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- EMDB-10124: Structure of ZEBOV GP in complex with 5T0180 antibody -

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Basic information

Entry
Database: EMDB / ID: EMD-10124
TitleStructure of ZEBOV GP in complex with 5T0180 antibody
Map dataLocally Filtered - Z flipped
Sample
  • Complex: EBOV-GP in complex with 3T0265 antibody
    • Complex: EBOV-GP
      • Protein or peptide: Envelope Glycoprotein 1
      • Protein or peptide: Envelope glycoprotein
    • Complex: 5T0180 antibody
      • Protein or peptide: Light Chain
      • Protein or peptide: Heavy Chain
  • Ligand: water
KeywordsEbola / glycoprotein / antibodies / VIRAL PROTEIN
Function / homology
Function and homology information


host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / symbiont entry into host cell / fusion of virus membrane with host endosome membrane ...host cell endoplasmic reticulum / viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / symbiont-mediated-mediated suppression of host tetherin activity / host cell cytoplasm / entry receptor-mediated virion attachment to host cell / symbiont-mediated suppression of host innate immune response / membrane raft / symbiont entry into host cell / fusion of virus membrane with host endosome membrane / lipid binding / viral envelope / host cell plasma membrane / virion membrane / extracellular region / identical protein binding / 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 speciesEbola virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsDiskin R / Cohen-Dvashi H
CitationJournal: Cell Host Microbe / Year: 2020
Title: Structural Basis for a Convergent Immune Response against Ebola Virus.
Authors: Hadas Cohen-Dvashi / Matthias Zehner / Stefanie Ehrhardt / Michael Katz / Nadav Elad / Florian Klein / Ron Diskin /
Abstract: Ebola virus disease is a severe health problem in Africa. Vaccines that display the Zaire ebolavirus glycoprotein spike complex are a prime component for the effort to combat it. The V3-15/V1-40- ...Ebola virus disease is a severe health problem in Africa. Vaccines that display the Zaire ebolavirus glycoprotein spike complex are a prime component for the effort to combat it. The V3-15/V1-40-based class of antibodies was recently discovered to be a common response in individuals who received the Ebola virus vaccines. These antibodies display attractive properties, and thus likely contribute to the efficacy of the vaccines. Here, we use cryo-EM to elucidate how three V3-15/V1-40 antibodies from different individuals target the virus and found a convergent mechanism against a partially conserved site on the spike complex. Our study rationalizes the selection of the V3-15/V1-40 germline genes for specifically targeting this site and highlights Ebolavirus species-specific sequence divergences that may restrict breadth of V3-15/V1-40-based humoral response. The results from this study could help develop improved immunization schemes and further enable the design of immunogens that would be efficacious against a broader set of Ebolavirus species.
History
DepositionJul 10, 2019-
Header (metadata) releaseFeb 12, 2020-
Map releaseFeb 12, 2020-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6s8j
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10124.png

Downloads & links

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Map

FileDownload / File: emd_10124.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally Filtered - Z flipped
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 256 pix.
= 217.344 Å		0.85 Å/pix.
x 256 pix.
= 217.344 Å		0.85 Å/pix.
x 256 pix.
= 217.344 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.849 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.21 / Movie #1: 0.6
Minimum - Maximum-4.5410633 - 6.900273
Average (Standard dev.)0.008410051 (±0.19395456)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.344 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8490.8490.849
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z217.344217.344217.344
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-4.5416.9000.008

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Supplemental data

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Half map: Half map B

Fileemd_10124_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_10124_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : EBOV-GP in complex with 3T0265 antibody

EntireName: EBOV-GP in complex with 3T0265 antibody
Components
  • Complex: EBOV-GP in complex with 3T0265 antibody
    • Complex: EBOV-GP
      • Protein or peptide: Envelope Glycoprotein 1
      • Protein or peptide: Envelope glycoprotein
    • Complex: 5T0180 antibody
      • Protein or peptide: Light Chain
      • Protein or peptide: Heavy Chain
  • Ligand: water

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Supramolecule #1: EBOV-GP in complex with 3T0265 antibody

SupramoleculeName: EBOV-GP in complex with 3T0265 antibody / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: EBOV-GP

SupramoleculeName: EBOV-GP / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Ebola virus

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Supramolecule #3: 5T0180 antibody

SupramoleculeName: 5T0180 antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2 / Details: A fab portion generated by cleavage
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Light Chain

MacromoleculeName: Light Chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.130488 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSV SGAPGQRVTI SCTGSSSNIG AGYDVQWYQQ LPGTAPKVLI YGNNNRPSGV PDRFSGSKSG SSASLAITGL QAEDEADYY CQTYDSRLRD QWVFGGGTKL TVLGQPKAAP SVTLFPPSSE ELQANKATLV CLISDFYPGA VTVAWKADSS P VKAGVETT ...String:
QSVLTQPPSV SGAPGQRVTI SCTGSSSNIG AGYDVQWYQQ LPGTAPKVLI YGNNNRPSGV PDRFSGSKSG SSASLAITGL QAEDEADYY CQTYDSRLRD QWVFGGGTKL TVLGQPKAAP SVTLFPPSSE ELQANKATLV CLISDFYPGA VTVAWKADSS P VKAGVETT TPSKQSNNKY AASSYLSLTP EQWKSHRSYS CQVTHEGSTV EKTVAPTECS

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Macromolecule #2: Heavy Chain

MacromoleculeName: Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.636709 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVKPGGSLRL SCAASGFSFG NAWMNWVRQA PGKGLEWVGR IKSKSDGGTT DYAAPVKDRF IISRDDSKKT LYLQMNSLR REDTAVYYCV RGPFYCDTCG PNDYWGQGTL VTVSSGSTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
EVQLVESGGG LVKPGGSLRL SCAASGFSFG NAWMNWVRQA PGKGLEWVGR IKSKSDGGTT DYAAPVKDRF IISRDDSKKT LYLQMNSLR REDTAVYYCV RGPFYCDTCG PNDYWGQGTL VTVSSGSTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKRVEPKSCD KTH

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Macromolecule #3: Envelope Glycoprotein 1

MacromoleculeName: Envelope Glycoprotein 1 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
Molecular weightTheoretical: 35.706977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ETGRSIPLGV IHNSALQVSD VDKLVCRDKL SSTNQLRSVG LNLEGNGVAT DVPSATKRWG FRSGVPPKVV NYEAGEWAEN CYNLEIKKP DGSECLPAAP DGIRGFPRCR YVHKVSGTGP CAGDFAFHKE GAFFLYDRLA STVIYRGTTF AEGVVAFLIL P QAKKDFFS ...String:
ETGRSIPLGV IHNSALQVSD VDKLVCRDKL SSTNQLRSVG LNLEGNGVAT DVPSATKRWG FRSGVPPKVV NYEAGEWAEN CYNLEIKKP DGSECLPAAP DGIRGFPRCR YVHKVSGTGP CAGDFAFHKE GAFFLYDRLA STVIYRGTTF AEGVVAFLIL P QAKKDFFS SHPLREPVNA TEDPSSGYYS TTIRYQATGF GTNETEYLFE VDNLTYVQLE SRFTPQFLLQ LNETIYTSGK RS NTTGKLI WKVNPEIDTT IGEWAFWETK KNLTRKIRSE ELSFTVVSTH HQDTGEESAS SGKLGLITNT IAGVAGLITG GRR TRR

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Macromolecule #4: Envelope glycoprotein

MacromoleculeName: Envelope glycoprotein / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ebola virus
Molecular weightTheoretical: 18.989391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EAIVNAQPKC NPNLHYWTTQ DEGAAIGLAW IPYFGPAAEG IYIEGLMHNQ DGLICGLRQL ANETTQALQL FLRATTELRT FSILNRKAI DFLLQRWGGT CHILGPDCCI EPHDWTKNIT DKIDQIIHDF VDGSGYIPEA PRDGQAYVRK DGEWVLLSTF L GTHHHHHH

UniProtKB: Envelope glycoprotein

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 163 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.6
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 27.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. V2) / Number images used: 100499
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. V2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5jq3


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-6s8j:
Structure of ZEBOV GP in complex with 5T0180 antibody

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