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- EMDB-22852: Ebola virus GP (mucin deleted, Makona strain) bound to antibody F... -

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Basic information

Entry
Database: EMDB / ID: EMD-22852
TitleEbola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-237 and EBOV-515
Map dataEbola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-237 and EBOV-515
Sample
  • Complex: Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-237 and EBOV-515
    • Complex: Antibody Fab EBOV-237
      • Protein or peptide: Antibody Fab EBOV-237 heavy chain
      • Protein or peptide: Antibody Fab EBOV-237 light chain
    • Complex: Ebola virus GP (mucin deleted, Makona strain)
      • Protein or peptide: Ebola virus GP1 (mucin deleted, Makona strain)
      • Protein or peptide: Ebola virus GP2 (Makona strain)
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 speciesEbola virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.9 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-
UpdateApr 28, 2021-
Current statusApr 28, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0185
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0185
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22852.png

Downloads & links

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Map

FileDownload / File: emd_22852.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-237 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: 0.0185 / Movie #1: 0.0185
Minimum - Maximum-0.025578042 - 0.083205916
Average (Standard dev.)0.00034930787 (±0.002714404)
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-0.0260.0830.000

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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-237 and EBOV-515
Components
  • Complex: Ebola virus GP (mucin deleted, Makona strain) bound to antibody Fab EBOV-237 and EBOV-515
    • Complex: Antibody Fab EBOV-237
      • Protein or peptide: Antibody Fab EBOV-237 heavy chain
      • Protein or peptide: Antibody Fab EBOV-237 light chain
    • Complex: Ebola virus GP (mucin deleted, Makona strain)
      • Protein or peptide: Ebola virus GP1 (mucin deleted, Makona strain)
      • Protein or peptide: Ebola virus GP2 (Makona strain)

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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-237 and EBOV-515
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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: Antibody Fab EBOV-237

SupramoleculeName: Antibody Fab EBOV-237 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#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: #1-#2
Source (natural)Organism: Ebola virus

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Macromolecule #1: Ebola virus GP1 (mucin deleted, Makona strain)

MacromoleculeName: Ebola virus GP1 (mucin deleted, Makona strain) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARSIPLG VIHNSTLQVS DVDKLVCRDK LSSTNQLRSV GLNLEGNGVA TDVPSVTKRW GFRSGVPPKV VNYEAGEWAE NCYNLEIKKP DGSECLPAAP DGIRGFPRCR YVHKVSGTGP CAGDFAFHKE GAFFLYDRLA ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARSIPLG VIHNSTLQVS DVDKLVCRDK LSSTNQLRSV GLNLEGNGVA TDVPSVTKRW GFRSGVPPKV VNYEAGEWAE NCYNLEIKKP DGSECLPAAP DGIRGFPRCR YVHKVSGTGP CAGDFAFHKE GAFFLYDRLA STVIYRGTTF AEGVVAFLIL PQAKKDFFSS HPLREPVNAT EDPSSGYYST TIRYQATGFG TNETEYLFEV DNLTYVQLES RFTPQFLLQL NETIYASGKR SNTTGKLIWK VNPEIDTTIG EWAFWETKKN LTRKIRSEEL SFT

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Macromolecule #2: Ebola virus GP2 (Makona strain)

MacromoleculeName: Ebola virus GP2 (Makona strain) / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NNNTHHQDTG EESASSGKLG LITNTIAGVA GLITGGRRTR REVIVNAQPK CNPNLHYWTT QDEGAAIGLA WIPYFGPAAE GIYTEGLMHN QDGLICGLRQ LANETTQALQ LFLRATTELR TFSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDD ...String:
NNNTHHQDTG EESASSGKLG LITNTIAGVA GLITGGRRTR REVIVNAQPK CNPNLHYWTT QDEGAAIGLA WIPYFGPAAE GIYTEGLMHN QDGLICGLRQ LANETTQALQ LFLRATTELR TFSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDD DDKAGWSHPQ FEKGGGSGGG SGGGSWSHPQ FEK

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Macromolecule #3: Antibody Fab EBOV-237 heavy chain

MacromoleculeName: Antibody Fab EBOV-237 heavy chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSGTLSL TCAVSGGSIS NGIWWSWVRQ PPGKGLEWIG EIYHSGSTNY SPSLKSRVTI SLDKSKNQFS LKLNSVTAAD TAVYYCARAP SQFDFSDWLV PQGAMFRGHY IDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP ...String:
QVQLQESGPG LVKPSGTLSL TCAVSGGSIS NGIWWSWVRQ PPGKGLEWIG EIYHSGSTNY SPSLKSRVTI SLDKSKNQFS LKLNSVTAAD TAVYYCARAP SQFDFSDWLV PQGAMFRGHY IDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSCD

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Macromolecule #4: Antibody Fab EBOV-237 light chain

MacromoleculeName: Antibody Fab EBOV-237 light chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQSPDS LAVSLGERAT INCKSSQSVL YNSNNKNYLA WYQQKPGQPP KLLIYWASTR ESGVPDRFSG SGSGTDFTLA ISSLRAEDVA VYYCQQYYSA PYTFGQGTKM EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL QSGNSQESVT ...String:
DIVMTQSPDS LAVSLGERAT INCKSSQSVL YNSNNKNYLA WYQQKPGQPP KLLIYWASTR ESGVPDRFSG SGSGTDFTLA ISSLRAEDVA VYYCQQYYSA PYTFGQGTKM EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL QSGNSQESVT EQDSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC

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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: 9.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17244
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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