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- PDB-9tgc: Structure of B10 anti-stem antibody in complex with ZEBOV spike c... -

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Basic information

Entry
Database: PDB / ID: 9tgc
TitleStructure of B10 anti-stem antibody in complex with ZEBOV spike complex
Components
  • GP2
  • Heavy chain
  • Light chain
KeywordsVIRAL PROTEIN / Antibody / spike complex / epitope
Function / homology
Function and homology information


symbiont-mediated killing of host cell / viral budding from plasma membrane / symbiont-mediated-mediated suppression of host tetherin activity / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / lipid binding / fusion of virus membrane with host endosome membrane ...symbiont-mediated killing of host cell / viral budding from plasma membrane / symbiont-mediated-mediated suppression of host tetherin activity / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / lipid binding / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / host cell cytoplasm / 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 speciesHomo sapiens (human)
Ebola virus - Mayinga
Zaire (virus)
1976
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsDiskin, R. / Cohen-Dvashi, H. / Shuker, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Nat Commun / Year: 2026
Title: Identification of a pan-orthoebolavirus-reactive antibody from an rVSV-EBOV vaccinated individual
Authors: Tarnow, P. / Cohen-Dvashi, H. / Rohde, C. / Krahling, V. / Ullrich, L. / Gieselmann, L. / Zar Shuker, H. / Amatya, S. / Fathi, A. / Kupke, A. / Kreer, C. / Koch, M. / Addo, M.M. / Becker, S. ...Authors: Tarnow, P. / Cohen-Dvashi, H. / Rohde, C. / Krahling, V. / Ullrich, L. / Gieselmann, L. / Zar Shuker, H. / Amatya, S. / Fathi, A. / Kupke, A. / Kreer, C. / Koch, M. / Addo, M.M. / Becker, S. / Diskin, R. / Zehner, M. / Klein, F.
#1: Journal: Biorxiv / Year: 2026
Title: Identification of a pan-orthoebolavirus-reactive antibody from an rVSV-EBOV vaccinated individual
Authors: Tarnow, P. / Cohen-Dvashi, H. / Rohde, C. / Krahling, V. / Ullrich, L. / Gieselmann, L. / Zar Shuker, H. / Amatya, S. / Fathi, A. / Kupke, A. / Kreer, C. / Koch, M. / Addo, M.M. / Becker, S. ...Authors: Tarnow, P. / Cohen-Dvashi, H. / Rohde, C. / Krahling, V. / Ullrich, L. / Gieselmann, L. / Zar Shuker, H. / Amatya, S. / Fathi, A. / Kupke, A. / Kreer, C. / Koch, M. / Addo, M.M. / Becker, S. / Diskin, R. / Zehner, M. / Klein, F.
History
DepositionNov 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 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
H: Heavy chain
L: Light chain
X: GP2
Y: GP2
Z: GP2
B: Light chain
D: Light chain
A: Heavy chain
C: Heavy chain


Theoretical massNumber of molelcules
Total (without water)201,2229
Polymers201,2229
Non-polymers00
Water9,872548
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 Heavy chain


Mass: 25003.145 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody Light chain


Mass: 23081.592 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Protein GP2


Mass: 18989.391 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ebola virus - Mayinga, Zaire, 1976 / Cell line: HEK293F / Gene: GP / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q05320
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 548 / Source method: isolated from a natural source / Formula: H2O
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 neutralizing antibody B10 with the ZEBOV spike complex
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F
Buffer solutionpH: 8
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: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 37 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIXdev_5430model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1649385 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 30.36 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00355938
ELECTRON MICROSCOPYf_angle_d0.53678051
ELECTRON MICROSCOPYf_chiral_restr0.0432875
ELECTRON MICROSCOPYf_plane_restr0.00421029
ELECTRON MICROSCOPYf_dihedral_angle_d6.6276836

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