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- EMDB-22839: BDBV-289 bound to EBOV GPdMuc Makona -

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Basic information

Entry
Database: EMDB / ID: EMD-22839
TitleBDBV-289 bound to EBOV GPdMuc Makona
Map dataEbola virus GP (mucin deleted, Makona strain) bound to antibody Fab BDBV-289
Sample
  • Complex: Complex of Ebola virus GP (mucin-deleted Makona strain) bound to BDBV-289 Fab
    • Protein or peptide: Virion spike glycoprotein
    • Protein or peptide: Antibody Fab heavy chain (HC) BDBV-289
    • Protein or peptide: Antibody Fab light chain (LC) BDBV-289
    • Protein or peptide: Virion spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsebolavirus / glycan cap / antibody / broadly neutralizing / filovirus / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homologyFiloviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / Envelope glycoprotein GP2-like, HR1-HR2 / extracellular region / membrane / Virion spike glycoprotein / Virion spike glycoprotein
Function and homology information
Biological speciesHomo sapiens (human) / Ebola virus / Zaire ebolavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsMurin CD / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI109762 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142785 United States
CitationJournal: Cell Rep / Year: 2021
Title: Convergence of a common solution for broad ebolavirus neutralization by glycan cap-directed human antibodies.
Authors: Charles D Murin / Pavlo Gilchuk / Philipp A Ilinykh / Kai Huang / Natalia Kuzmina / Xiaoli Shen / Jessica F Bruhn / Aubrey L Bryan / Edgar Davidson / Benjamin J Doranz / Lauren E Williamson ...Authors: Charles D Murin / Pavlo Gilchuk / Philipp A Ilinykh / Kai Huang / Natalia Kuzmina / Xiaoli Shen / Jessica F Bruhn / Aubrey L Bryan / Edgar Davidson / Benjamin J Doranz / Lauren E Williamson / Jeffrey Copps / Tanwee Alkutkar / Andrew I Flyak / Alexander Bukreyev / James E Crowe / Andrew B Ward /
Abstract: Antibodies that target the glycan cap epitope on the ebolavirus glycoprotein (GP) are common in the adaptive response of survivors. A subset is known to be broadly neutralizing, but the details of ...Antibodies that target the glycan cap epitope on the ebolavirus glycoprotein (GP) are common in the adaptive response of survivors. A subset is known to be broadly neutralizing, but the details of their epitopes and basis for neutralization are not well understood. Here, we present cryoelectron microscopy (cryo-EM) structures of diverse glycan cap antibodies that variably synergize with GP base-binding antibodies. These structures describe a conserved site of vulnerability that anchors the mucin-like domains (MLDs) to the glycan cap, which we call the MLD anchor and cradle. Antibodies that bind to the MLD cradle share common features, including use of IGHV1-69 and IGHJ6 germline genes, which exploit hydrophobic residues and form β-hairpin structures to mimic the MLD anchor, disrupt MLD attachment, destabilize GP quaternary structure, and block cleavage events required for receptor binding. Our results provide a molecular basis for ebolavirus neutralization by broadly reactive glycan cap antibodies.
History
DepositionOct 11, 2020-
Header (metadata) releaseJun 23, 2021-
Map releaseJun 23, 2021-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0397
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0397
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kej
  • Surface level: 0.0397
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22839.png

Downloads & links

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Map

FileDownload / File: emd_22839.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEbola virus GP (mucin deleted, Makona strain) bound to antibody Fab BDBV-289
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 288 pix.
= 296.64 Å		1.03 Å/pix.
x 288 pix.
= 296.64 Å		1.03 Å/pix.
x 288 pix.
= 296.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0397 / Movie #1: 0.0397
Minimum - Maximum-0.0889489 - 0.1811844
Average (Standard dev.)0.00041069926 (±0.0039929375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 296.63998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z296.640296.640296.640
α/β/γ90.00090.00090.000
start NX/NY/NZ192139186
NX/NY/NZ211274246
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0890.1810.000

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Supplemental data

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Sample components

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Entire : Complex of Ebola virus GP (mucin-deleted Makona strain) bound to ...

EntireName: Complex of Ebola virus GP (mucin-deleted Makona strain) bound to BDBV-289 Fab
Components
  • Complex: Complex of Ebola virus GP (mucin-deleted Makona strain) bound to BDBV-289 Fab
    • Protein or peptide: Virion spike glycoprotein
    • Protein or peptide: Antibody Fab heavy chain (HC) BDBV-289
    • Protein or peptide: Antibody Fab light chain (LC) BDBV-289
    • Protein or peptide: Virion spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of Ebola virus GP (mucin-deleted Makona strain) bound to ...

SupramoleculeName: Complex of Ebola virus GP (mucin-deleted Makona strain) bound to BDBV-289 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Fab and GP expressed in HEK 293F cells, complexed and purified by size exclusion chromatography
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Virion spike glycoprotein

MacromoleculeName: Virion spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
Molecular weightTheoretical: 34.978613 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARSIPLG VIHNSTLQVS DVDKLVCRDK LSSTNQLRSV GLNLEGNGVA TDVPSVTKR WGFRSGVPPK VVNYEAGEWA ENCYNLEIKK PDGSECLPAA PDGIRGFPRC RYVHKVSGTG PCAGDFAFHK E GAFFLYDR ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARSIPLG VIHNSTLQVS DVDKLVCRDK LSSTNQLRSV GLNLEGNGVA TDVPSVTKR WGFRSGVPPK VVNYEAGEWA ENCYNLEIKK PDGSECLPAA PDGIRGFPRC RYVHKVSGTG PCAGDFAFHK E GAFFLYDR LASTVIYRGT TFAEGVVAFL ILPQAKKDFF SSHPLREPVN ATEDPSSGYY STTIRYQATG FGTNETEYLF EV DNLTYVQ LESRFTPQFL LQLNETIYAS GKRSNTTGKL IWKVNPEIDT TIGEWAFWET KKNLTRKIRS EELSFT

UniProtKB: Virion spike glycoprotein

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Macromolecule #2: Antibody Fab heavy chain (HC) BDBV-289

MacromoleculeName: Antibody Fab heavy chain (HC) BDBV-289 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.864316 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MELGLRWVFL VAILEGVQCQ VQLVQSGAEV KKPGSSVKVS CKASGATFGS DTVTWVRQAP GQGLEWMGGI IPFFGEANYA QRFQGRVTI TADKSTNTAY MELSSLRSED TAVYFCARQI NEMATFGEIH YYTYMDVWGQ GTLVTVSSAS TKGPSVFPLA P SSKSTSGG ...String:
MELGLRWVFL VAILEGVQCQ VQLVQSGAEV KKPGSSVKVS CKASGATFGS DTVTWVRQAP GQGLEWMGGI IPFFGEANYA QRFQGRVTI TADKSTNTAY MELSSLRSED TAVYFCARQI NEMATFGEIH YYTYMDVWGQ GTLVTVSSAS TKGPSVFPLA P SSKSTSGG TAALGCLVKD YFPEPVTVSW NSGALTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY ICNVNHKPSN TK VDKRVEP KSCD

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Macromolecule #3: Antibody Fab light chain (LC) BDBV-289

MacromoleculeName: Antibody Fab light chain (LC) BDBV-289 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.725422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHGS ELTQDPAVSV ALGQTVRITC QGDSLRNYYA SWYQQKPRQA PVLVFYGKNN RPSGIPDRFS GSSSGNTAS LTISGAQAED EADYYCNSRD SSSNHLVFGG GTKLTVLSQP KAAPSVTLFP PSSEELQANK ATLVCLISDF Y PGAVTVAW ...String:
MGWSCIILFL VATATGVHGS ELTQDPAVSV ALGQTVRITC QGDSLRNYYA SWYQQKPRQA PVLVFYGKNN RPSGIPDRFS GSSSGNTAS LTISGAQAED EADYYCNSRD SSSNHLVFGG GTKLTVLSQP KAAPSVTLFP PSSEELQANK ATLVCLISDF Y PGAVTVAW KADSSPVKAG VETTTPSKQS NNKYAASSYL SLTPEQWKSH RSYSCQVTHE GSTVEKTVAP TEC

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Macromolecule #4: Virion spike glycoprotein

MacromoleculeName: Virion spike glycoprotein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Zaire ebolavirus
Molecular weightTheoretical: 22.158592 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NNNTHHQDTG EESASSGKLG LITNTIAGVA GLITGGRRTR REVIVNAQPK CNPNLHYWTT QDEGAAIGLA WIPYFGPAAE GIYTEGLMH NQDGLICGLR QLANETTQAL QLFLRATTEL RTFSILNRKA IDFLLQRWGG TCHILGPDCC IEPHDWTKNI T DKIDQIIH ...String:
NNNTHHQDTG EESASSGKLG LITNTIAGVA GLITGGRRTR REVIVNAQPK CNPNLHYWTT QDEGAAIGLA WIPYFGPAAE GIYTEGLMH NQDGLICGLR QLANETTQAL QLFLRATTEL RTFSILNRKA IDFLLQRWGG TCHILGPDCC IEPHDWTKNI T DKIDQIIH DDDDKAGWSH PQFEKGGGSG GGSGGGSWSH PQFEK

UniProtKB: Virion spike glycoprotein

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 9 / 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: 3D classification
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 32108
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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