Virion spike glycoprotein ...) x 2
  • 11883 heavy chain
  • 11883 light chain
  • 11886 heavy chain
  • 11886 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / Ebola / 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 speciesOryctolagus cuniculus (rabbit)
Ebolavirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsDonnellan, F.R. / Rayaprolu, V. / Rijal, P. / O'Dowd, V. / Parvate, A. / Callaway, H. / Hariharan, C. / Parekh, D. / Hui, S. / Shaffer, K. ...Donnellan, F.R. / 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, E.O. / Lightwood, D.J. / Townsend, A.R. / Draper, S.J.
Funding support United Kingdom, 1items
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, F.R. / 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. / ...Authors: Donnellan, F.R. / 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, E.O. / Lightwood, D.J. / Townsend, A.R. / Draper, S.J.
History
DepositionMay 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 11883 heavy chain
B: 11883 light chain
M: 11886 heavy chain
N: 11886 light chain
O: 11886 heavy chain
P: 11886 light chain
S: Virion spike glycoprotein GP1
V: Virion spike glycoprotein GP2
C: 11883 heavy chain
E: 11883 heavy chain
D: 11883 light chain
F: 11883 light chain
W: Virion spike glycoprotein GP2
X: Virion spike glycoprotein GP2
T: Virion spike glycoprotein GP1
U: Virion spike glycoprotein GP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)298,51528
Polymers293,79216
Non-polymers4,72312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 5 molecules ACEMO

#1: Protein 11883 heavy chain


Mass: 15837.846 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell: Splenocytes / Organ: Spleen / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Protein 11886 heavy chain


Mass: 15854.976 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)

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Virion spike glycoprotein ... , 2 types, 6 molecules STUVWX

#5: Protein Virion spike glycoprotein GP1


Mass: 31256.092 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebolavirus / Gene: GP / Variant: Mayinga / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A8G0KJC2
#6: Protein Virion spike glycoprotein GP2


Mass: 15206.248 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebolavirus / Gene: GP / Variant: Mayinga / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A8G0KMX8

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Antibody , 2 types, 5 molecules BDFNP

#2: Antibody 11883 light chain


Mass: 14970.940 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): ExpiCHO-S / Production host: Homo sapiens (human)
#4: Antibody 11886 light chain


Mass: 15134.112 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Cell line (production host): ExpiCHO-S / Production host: Homo sapiens (human)

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Sugars , 2 types, 12 molecules

#7: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Zaire Ebola Glycoprotein dTM (GP1 and GP2 including MLD) complexed with 11883 and 11886COMPLEX#1-#60MULTIPLE SOURCES
2Zaire ebolavirus glycoprotein containing MLDCOMPLEX#5-#61RECOMBINANT
311883 Fab heavy and light chainsCOMPLEX#1-#21RECOMBINANT
411886 Fab heavy and light chainsCOMPLEX#3-#41RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.45 MDaNO
220.18 MDaNO
330.1 MDaNO
440.1 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Ebola virus1570291
23Oryctolagus cuniculus (rabbit)9986
34Oryctolagus cuniculus (rabbit)9986
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
12Drosophila melanogaster (fruit fly)7227
23Homo sapiens (human)9606HEK293F, Expi-CHO
34Homo sapiens (human)9606HEK293F, Expi-CHO
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris1
2150 mMsodium chlorideNaCl1
320 uMLMNG1
SpecimenConc.: 1.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Details: Total dose of 50e/A2
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 75000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9552
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 66500 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00217257
ELECTRON MICROSCOPYf_angle_d0.4423512
ELECTRON MICROSCOPYf_dihedral_angle_d3.9712512
ELECTRON MICROSCOPYf_chiral_restr0.042699
ELECTRON MICROSCOPYf_plane_restr0.0032962

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