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- PDB-8y3u: Ebola virus glycoprotein in complex with a broadly neutralizing a... -

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Basic information

Entry
Database: PDB / ID: 8y3u
TitleEbola virus glycoprotein in complex with a broadly neutralizing antibody 2G1
Components
  • 2G1 VH
  • 2G1 VL
  • SGP
  • Virion spike glycoprotein
KeywordsANTIVIRAL PROTEIN
Function / homologyFiloviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 / extracellular region / membrane / SGP / Virion spike glycoprotein
Function and homology information
Biological speciesHomo sapiens (human)
Ebola virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsFan, P.F. / Yu, C.M. / Chen, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82204260 China
CitationJournal: To Be Published
Title: Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1
Authors: Fan, P.F. / Yu, C.M. / Chen, W.
History
DepositionJan 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2G1 VH
B: 2G1 VL
C: Virion spike glycoprotein
D: SGP
E: 2G1 VH
F: 2G1 VL
G: Virion spike glycoprotein
H: SGP
I: 2G1 VH
J: 2G1 VL
K: Virion spike glycoprotein
L: SGP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,96815
Polymers158,23612
Non-polymers2,7323
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody 2G1 VH


Mass: 13535.075 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody 2G1 VL


Mass: 11342.541 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein Virion spike glycoprotein


Mass: 10883.393 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus / Gene: GP / Production host: Homo sapiens (human) / References: UniProt: A0A1C4HDV6
#4: Protein SGP


Mass: 16984.287 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus / Gene: GP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: A0A1C4HDL5
#5: 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-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
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

Component
IDNameTypeEntity IDParent-IDSource
1Ebola virus glycoprotein in complex with a broadly neutralizing antibody 2G1COMPLEX#1-#40RECOMBINANT
2Ebola virus glycoproteinCOMPLEX#3-#41RECOMBINANT
32G1 FabCOMPLEX#1-#21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Henipavirus nipahense3052225
32Ebola virus1570291
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Buffer solutionpH: 7.4 / Details: 137 mM NaCl, 2.7mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4
SpecimenConc.: 1 mg/ml / Embedding 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: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of real images: 8926

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 326558 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00311531
ELECTRON MICROSCOPYf_angle_d0.61915646
ELECTRON MICROSCOPYf_dihedral_angle_d4.881702
ELECTRON MICROSCOPYf_chiral_restr0.0431765
ELECTRON MICROSCOPYf_plane_restr0.0061984

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