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- EMDB-8936: Bundibugyo virus GP (mucin-deleted) in complex with pan-ebolaviru... -

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Basic information

Entry
Database: EMDB / ID: EMD-8936
TitleBundibugyo virus GP (mucin-deleted) in complex with pan-ebolavirus human antibody ADI-15878 Fab
Map dataBundibugyo virus glycoprotein (mucin-deleted) ectodomain bound to human survivor antibody ADI-15878 Fab
Sample
  • Complex: Bundibugyo virus glycoprotein (mucin-deleted) ectodomain bound to human survivor antibody ADI-15878 Fab
    • Complex: Bundibugyo virus glycoprotein (mucin-deleted) ectodomain
      • Protein or peptide: Bundibugyo virus GP2
    • Complex: Human survivor antibody ADI-15878 Fab
      • Protein or peptide: Antibody ADI-15878 Fab, light chain
      • Protein or peptide: Antibody ADI-15878 Fab, heavy chain
  • Protein or peptide: Bundibugyo virus GP1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsantibody / pan-ebolavirus / internal fusion loop / HR1 / glycoprotein / VIRAL PROTEIN
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 / 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
Similarity search - Domain/homology
Envelope glycoprotein
Similarity search - Component
Biological speciesEbola virus / Bundibugyo virus / Homo sapiens (human) / Bundibugyo ebolavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.29 Å
AuthorsMurin CD / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI109762 United States
CitationJournal: Cell Rep / Year: 2018
Title: Structural Basis of Pan-Ebolavirus Neutralization by an Antibody Targeting the Glycoprotein Fusion Loop.
Authors: Charles D Murin / Jessica F Bruhn / Zachary A Bornholdt / Jeffrey Copps / Robyn Stanfield / Andrew B Ward /
Abstract: Monoclonal antibodies (mAbs) with pan-ebolavirus cross-reactivity are highly desirable, but development of such mAbs is limited by a lack of a molecular understanding of cross-reactive epitopes. The ...Monoclonal antibodies (mAbs) with pan-ebolavirus cross-reactivity are highly desirable, but development of such mAbs is limited by a lack of a molecular understanding of cross-reactive epitopes. The antibody ADI-15878 was previously identified from a human survivor of Ebola virus Makona variant (EBOV/Mak) infection. This mAb demonstrated potent neutralizing activity against all known ebolaviruses and provided protection in rodent and ferret models against three ebolavirus species. Here, we describe the unliganded crystal structure of ADI-15878 as well as the cryo-EM structures of ADI-15878 in complex with the EBOV/Mak and Bundibugyo virus (BDBV) glycoproteins (GPs). ADI-15878 binds through an induced-fit mechanism by targeting highly conserved residues in the internal fusion loop (IFL), bridging across GP protomers via the heptad repeat 1 (HR1) region. Our structures provide a more complete description of the ebolavirus immunogenic landscape, as well as a molecular basis for how rare but potent antibodies target conserved filoviral fusion machinery.
History
DepositionJul 5, 2018-
Header (metadata) releaseSep 12, 2018-
Map releaseSep 12, 2018-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0393
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0393
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6dzm
  • Surface level: 0.0393
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6dzm
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8936.png

Downloads & links

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Map

FileDownload / File: emd_8936.map.gz / Format: CCP4 / Size: 134.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBundibugyo virus glycoprotein (mucin-deleted) ectodomain bound to human survivor antibody ADI-15878 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 328 pix.
= 429.68 Å		1.31 Å/pix.
x 328 pix.
= 429.68 Å		1.31 Å/pix.
x 328 pix.
= 429.68 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0393 / Movie #1: 0.0393
Minimum - Maximum-0.045263845 - 0.12573333
Average (Standard dev.)0.00022437646 (±0.0031417415)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions328328328
Spacing328328328
CellA=B=C: 429.68 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z328328328
origin x/y/z0.0000.0000.000
length x/y/z429.680429.680429.680
α/β/γ90.00090.00090.000
start NX/NY/NZ-69-50-137
NX/NY/NZ136114193
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS328328328
D min/max/mean-0.0450.1260.000

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Supplemental data

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Sample components

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Entire : Bundibugyo virus glycoprotein (mucin-deleted) ectodomain bound to...

EntireName: Bundibugyo virus glycoprotein (mucin-deleted) ectodomain bound to human survivor antibody ADI-15878 Fab
Components
  • Complex: Bundibugyo virus glycoprotein (mucin-deleted) ectodomain bound to human survivor antibody ADI-15878 Fab
    • Complex: Bundibugyo virus glycoprotein (mucin-deleted) ectodomain
      • Protein or peptide: Bundibugyo virus GP2
    • Complex: Human survivor antibody ADI-15878 Fab
      • Protein or peptide: Antibody ADI-15878 Fab, light chain
      • Protein or peptide: Antibody ADI-15878 Fab, heavy chain
  • Protein or peptide: Bundibugyo virus GP1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Bundibugyo virus glycoprotein (mucin-deleted) ectodomain bound to...

SupramoleculeName: Bundibugyo virus glycoprotein (mucin-deleted) ectodomain bound to human survivor antibody ADI-15878 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3-#4
Source (natural)Organism: Ebola virus
Molecular weightTheoretical: 45 KDa

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Supramolecule #2: Bundibugyo virus glycoprotein (mucin-deleted) ectodomain

SupramoleculeName: Bundibugyo virus glycoprotein (mucin-deleted) ectodomain
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Bundibugyo virus

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Supramolecule #3: Human survivor antibody ADI-15878 Fab

SupramoleculeName: Human survivor antibody ADI-15878 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4 / Details: Fab was generated by papain digestion of IgG
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Bundibugyo virus GP1

MacromoleculeName: Bundibugyo virus GP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bundibugyo ebolavirus
Molecular weightTheoretical: 34.697938 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: IPLGVVHNNT LQVSDIDKLV CRDKLSSTSQ LKSVGLNLEG NGVATDVPTA TKRWGFRAGV PPKVVNYEAG EWAENCYNLD IKKADGSEC LPEAPEGVRG FPRCRYVHKV SGTGPCPEGY AFHKEGAFFL YDRLASTIIY RSTTFSEGVV AFLILPETKK D FFQSPPLH ...String:
IPLGVVHNNT LQVSDIDKLV CRDKLSSTSQ LKSVGLNLEG NGVATDVPTA TKRWGFRAGV PPKVVNYEAG EWAENCYNLD IKKADGSEC LPEAPEGVRG FPRCRYVHKV SGTGPCPEGY AFHKEGAFFL YDRLASTIIY RSTTFSEGVV AFLILPETKK D FFQSPPLH EPANMTTDPS SYYHTVTLNY VADNFGTNMT NFLFQVDHLT YVQLEPRFTP QFLVQLNETI YTNGRRSNTT GT LIWKVNP TVDTGVGEWA FWENKKNFTK TLSSEELSVI FVPIDISEST EPGPLTNTTR GAANLLTGSR RTRR

UniProtKB: Envelope glycoprotein

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Macromolecule #2: Bundibugyo virus GP2

MacromoleculeName: Bundibugyo virus GP2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bundibugyo ebolavirus
Molecular weightTheoretical: 19.683902 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EITLRTQAKC NPNLHYWTTQ DEGAAIGLAW IPYFGPAAEG IYTEGIMHNQ NGLICGLRQL ANETTQALQL FLRATTELRT FSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDF IDKPLPDQTD VEVDDDDKAG WSHPQFEKGG G SGGGSGGG SWSHPQFEK

UniProtKB: Envelope glycoprotein

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Macromolecule #3: Antibody ADI-15878 Fab, light chain

MacromoleculeName: Antibody ADI-15878 Fab, light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.333459 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString:
DIVLTQSPST LSASVGDRVT ITCRASQSIS SWLAWYQQKP GEAPKLLISD ASSLESGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QYYSSPTFGG GTKVEIK

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Macromolecule #4: Antibody ADI-15878 Fab, heavy chain

MacromoleculeName: Antibody ADI-15878 Fab, heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.043574 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString:
VQLVQSGVTL VQPGGSLRVS CAASGFTFSS YAMSWVRQAP GKGLEWVSAI SGLGGSTYYA DSVKGRFTIS RDNSKNTLYL QMNSLRAED TAVYYCAKDH RVWAAGYHFD YWGQGALVTV S

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 milimolarNaClsodium chloride
20.0 milimolarTrisTris

Details: Solutions were made fresh from 10X concentrate and filtered with a 0.2 micrometer filter into a sterile glass container.
GridSupport film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec. / Pretreatment - Atmosphere: OTHER / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details: 3.5s blot on both sides of the grid using Whattman No. 1 filter paper.
DetailsAntibody ADI-15878 Fab was added in 10 molar excess to glycoprotein and allowed to incubate overnight at 4 degrees Celsius followed by size exclusion chromatography to purify the complex and rid of excess Fab.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsPreliminary grid screening was performed manually
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 38167 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

8700


Details: Starting model was a negative stain reconstruction and low pass filtered
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.29 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 35961
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
Details: Particles were initially classified with 3D classification in Relion
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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