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- PDB-7swd: Structure of EBOV GP lacking the mucin-like domain with 1C11 scFv... -

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Basic information

Entry
Database: PDB / ID: 7swd
TitleStructure of EBOV GP lacking the mucin-like domain with 1C11 scFv and 1C3 Fab bound
Components
  • (Virion spike glycoprotein ...) x 2
  • 1C11 scFv
  • 1C3 heavy chain
  • 1C3 light chain
KeywordsVIRAL PROTEIN/Immune System / VIRAL PROTEIN / glycoprotein / immune system / antibody / Ebola virus / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein / Envelope glycoprotein
Similarity search - Component
Biological speciesEbola virus - Gabon
Zaire ebolavirus
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsMilligan, J.C. / Yu, X. / Saphire, E.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5 U19 AI142790 United States
CitationJournal: Cell / Year: 2022
Title: Asymmetric and non-stoichiometric glycoprotein recognition by two distinct antibodies results in broad protection against ebolaviruses.
Authors: Jacob C Milligan / Carl W Davis / Xiaoying Yu / Philipp A Ilinykh / Kai Huang / Peter J Halfmann / Robert W Cross / Viktoriya Borisevich / Krystle N Agans / Joan B Geisbert / Chakravarthy ...Authors: Jacob C Milligan / Carl W Davis / Xiaoying Yu / Philipp A Ilinykh / Kai Huang / Peter J Halfmann / Robert W Cross / Viktoriya Borisevich / Krystle N Agans / Joan B Geisbert / Chakravarthy Chennareddy / Arthur J Goff / Ashley E Piper / Sean Hui / Kelly C L Shaffer / Tierra Buck / Megan L Heinrich / Luis M Branco / Ian Crozier / Michael R Holbrook / Jens H Kuhn / Yoshihiro Kawaoka / Pamela J Glass / Alexander Bukreyev / Thomas W Geisbert / Gabriella Worwa / Rafi Ahmed / Erica Ollmann Saphire /
Abstract: Several ebolaviruses cause outbreaks of severe disease. Vaccines and monoclonal antibody cocktails are available to treat Ebola virus (EBOV) infections, but not Sudan virus (SUDV) or other ...Several ebolaviruses cause outbreaks of severe disease. Vaccines and monoclonal antibody cocktails are available to treat Ebola virus (EBOV) infections, but not Sudan virus (SUDV) or other ebolaviruses. Current cocktails contain antibodies that cross-react with the secreted soluble glycoprotein (sGP) that absorbs virus-neutralizing antibodies. By sorting memory B cells from EBOV infection survivors, we isolated two broadly reactive anti-GP monoclonal antibodies, 1C3 and 1C11, that potently neutralize, protect rodents from disease, and lack sGP cross-reactivity. Both antibodies recognize quaternary epitopes in trimeric ebolavirus GP. 1C11 bridges adjacent protomers via the fusion loop. 1C3 has a tripartite epitope in the center of the trimer apex. One 1C3 antigen-binding fragment anchors simultaneously to the three receptor-binding sites in the GP trimer, and separate 1C3 paratope regions interact differently with identical residues on the three protomers. A cocktail of both antibodies completely protected nonhuman primates from EBOV and SUDV infections, indicating their potential clinical value.
History
DepositionNov 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.0Apr 6, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 6, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 6, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 6, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 6, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Apr 6, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 6, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 2.0Aug 10, 2022Group: Advisory / Database references ...Advisory / Database references / Polymer sequence / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref / struct_ref_seq
Item: _entity.formula_weight / _entity.pdbx_description ..._entity.formula_weight / _entity.pdbx_description / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Revision 2.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 2.2May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Virion spike glycoprotein GP1
B: Virion spike glycoprotein GP2
C: Virion spike glycoprotein GP1
D: Virion spike glycoprotein GP2
E: Virion spike glycoprotein GP1
F: Virion spike glycoprotein GP2
G: 1C11 scFv
H: 1C11 scFv
I: 1C11 scFv
J: 1C3 heavy chain
K: 1C3 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,20414
Polymers232,44411
Non-polymers1,7603
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: Protein Virion spike glycoprotein GP1


Mass: 31297.158 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus - Gabon (1994-1997) / Strain: Mayinga-76 / Gene: GP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A089X075
#2: Protein Virion spike glycoprotein GP2


Mass: 10756.211 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zaire ebolavirus / Gene: GP / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: A0A7S6GAH2

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Antibody , 3 types, 5 molecules GHIJK

#3: Antibody 1C11 scFv


Mass: 26783.773 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly)
#4: Antibody 1C3 heavy chain


Mass: 13308.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#5: Antibody 1C3 light chain


Mass: 12624.050 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 1 types, 3 molecules

#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Details

Has ligand of interestN
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

ComponentName: Complex of EBOV GP lacking the mucin-like-domain with 1C11 scFv and 1C3 Fab
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Drosophila (fruit flies)
Buffer solutionpH: 7.4
Buffer componentName: TBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Alignment procedure: COMA FREE
Image recordingAverage exposure time: 54.95 sec. / Electron dose: 34.97 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameCategory
1RELIONparticle selection
2RELIONimage acquisition
9PHENIXmodel refinement
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 75948 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00513134
ELECTRON MICROSCOPYf_angle_d0.73817835
ELECTRON MICROSCOPYf_dihedral_angle_d15.0664732
ELECTRON MICROSCOPYf_chiral_restr0.0471982
ELECTRON MICROSCOPYf_plane_restr0.0062282

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