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- EMDB-8694: Negative stain EM map of CA45 Fab bound to EBOV GPdTM -

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Basic information

Entry
Database: EMDB / ID: EMD-8694
TitleNegative stain EM map of CA45 Fab bound to EBOV GPdTM
Map dataNegative stain EM map of CA45 Fab bound to EBOV GPdTM
Sample
  • Complex: CA45 Fab bound to EBOV GPdTM
Biological speciesMacaca fascicularis (crab-eating macaque)
Methodsingle particle reconstruction / negative staining / Resolution: 11.0 Å
AuthorsTurner HL / Ward AB
CitationJournal: Cell / Year: 2017
Title: Immunization-Elicited Broadly Protective Antibody Reveals Ebolavirus Fusion Loop as a Site of Vulnerability.
Authors: Xuelian Zhao / Katie A Howell / Shihua He / Jennifer M Brannan / Anna Z Wec / Edgar Davidson / Hannah L Turner / Chi-I Chiang / Lin Lei / J Maximilian Fels / Hong Vu / Sergey Shulenin / ...Authors: Xuelian Zhao / Katie A Howell / Shihua He / Jennifer M Brannan / Anna Z Wec / Edgar Davidson / Hannah L Turner / Chi-I Chiang / Lin Lei / J Maximilian Fels / Hong Vu / Sergey Shulenin / Ashley N Turonis / Ana I Kuehne / Guodong Liu / Mi Ta / Yimeng Wang / Christopher Sundling / Yongli Xiao / Jennifer S Spence / Benjamin J Doranz / Frederick W Holtsberg / Andrew B Ward / Kartik Chandran / John M Dye / Xiangguo Qiu / Yuxing Li / M Javad Aman /
Abstract: While neutralizing antibodies are highly effective against ebolavirus infections, current experimental ebolavirus vaccines primarily elicit species-specific antibody responses. Here, we describe an ...While neutralizing antibodies are highly effective against ebolavirus infections, current experimental ebolavirus vaccines primarily elicit species-specific antibody responses. Here, we describe an immunization-elicited macaque antibody (CA45) that clamps the internal fusion loop with the N terminus of the ebolavirus glycoproteins (GPs) and potently neutralizes Ebola, Sudan, Bundibugyo, and Reston viruses. CA45, alone or in combination with an antibody that blocks receptor binding, provided full protection against all pathogenic ebolaviruses in mice, guinea pigs, and ferrets. Analysis of memory B cells from the immunized macaque suggests that elicitation of broadly neutralizing antibodies (bNAbs) for ebolaviruses is possible but difficult, potentially due to the rarity of bNAb clones and their precursors. Unexpectedly, germline-reverted CA45, while exhibiting negligible binding to full-length GP, bound a proteolytically remodeled GP with picomolar affinity, suggesting that engineered ebolavirus vaccines could trigger rare bNAb precursors more robustly. These findings have important implications for developing pan-ebolavirus vaccine and immunotherapeutic cocktails.
History
DepositionApr 18, 2017-
Header (metadata) releaseJun 7, 2017-
Map releaseJun 7, 2017-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 34.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 34.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_8694.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of CA45 Fab bound to EBOV GPdTM
Voxel sizeX=Y=Z: 2.05 Å
Density
Contour LevelBy AUTHOR: 34.299999999999997 / Movie #1: 34.3
Minimum - Maximum-45.593783999999999 - 119.432299999999998
Average (Standard dev.)1.1776823 (±9.795814500000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 262.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z262.400262.400262.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-45.594119.4321.178

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Supplemental data

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Sample components

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Entire : CA45 Fab bound to EBOV GPdTM

EntireName: CA45 Fab bound to EBOV GPdTM
Components
  • Complex: CA45 Fab bound to EBOV GPdTM

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Supramolecule #1: CA45 Fab bound to EBOV GPdTM

SupramoleculeName: CA45 Fab bound to EBOV GPdTM / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.376 mg/mL
BufferpH: 7.4 / Component - Formula: TBS
StainingType: NEGATIVE / Material: Uranyl Formate
GridModel: EMS / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus min: 1.5 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 e/Å2
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
In silico model: Model derived from common lines using seven hand-picked 2D classes.
Initial angle assignmentType: COMMON LINE / Software - Name: EMAN (ver. 2.1)
Final 3D classificationNumber classes: 130 / Avg.num./class: 130
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPARX (ver. 3.0) / Number images used: 16842

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