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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 / ebolavirus
Function / homology
Function and homology information


symbiont-mediated-mediated suppression of host tetherin activity / clathrin-dependent endocytosis of virus by host cell / 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
Similarity search - Function
Filoviruses glycoprotein / : / Filoviruses glycoprotein, extracellular domain / 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: Npj Viruses / Year: 2026
Title: A broadly-neutralizing antibody against Orthoebolavirus glycoprotein that potentiates the breadth and neutralization of other antibodies.
Authors: Francesca R Donnellan / Vamseedhar Rayaprolu / Pramila Rijal / Victoria O'Dowd / Amar Parvate / Heather Callaway / Chitra Hariharan / Dipti Parekh / Sean Hui / Kelly C L Shaffer / Ruben Diaz ...Authors: Francesca R Donnellan / Vamseedhar Rayaprolu / Pramila Rijal / Victoria O'Dowd / Amar Parvate / Heather Callaway / Chitra Hariharan / Dipti Parekh / Sean Hui / Kelly C L Shaffer / Ruben Diaz Avalos / Kathryn M Hastie / Lisa Schimanski / Helena Müller-Kräuter / Thomas Strecker / Ariane Balaram / Peter Halfmann / Erica Ollmann Saphire / Daniel J Lightwood / Alain R Townsend / Simon J Draper /
Abstract: Ebolavirus disease (EVD) is caused by multiple species of orthoebolavirus. Monoclonal antibodies (mAbs) against the virus glycoprotein (GP) are the only class of therapeutic approved for treatment of ...Ebolavirus disease (EVD) is caused by multiple species of orthoebolavirus. Monoclonal antibodies (mAbs) against the virus glycoprotein (GP) are the only class of therapeutic approved for treatment of EVD caused by Orthoebolavirus zairense (Ebola virus, EBOV). Therefore, mAbs targeting multiple orthoebolavirus species may represent the next generation of EVD therapeutics. Broadly reactive anti-GP mAbs were produced; among these, mAbs 11886 and 11883 were broadly neutralizing in vitro. A 3.0 Å cryo-electron microscopy structure of EBOV GP bound to both mAbs shows that 11886 binds a novel epitope bridging the glycan cap (GC), 3 pocket and GP2 N-terminus, whereas 11883 binds the receptor binding region (RBR) and GC. In vitro, 11886 synergized with a range of mAbs with epitope specificities spanning the RBR/GC, including 11883. Notably, 11886 increased the breadth of neutralization by partner mAbs against different orthoebolavirus species. These data provide a strategic route to design improved mAb-based next-generation EVD therapeutics.
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
Revision 1.1May 20, 2026Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / struct_keywords
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update / _struct_keywords.text
Revision 1.1May 20, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / EM metadata
Group: Database references / Experimental summary / Structure summary
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
Category: citation / citation_author ...citation / citation_author / em_admin / struct_keywords
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update / _struct_keywords.text

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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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