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- EMDB-27638: Structure of EBOV GP lacking the mucin-like domain with 9.20.1A2 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-27638
TitleStructure of EBOV GP lacking the mucin-like domain with 9.20.1A2 Fab and 6D6 scFv bound
Map dataStructure of EBOV GP lacking the mucin-like domain with 9.20.1A2 Fab and 6D6 scFv bound
Sample
  • Complex: Complex of Ebola virus glycoprotein trimer with 1A2 antibody Fab and 6D6 antibody scFv
    • Complex: Antibody 9.20.1A2 Fab
      • Protein or peptide: Antibody 9.20.1A2 Fab heavy chain
      • Protein or peptide: Antibody 9.20.1A2 Fab light chain
    • Protein or peptide: Glycoprotein GP1
    • Protein or peptide: Glycoprotein GP2
    • Protein or peptide: Antibody 6D6 scFv
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsAntibody / Viral protein / glycoprotein / immune system / Ebola virus / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / suppression by virus of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / membrane raft / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / host cell plasma membrane / virion membrane / extracellular region / membrane / identical protein binding
Similarity search - Function
Filoviruses glycoprotein, extracellular domain / Filoviruses glycoprotein / Filovirus glycoprotein
Similarity search - Domain/homology
Envelope glycoprotein / Envelope glycoprotein
Similarity search - Component
Biological speciesEbola virus - Mayinga, Zaire, 1976 / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsYu X / Saphire EO
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI142790 United States
National Science Foundation (NSF, United States)NSF 1531991 United States
CitationJournal: Cell Rep / Year: 2023
Title: The evolution and determinants of neutralization of potent head-binding antibodies against Ebola virus.
Authors: Xiaoying Yu / Kathryn M Hastie / Carl W Davis / Ruben Diaz Avalos / Dewight Williams / Diptiben Parekh / Sean Hui / Colin Mann / Chitra Hariharan / Ayato Takada / Rafi Ahmed / Erica Ollmann Saphire /
Abstract: Monoclonal antibodies against the Ebola virus (EBOV) surface glycoprotein are effective treatments for EBOV disease. Antibodies targeting the EBOV glycoprotein (GP) head epitope have potent ...Monoclonal antibodies against the Ebola virus (EBOV) surface glycoprotein are effective treatments for EBOV disease. Antibodies targeting the EBOV glycoprotein (GP) head epitope have potent neutralization and Fc effector function activity and thus are of high interest as therapeutics and for vaccine design. Here we focus on the head-binding antibodies 1A2 and 1D5, which have been identified previously in a longitudinal study of survivors of EBOV infection. 1A2 and 1D5 have the same heavy- and light-chain germlines despite being isolated from different individuals and at different time points after recovery from infection. Cryoelectron microscopy analysis of each antibody in complex with the EBOV surface GP reveals key amino acid substitutions in 1A2 that contribute to greater affinity, improved neutralization potency, and enhanced breadth as well as two strategies for antibody evolution from a common site.
History
DepositionJul 15, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateNov 22, 2023-
Current statusNov 22, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27638.png

Downloads & links

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Map

FileDownload / File: emd_27638.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of EBOV GP lacking the mucin-like domain with 9.20.1A2 Fab and 6D6 scFv bound
Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.014
Minimum - Maximum-0.026904112 - 0.07591871
Average (Standard dev.)-0.000058027792 (±0.0015862864)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 403.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map 1

Fileemd_27638_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_27638_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Ebola virus glycoprotein trimer with 1A2 antibody Fab ...

EntireName: Complex of Ebola virus glycoprotein trimer with 1A2 antibody Fab and 6D6 antibody scFv
Components
  • Complex: Complex of Ebola virus glycoprotein trimer with 1A2 antibody Fab and 6D6 antibody scFv
    • Complex: Antibody 9.20.1A2 Fab
      • Protein or peptide: Antibody 9.20.1A2 Fab heavy chain
      • Protein or peptide: Antibody 9.20.1A2 Fab light chain
    • Protein or peptide: Glycoprotein GP1
    • Protein or peptide: Glycoprotein GP2
    • Protein or peptide: Antibody 6D6 scFv
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of Ebola virus glycoprotein trimer with 1A2 antibody Fab ...

SupramoleculeName: Complex of Ebola virus glycoprotein trimer with 1A2 antibody Fab and 6D6 antibody scFv
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976

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Supramolecule #2: Antibody 9.20.1A2 Fab

SupramoleculeName: Antibody 9.20.1A2 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #4-#5
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Glycoprotein GP1

MacromoleculeName: Glycoprotein GP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976 / Strain: Mayinga-76
Molecular weightTheoretical: 31.297158 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: IPLGVIHNST LQVSDVDKLV CRDKLSSTNQ LRSVGLNLEG NGVATDVPSA TKRWGFRSGV PPKVVNYEAG EWAENCYNLE IKKPDGSEC LPAAPDGIRG FPRCRYVHKV SGTGPCAGDF AFHKEGAFFL YDRLASTVIY RGTTFAEGVV AFLILPQAKK D FFSSHPLR ...String:
IPLGVIHNST LQVSDVDKLV CRDKLSSTNQ LRSVGLNLEG NGVATDVPSA TKRWGFRSGV PPKVVNYEAG EWAENCYNLE IKKPDGSEC LPAAPDGIRG FPRCRYVHKV SGTGPCAGDF AFHKEGAFFL YDRLASTVIY RGTTFAEGVV AFLILPQAKK D FFSSHPLR EPVNATEDPS SGYYSTTIRY QATGFGTNET EYLFEVDNLT YVQLESRFTP QFLLQLNETI YTSGKRSNTT GK LIWKVNP EIDTTIGEWA FWETKKNLTR KIRSEELSFT VVS

UniProtKB: Envelope glycoprotein

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Macromolecule #2: Glycoprotein GP2

MacromoleculeName: Glycoprotein GP2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus - Mayinga, Zaire, 1976
Molecular weightTheoretical: 15.335362 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString:
EAIVNAQPKC NPNLHYWTTQ DEGAAIGLAW IPYFGPAAEG IYTEGLMHNQ DGLICGLRQL ANETTQALQL FLRATTELRT FSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDF VDKTLPD

UniProtKB: Envelope glycoprotein

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Macromolecule #3: Antibody 6D6 scFv

MacromoleculeName: Antibody 6D6 scFv / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.853459 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: QVQLQQSGTE LVKPGASVKL SCKASGYTFT SYWMHWVKQR PGQGLEWIGE INPRNGRTDF SEKFKSKATL TVDTSSSTAF IQLSSLTSE DSAVYYCARW GYYGSSDYWG QGTALTVSSG TGGSGGGGSG GGGSGGGASD IVVTQSHKFM STSVGDRVSI T CKASQDVS ...String:
QVQLQQSGTE LVKPGASVKL SCKASGYTFT SYWMHWVKQR PGQGLEWIGE INPRNGRTDF SEKFKSKATL TVDTSSSTAF IQLSSLTSE DSAVYYCARW GYYGSSDYWG QGTALTVSSG TGGSGGGGSG GGGSGGGASD IVVTQSHKFM STSVGDRVSI T CKASQDVS VAVAWYQQKT GQSPKLLIYS ASYRITGVPD RFTGSGSGTD FTFTISSVQA EDMAVYYCQQ HYSTPPWTFG GG TKL

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Macromolecule #4: Antibody 9.20.1A2 Fab heavy chain

MacromoleculeName: Antibody 9.20.1A2 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.340016 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVQLVESGGD LVQPGGSLRL SCAASGITLS GVWMNWVRQA PGKGLEWIGR IKSTSDGGRA DFAAPARGRF TMSRDESKNK LFLQMNNLG IEDTGMYYCF TRVQRDGTKD DFWGRGTLVT VSS

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Macromolecule #5: Antibody 9.20.1A2 Fab light chain

MacromoleculeName: Antibody 9.20.1A2 Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.985138 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QSVLTQPPSV SGAPGQTVTI SCTGSYSNIG AGYDVQWYQH LPGTAPKLLI YDNVHRPSGV PDRFSGSKSG TSASLAITGL QTEDEADYY CQSYDSRLRD QWVFGGGTKL TVL

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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: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81175
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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