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- EMDB-22841: Bundibugyo virus GP (mucin deleted) bound to antibody Fab BDBV-43... -

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Basic information

Entry
Database: EMDB / ID: EMD-22841
TitleBundibugyo virus GP (mucin deleted) bound to antibody Fab BDBV-43 and ADI-15878
Map dataBundibugyo virus GP (mucin deleted) bound to antibody Fab BDBV-43 and ADI-15878
Sample
  • Complex: Complex of Bundibugyo virus GP (mucin deleted) bound to the antibody Fab BDBV-43 and ADI-15878
    • Complex: Bundibugyo virus GP (mucin deleted)
      • Protein or peptide: Spike glycoprotein 1
      • Protein or peptide: Envelope glycoprotein 2
    • Complex: BDBV-43 Fab
      • Protein or peptide: BDBV-43 Fab heavy chain
      • Protein or peptide: BDBV-43 Fab light 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


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: 4.16 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: 0.41
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.41
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kew
  • Surface level: 0.41
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kew
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22841.png

Downloads & links

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Map

FileDownload / File: emd_22841.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-43 and ADI-15878
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: 0.41 / Movie #1: 0.41
Minimum - Maximum-1.1500407 - 2.1496599
Average (Standard dev.)0.006688564 (±0.07157642)
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/NZ278280246
NX/NY/NZ474891
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-1.1502.1500.007

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Supplemental data

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Sample components

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Entire : Complex of Bundibugyo virus GP (mucin deleted) bound to the antib...

EntireName: Complex of Bundibugyo virus GP (mucin deleted) bound to the antibody Fab BDBV-43 and ADI-15878
Components
  • Complex: Complex of Bundibugyo virus GP (mucin deleted) bound to the antibody Fab BDBV-43 and ADI-15878
    • Complex: Bundibugyo virus GP (mucin deleted)
      • Protein or peptide: Spike glycoprotein 1
      • Protein or peptide: Envelope glycoprotein 2
    • Complex: BDBV-43 Fab
      • Protein or peptide: BDBV-43 Fab heavy chain
      • Protein or peptide: BDBV-43 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of Bundibugyo virus GP (mucin deleted) bound to the antib...

SupramoleculeName: Complex of Bundibugyo virus GP (mucin deleted) bound to the antibody Fab BDBV-43 and ADI-15878
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: Bundibugyo ebolavirus

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Supramolecule #2: Bundibugyo virus GP (mucin deleted)

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

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Supramolecule #3: BDBV-43 Fab

SupramoleculeName: BDBV-43 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike glycoprotein 1

MacromoleculeName: Spike glycoprotein 1 / type: protein_or_peptide / ID: 1 / 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 #2: BDBV-43 Fab heavy chain

MacromoleculeName: BDBV-43 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.233672 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MELGLRWVFL VAILEGVQCQ VQLVQSGAEV KKPGSSVKVS CRASGDSFSR KYGISWVRQA PGQGFEWMGT IMPIVGLTTS AQKFQGRVT ITADKSTSTA HMELNSLTSE DTAIYYCARD EIIGARPHWF DSWGQGTLVT VSSASTKGPS VFPLAPSSKS T SGGTAALG ...String:
MELGLRWVFL VAILEGVQCQ VQLVQSGAEV KKPGSSVKVS CRASGDSFSR KYGISWVRQA PGQGFEWMGT IMPIVGLTTS AQKFQGRVT ITADKSTSTA HMELNSLTSE DTAIYYCARD EIIGARPHWF DSWGQGTLVT VSSASTKGPS VFPLAPSSKS T SGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RV EPKSCD

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Macromolecule #3: BDBV-43 Fab light chain

MacromoleculeName: BDBV-43 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.397576 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHEI VMTQSPAIMS VSPGKRATLS CRASQSVSSN LAWYQRKPGQ APRLLIYGSS TRATGIPARF SGSGSGTEF TLTISSLQSE DFAVYYCLQY YNWPRTFGQG TKVEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP R EAKVQWKV ...String:
MGWSCIILFL VATATGVHEI VMTQSPAIMS VSPGKRATLS CRASQSVSSN LAWYQRKPGQ APRLLIYGSS TRATGIPARF SGSGSGTEF TLTISSLQSE DFAVYYCLQY YNWPRTFGQG TKVEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP R EAKVQWKV DNALQSGNSQ ESVTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LSSPVTKSFN RGEC

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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: 3 / 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: 4.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 383783
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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