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- PDB-9pel: Structure of EBOV GP, MWAC-3634, and Nanosota-EB2 ternary complex -

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Basic information

Entry
Database: PDB / ID: 9pel
TitleStructure of EBOV GP, MWAC-3634, and Nanosota-EB2 ternary complex
Components
  • (Envelope glycoprotein ...) x 2
  • Nanosota-EB2
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / EBOV / glycoprotein / inhibitor / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated killing of host cell / host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / fusion of virus membrane with host endosome membrane ...symbiont-mediated killing of host cell / host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / lipid binding / host cell plasma membrane / virion membrane / extracellular region / identical protein binding
Similarity search - Function
Filoviruses glycoprotein / : / Filoviruses glycoprotein, extracellular domain / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2
Similarity search - Domain/homology
: / Envelope glycoprotein
Similarity search - Component
Biological speciesVicugna pacos (alpaca)
Ebola virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsBu, F. / Ye, G. / Li, F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI171954 United States
CitationJournal: To Be Published
Title: Structure of EBOV GP, MWAC-3634, and Nanosota-EB2 ternary complex
Authors: Bu, F. / Ye, G. / Li, F.
History
DepositionJul 2, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Nanosota-EB2
H: Nanosota-EB2
J: Nanosota-EB2
A: Envelope glycoprotein GP1
a: Envelope glycoprotein GP2
B: Envelope glycoprotein GP1
b: Envelope glycoprotein GP2
C: Envelope glycoprotein GP1
c: Envelope glycoprotein GP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,91615
Polymers216,8259
Non-polymers5,0916
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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Envelope glycoprotein ... , 2 types, 6 molecules ABCabc

#2: Protein Envelope glycoprotein GP1


Mass: 37664.500 Da / Num. of mol.: 3 / Mutation: residues 313-463 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus / Strain: Mayinga, Zaire, 1976 / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q05320
#3: Protein Envelope glycoprotein GP2


Mass: 18888.287 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus / Strain: Mayinga, Zaire, 1976 / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: Q05320

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Antibody / Non-polymers , 2 types, 6 molecules DHJ

#1: Antibody Nanosota-EB2


Mass: 15722.139 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)
#7: Chemical ChemComp-A1CIK / (3S,4R)-1-{(2P)-2-(6-chloroquinolin-4-yl)-1-[(1R)-1-(naphthalen-1-yl)ethyl]-1H-1,3-benzimidazole-6-carbonyl}-N-methyl-4-[3-(trifluoromethyl)phenyl]pyrrolidine-3-carboxamide


Mass: 732.192 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C42H33ClF3N5O2 / Feature type: SUBJECT OF INVESTIGATION

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Sugars , 3 types, 3 molecules

#4: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[beta-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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]/1-1-2-3-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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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
1EBOV GP, MWAC-3634, and Nanosota-EB2 ternary complexCOMPLEX#1-#30MULTIPLE SOURCES
2EBOV GPCOMPLEX#2-#31RECOMBINANT
3Nanosota-EB2COMPLEX#11RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Ebola virus - Mayinga, Zaire, 1976128952
33Vicugna pacos (alpaca)30538
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 54.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 6106

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1particle selection
2PHENIX1.21.1_5286:model refinement
13cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 257283 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00310001
ELECTRON MICROSCOPYf_angle_d0.6513614
ELECTRON MICROSCOPYf_dihedral_angle_d15.0763630
ELECTRON MICROSCOPYf_chiral_restr0.1361505
ELECTRON MICROSCOPYf_plane_restr0.0051740

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