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- EMDB-55896: Structure of B10 anti-stem antibody in complex with ZEBOV spike c... -

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Basic information

Entry
Database: EMDB / ID: EMD-55896
TitleStructure of B10 anti-stem antibody in complex with ZEBOV spike complex
Map dataUnfiltered map
Sample
  • Complex: Complex of neutralizing antibody B10 with the ZEBOV spike complex
    • Protein or peptide: Heavy chain
    • Protein or peptide: Light chain
    • Protein or peptide: GP2
  • Ligand: water
KeywordsAntibody / spike complex / epitope / VIRAL PROTEIN
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, 1976
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsDiskin R / Cohen-Dvashi H / Shuker H
Funding support1 items
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 MM / 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 MM / Becker S / Diskin R / Zehner M / Klein F
History
DepositionNov 30, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55896.png

Downloads & links

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Map

FileDownload / File: emd_55896.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnfiltered map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.23866752 - 0.53115064
Average (Standard dev.)0.00033141018 (±0.016783876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local filtered map

Fileemd_55896_additional_1.map
AnnotationLocal filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_55896_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_55896_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of neutralizing antibody B10 with the ZEBOV spike complex

EntireName: Complex of neutralizing antibody B10 with the ZEBOV spike complex
Components
  • Complex: Complex of neutralizing antibody B10 with the ZEBOV spike complex
    • Protein or peptide: Heavy chain
    • Protein or peptide: Light chain
    • Protein or peptide: GP2
  • Ligand: water

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Supramolecule #1: Complex of neutralizing antibody B10 with the ZEBOV spike complex

SupramoleculeName: Complex of neutralizing antibody B10 with the ZEBOV spike complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Heavy chain

MacromoleculeName: Heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.003145 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKASGYTFA SYYMHWVRQA PGQGPEWIGR INCSGGATRY AEKFQGRVTV TRDTSTSTVY MELSSLRHD DTAVYYCARL KGETVGGPHI YQFGMDVWGH GTMVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW ...String:
QVQLVQSGAE VKKPGASVKV SCKASGYTFA SYYMHWVRQA PGQGPEWIGR INCSGGATRY AEKFQGRVTV TRDTSTSTVY MELSSLRHD DTAVYYCARL KGETVGGPHI YQFGMDVWGH GTMVTVSSAS TKGPSVFPLA PSSKSTSGGT AALGCLVKDY F PEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TKVDKRVEPK SCDKTH

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Macromolecule #2: Light chain

MacromoleculeName: Light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.081592 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVLTQSPGT LSLSPGERAT LSCRASQSVS TTYLAWYQQK PGQAPRLLIY GASNRAAGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC HQYAGTFGQG TKVEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP REAKVQWKVD NALQSGNSQE S VTEQDSKD ...String:
DIVLTQSPGT LSLSPGERAT LSCRASQSVS TTYLAWYQQK PGQAPRLLIY GASNRAAGIP DRFSGSGSGT DFTLTISRLE PEDFAVYYC HQYAGTFGQG TKVEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP REAKVQWKVD NALQSGNSQE S VTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LSSPVTKSFN RGEC

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Macromolecule #3: GP2

MacromoleculeName: GP2 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Molecular weightTheoretical: 18.989391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EAIVNAQPKC NPNLHYWTTQ DEGAAIGLAW IPYFGPAAEG IYIEGLMHNQ DGLICGLRQL ANETTQALQL FLRATTELRT FSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDF VDGSGYIPEA PRDGQAYVRK DGEWVLLSTF L GTHHHHHH

UniProtKB: Envelope glycoprotein

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 548 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 1649385
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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