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- EMDB-22847: Ebola virus GP (mucin deleted, Makona strain) bound to antibody F... -

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Basic information

Entry
Database: EMDB / ID: EMD-22847
TitleEbola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-296 and EBOV-515
Map dataEbola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-296 and EBOV-515
Sample
  • Complex: Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-296 and EBOV-515
    • Complex: EBOV-296 Fab
      • Protein or peptide: Antibody Fab EBOV-296 heavy chain
      • Protein or peptide: Antibody Fab EBOV-296 light chain
    • Complex: Ebola virus GP (mucin deleted, Makona strain)
      • Protein or peptide: Virion spike glycoprotein 1
      • Protein or peptide: Virion spike glycoprotein 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsebolavirus / antibody / broadly neutralizing / glycan cap / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyEnvelope glycoprotein GP2-like, HR1-HR2 / Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein / extracellular region / membrane / Virion spike glycoprotein / Virion spike glycoprotein
Function and homology information
Biological speciesEbola virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 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) 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 13, 2020-
Header (metadata) releaseApr 28, 2021-
Map releaseApr 28, 2021-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.478
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.478
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kf9
  • Surface level: 0.478
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kf9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22847.png

Downloads & links

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Map

FileDownload / File: emd_22847.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 EBOV-296 and EBOV-515
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 288 pix.
= 331.2 Å		1.15 Å/pix.
x 288 pix.
= 331.2 Å		1.15 Å/pix.
x 288 pix.
= 331.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.478 / Movie #1: 0.478
Minimum - Maximum-0.352563 - 1.4509231
Average (Standard dev.)0.0011454956 (±0.07200078)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 331.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z331.200331.200331.200
α/β/γ90.00090.00090.000
start NX/NY/NZ278280246
NX/NY/NZ474891
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.3531.4510.001

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Supplemental data

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Sample components

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Entire : Ebola virus GP (mucin deleted, Makona strain) bound to antibody F...

EntireName: Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-296 and EBOV-515
Components
  • Complex: Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-296 and EBOV-515
    • Complex: EBOV-296 Fab
      • Protein or peptide: Antibody Fab EBOV-296 heavy chain
      • Protein or peptide: Antibody Fab EBOV-296 light chain
    • Complex: Ebola virus GP (mucin deleted, Makona strain)
      • Protein or peptide: Virion spike glycoprotein 1
      • Protein or peptide: Virion spike glycoprotein 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Ebola virus GP (mucin deleted, Makona strain) bound to antibody F...

SupramoleculeName: Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-296 and EBOV-515
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Parts of complex expressed and purified recombinantly, complexed and purified by gel filtration
Source (natural)Organism: Ebola virus

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Supramolecule #2: EBOV-296 Fab

SupramoleculeName: EBOV-296 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Ebola virus GP (mucin deleted, Makona strain)

SupramoleculeName: Ebola virus GP (mucin deleted, Makona strain) / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Ebola virus

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Macromolecule #1: Antibody Fab EBOV-296 heavy chain

MacromoleculeName: Antibody Fab EBOV-296 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.260855 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MELGLRWVFL VAILEGVQCQ VQLVESGPGL VKPSQTLSLI CTVSGGSISS GDFYWSWIRQ PPGKGLEWIG FFYYSGITYY NPSLKSRVS ISRDTSTNQF SLKLRSVTAA DTAVYYCARV RGGRITLGQG DMYYYSGMDV WGQGTLVTVS SASTKGPSVF P LAPSSKST ...String:
MELGLRWVFL VAILEGVQCQ VQLVESGPGL VKPSQTLSLI CTVSGGSISS GDFYWSWIRQ PPGKGLEWIG FFYYSGITYY NPSLKSRVS ISRDTSTNQF SLKLRSVTAA DTAVYYCARV RGGRITLGQG DMYYYSGMDV WGQGTLVTVS SASTKGPSVF P LAPSSKST SGGTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PS NTKVDKR VEPKSCD

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Macromolecule #2: Virion spike glycoprotein 1

MacromoleculeName: Virion spike glycoprotein 1 / type: protein_or_peptide / ID: 2 / 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 #3: Virion spike glycoprotein 2

MacromoleculeName: Virion spike glycoprotein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
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 #4: Antibody Fab EBOV-296 light chain

MacromoleculeName: Antibody Fab EBOV-296 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.794436 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHQS VLTQPPSASG TPGQRVSISC SGSRSNIGGN TVDWYQQLPG TDPKLLIYSN DQRPSGVPDR FSGSKSGTS ASLAISGLQS EDEADYYCAA WDDSLNGHWV FGGGTKLTVL QPKAAPSVTL FPPSSEELQA NKATLVCLIS D FYPGAVTV ...String:
MGWSCIILFL VATATGVHQS VLTQPPSASG TPGQRVSISC SGSRSNIGGN TVDWYQQLPG TDPKLLIYSN DQRPSGVPDR FSGSKSGTS ASLAISGLQS EDEADYYCAA WDDSLNGHWV FGGGTKLTVL QPKAAPSVTL FPPSSEELQA NKATLVCLIS D FYPGAVTV AWKADSSPVK AGVETTTPSK QSNNKYAASS YLSLTPEQWK SHRSYSCQVT HEGSTVEKTV APTECS

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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 TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: 3D classification
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69564
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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