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- EMDB-0486: Negative stain EM map of MERS 2 in complex with G2 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-0486
TitleNegative stain EM map of MERS 2 in complex with G2 Fab
Map dataNegative stain EM map of MERS S in complex with G2 fab
Sample
  • Complex: MERS S in complex with Fab G2
Biological speciesMiddle East respiratory syndrome coronavirus
Methodsingle particle reconstruction / negative staining / Resolution: 24.0 Å
AuthorsWard AB / Turner HL / McLellan JS / Wang N
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesR01AI127521 United States
CitationJournal: Cell Rep / Year: 2019
Title: Structural Definition of a Neutralization-Sensitive Epitope on the MERS-CoV S1-NTD.
Authors: Nianshuang Wang / Osnat Rosen / Lingshu Wang / Hannah L Turner / Laura J Stevens / Kizzmekia S Corbett / Charles A Bowman / Jesper Pallesen / Wei Shi / Yi Zhang / Kwanyee Leung / Robert N ...Authors: Nianshuang Wang / Osnat Rosen / Lingshu Wang / Hannah L Turner / Laura J Stevens / Kizzmekia S Corbett / Charles A Bowman / Jesper Pallesen / Wei Shi / Yi Zhang / Kwanyee Leung / Robert N Kirchdoerfer / Michelle M Becker / Mark R Denison / James D Chappell / Andrew B Ward / Barney S Graham / Jason S McLellan /
Abstract: Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into the human population in 2012 and has caused substantial morbidity and mortality. Potently neutralizing antibodies targeting the ...Middle East respiratory syndrome coronavirus (MERS-CoV) emerged into the human population in 2012 and has caused substantial morbidity and mortality. Potently neutralizing antibodies targeting the receptor-binding domain (RBD) on MERS-CoV spike (S) protein have been characterized, but much less is known about antibodies targeting non-RBD epitopes. Here, we report the structural and functional characterization of G2, a neutralizing antibody targeting the MERS-CoV S1 N-terminal domain (S1-NTD). Structures of G2 alone and in complex with the MERS-CoV S1-NTD define a site of vulnerability comprising two loops, each of which contain a residue mutated in G2-escape variants. Cell-surface binding studies and in vitro competition experiments demonstrate that G2 strongly disrupts the attachment of MERS-CoV S to its receptor, dipeptidyl peptidase-4 (DPP4), with the inhibition requiring the native trimeric S conformation. These results advance our understanding of antibody-mediated neutralization of coronaviruses and should facilitate the development of immunotherapeutics and vaccines against MERS-CoV.
History
DepositionJan 22, 2019-
Header (metadata) releaseJul 10, 2019-
Map releaseFeb 26, 2020-
UpdateSep 8, 2021-
Current statusSep 8, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.62
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.62
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0486.png

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Map

FileDownload / File: emd_0486.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain EM map of MERS S in complex with G2 fab
Voxel sizeX=Y=Z: 24 Å
Density
Contour LevelBy AUTHOR: 2.62 / Movie #1: 2.62
Minimum - Maximum-3.9095116 - 10.298336
Average (Standard dev.)-1.7145441e-09 (±0.999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 1920.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z242424
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z1920.0001920.0001920.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-3.91010.298-0.000

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Supplemental data

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Sample components

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Entire : MERS S in complex with Fab G2

EntireName: MERS S in complex with Fab G2
Components
  • Complex: MERS S in complex with Fab G2

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Supramolecule #1: MERS S in complex with Fab G2

SupramoleculeName: MERS S in complex with Fab G2 / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Middle East respiratory syndrome coronavirus
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: freestyle 293-F

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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

BufferpH: 7.4
StainingType: NEGATIVE / Material: Uranyl formate
GridMaterial: COPPER / Support film - topology: HOLEY / 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 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
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

Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE / Software - Name: EMAN2
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number images used: 6823

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