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- EMDB-22851: Bundibugyo virus GP (mucin deleted) bound to antibody Fab BDBV-32... -

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Basic information

Entry
Database: EMDB / ID: EMD-22851
TitleBundibugyo virus GP (mucin deleted) bound to antibody Fab BDBV-329 and EBOV-515
Map dataBundibugyo virus GP (mucin deleted) bound to antibody Fab BDBV-329 and EBOV-515
Sample
  • Complex: Bundibugyo virus GP (mucin deleted) bound to antibody Fab EBOV-329 and EBOV-515
    • Complex: Antibody Fab BDBV-329
      • Protein or peptide: Antibody BDBV-329 heavy chain
      • Protein or peptide: Antibody BDBV-329 light chain
    • Complex: Bundibugyo virus GP (mucin deleted)
      • Protein or peptide: Spike glycoprotein 1
      • Protein or peptide: Envelope glycoprotein 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsebolavirus / antibody / broadly neutralizing / glycan cap / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


membrane => GO:0016020 / 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
Spike glycoprotein / Envelope glycoprotein
Similarity search - Component
Biological speciesBundibugyo ebolavirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.6 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-
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: 0.0289
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0289
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kfe
  • Surface level: 0.0289
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kfe
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22851.png

Downloads & links

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Map

FileDownload / File: emd_22851.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBundibugyo virus GP (mucin deleted) bound to antibody Fab BDBV-329 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: 0.0289 / Movie #1: 0.0289
Minimum - Maximum-0.038358897 - 0.11573066
Average (Standard dev.)0.00031635436 (±0.0036480543)
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-0.0380.1160.000

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Supplemental data

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Sample components

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Entire : Bundibugyo virus GP (mucin deleted) bound to antibody Fab EBOV-32...

EntireName: Bundibugyo virus GP (mucin deleted) bound to antibody Fab EBOV-329 and EBOV-515
Components
  • Complex: Bundibugyo virus GP (mucin deleted) bound to antibody Fab EBOV-329 and EBOV-515
    • Complex: Antibody Fab BDBV-329
      • Protein or peptide: Antibody BDBV-329 heavy chain
      • Protein or peptide: Antibody BDBV-329 light chain
    • Complex: Bundibugyo virus GP (mucin deleted)
      • Protein or peptide: Spike glycoprotein 1
      • Protein or peptide: Envelope glycoprotein 2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Bundibugyo virus GP (mucin deleted) bound to antibody Fab EBOV-32...

SupramoleculeName: Bundibugyo virus GP (mucin deleted) bound to antibody Fab EBOV-329 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: Bundibugyo ebolavirus

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Supramolecule #2: Antibody Fab BDBV-329

SupramoleculeName: Antibody Fab BDBV-329 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Bundibugyo virus GP (mucin deleted)

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

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Macromolecule #1: Antibody BDBV-329 heavy chain

MacromoleculeName: Antibody BDBV-329 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.959318 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGSSVKV SCKASGGTFD TYAISWVRQA PGQGLEWMGG IIPVLGIVDY AQKFQGRVTI TAAKFTNIAY MELSSLRSE DAAVYYCARG LRSLSPRGQE GPTPAPGWRR AQYHYYYMDV WGTGTLVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL ...String:
QVQLVQSGAE VKKPGSSVKV SCKASGGTFD TYAISWVRQA PGQGLEWMGG IIPVLGIVDY AQKFQGRVTI TAAKFTNIAY MELSSLRSE DAAVYYCARG LRSLSPRGQE GPTPAPGWRR AQYHYYYMDV WGTGTLVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EP KSCD

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Macromolecule #2: Antibody BDBV-329 light chain

MacromoleculeName: Antibody BDBV-329 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.357906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVMTQSPGT LSLSPGERAT LSCRASQSVS SNYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGP DFTLTISRLE PEDFAVYYC QQYGSSPGTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
EIVMTQSPGT LSLSPGERAT LSCRASQSVS SNYLAWYQQK PGQAPRLLIY GASSRATGIP DRFSGSGSGP DFTLTISRLE PEDFAVYYC QQYGSSPGTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLRSPVTK SFNRGEC

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Macromolecule #3: Spike glycoprotein 1

MacromoleculeName: Spike glycoprotein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Bundibugyo ebolavirus
Molecular weightTheoretical: 38.579625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MVTSGILQLP RERFRKTSFF VWVIILFHKV FPIPLGVVHN NTLQVSDIDK LVCRDKLSST SQLKSVGLNL EGNGVATDVP TATKRWGFR AGVPPKVVNY EAGEWAENCY NLDIKKADGS ECLPEAPEGV RGFPRCRYVH KVSGTGPCPE GYAFHKEGAF F LYDRLAST ...String:
MVTSGILQLP RERFRKTSFF VWVIILFHKV FPIPLGVVHN NTLQVSDIDK LVCRDKLSST SQLKSVGLNL EGNGVATDVP TATKRWGFR AGVPPKVVNY EAGEWAENCY NLDIKKADGS ECLPEAPEGV RGFPRCRYVH KVSGTGPCPE GYAFHKEGAF F LYDRLAST IIYRSTTFSE GVVAFLILPE TKKDFFQSPP LHEPANMTTD PSSYYHTVTL NYVADNFGTN MTNFLFQVDH LT YVQLEPR FTPQFLVQLN ETIYTNGRRS NTTGTLIWKV NPTVDTGVGE WAFWENKKNF TKTLSSEELS VIFVPIDISE STE PGPLTN TTRGAANLLT GSRRTRR

UniProtKB: Spike glycoprotein

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Macromolecule #4: Envelope glycoprotein 2

MacromoleculeName: Envelope glycoprotein 2 / type: protein_or_peptide / ID: 4 / 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 #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 2 / 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: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 45640
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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