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- EMDB-22842: Ebola virus GP (mucin deleted, Makona strain) bound to antibody F... -

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Basic information

Entry
Database: EMDB / ID: EMD-22842
TitleEbola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-293
Map dataEbola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-293 and EBOV-515
Sample
  • Complex: Complex of Ebola virus GP (mucin deleted, Makona strain) bound to the antibody Fab EBOV-293 and EBOV-515
    • Complex: Ebola virus GP (mucin deleted, Makona strain)
      • Protein or peptide: Virion spike glycoprotein 1
      • Protein or peptide: Virion spike glycoprotein 2
    • Complex: EBOV-293 Fab
      • Protein or peptide: Antibody Fab EBOV-293 light chain
      • Protein or peptide: Antibody Fab EBOV-293 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsebolavirus / glycan cap / antibody / broadly neutralizing / filovirus / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / Envelope glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Ebola virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 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 13, 2020-
Header (metadata) releaseApr 28, 2021-
Map releaseApr 28, 2021-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.572
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.572
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kex
  • Surface level: 0.572
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kex
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22842.png

Downloads & links

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Map

FileDownload / File: emd_22842.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEbola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-293 and EBOV-515
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 320 pix.
= 368. Å		1.15 Å/pix.
x 320 pix.
= 368. Å		1.15 Å/pix.
x 320 pix.
= 368. 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: 0.572 / Movie #1: 0.572
Minimum - Maximum-0.7858056 - 2.3989308
Average (Standard dev.)-0.0016886538 (±0.08882748)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z368.000368.000368.000
α/β/γ90.00090.00090.000
start NX/NY/NZ278280246
NX/NY/NZ474891
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.7862.399-0.002

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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 the antibody Fab EBOV-293 and EBOV-515
Components
  • Complex: Complex of Ebola virus GP (mucin deleted, Makona strain) bound to the antibody Fab EBOV-293 and EBOV-515
    • Complex: Ebola virus GP (mucin deleted, Makona strain)
      • Protein or peptide: Virion spike glycoprotein 1
      • Protein or peptide: Virion spike glycoprotein 2
    • Complex: EBOV-293 Fab
      • Protein or peptide: Antibody Fab EBOV-293 light chain
      • Protein or peptide: Antibody Fab EBOV-293 heavy chain
  • 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 the antibody Fab EBOV-293 and EBOV-515
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Complex components were expressed in HEK 293F cells, complexed and purified by size exclusion chromatography. The Fab ADI-15878 was added to increase complex size and assist in angular ...Details: Complex components were expressed in HEK 293F cells, complexed and purified by size exclusion chromatography. The Fab ADI-15878 was added to increase complex size and assist in angular sampling but was not build in the associated model.
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Ebola virus GP (mucin deleted, Makona strain)

SupramoleculeName: Ebola virus GP (mucin deleted, Makona strain) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Ebola virus

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Supramolecule #3: EBOV-293 Fab

SupramoleculeName: EBOV-293 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Antibody Fab EBOV-293 light chain

MacromoleculeName: Antibody Fab EBOV-293 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.215092 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHQT VMTQSPGTLS LSPGERATLS CGVSQSISST YFAWYQQKVG QAPRLLIYGA SNRASGIPDR FSGSASGTD FTLTISRVEP EDFAVYYCQQ YGSSPTFGQG TRLEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP R EAKVQWKV ...String:
MGWSCIILFL VATATGVHQT VMTQSPGTLS LSPGERATLS CGVSQSISST YFAWYQQKVG QAPRLLIYGA SNRASGIPDR FSGSASGTD FTLTISRVEP EDFAVYYCQQ YGSSPTFGQG TRLEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP R EAKVQWKV DNALQSGNSQ ESVTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LSSPVTKSFN RGEC

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Macromolecule #2: Antibody Fab EBOV-293 heavy chain

MacromoleculeName: Antibody Fab EBOV-293 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.001475 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MELGLRWVFL VAILEGVQCQ VQLVQSGAEV KKPGSSVKVS CKASGGTFID YTYNWVRQAP GQGLVWMGRV VPGLGLSSYA QQFEDRVTI TAAKSTSTVY MELRGLTSED TAMYYCARDT ASFGWLPFAF WGQGTLVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL ...String:
MELGLRWVFL VAILEGVQCQ VQLVQSGAEV KKPGSSVKVS CKASGGTFID YTYNWVRQAP GQGLVWMGRV VPGLGLSSYA QQFEDRVTI TAAKSTSTVY MELRGLTSED TAMYYCARDT ASFGWLPFAF WGQGTLVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EP KSCD

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Macromolecule #3: Virion spike glycoprotein 1

MacromoleculeName: Virion spike glycoprotein 1 / type: protein_or_peptide / ID: 3 / 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: Envelope glycoprotein

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Macromolecule #4: Virion spike glycoprotein 2

MacromoleculeName: Virion spike glycoprotein 2 / type: protein_or_peptide / ID: 4 / 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: Envelope glycoprotein

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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

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: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 79722
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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