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- EMDB-20527: MERS S0 trimer in complex with antibody G2 -

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Basic information

Entry
Database: EMDB / ID: EMD-20527
TitleMERS S0 trimer in complex with antibody G2
Map data
SampleMERS S0 ectodomain trimer in complex with antibody G2:
MERS S0 ectodomain trimer / antibody G2 / (S protein) x 2 / G2 heavy chain / G2 light chain / (ligand) x 3
Function / homology
Function and homology information


membrane fusion / receptor-mediated virion attachment to host cell / viral envelope / integral component of membrane
Coronavirus S2 glycoprotein / Spike receptor binding domain / Coronovirus spike glycoprotein, heptad repeat 2 domain / Spike receptor binding domain superfamily / Spike glycoprotein / Coronavirus S2 glycoprotein / Spike receptor binding domain
S protein / Spike glycoprotein
Biological speciesMiddle East respiratory syndrome-related coronavirus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.19 Å
AuthorsBowman CA / Pallesen J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesAI127521 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 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.
Validation ReportPDB-ID: 6pz8

SummaryFull reportAbout validation report
History
DepositionJul 31, 2019-
Header (metadata) releaseSep 18, 2019-
Map releaseOct 9, 2019-
UpdateOct 9, 2019-
Current statusOct 9, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.264
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.264
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6pz8
  • Surface level: 0.264
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6pz8
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20527.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.02 Å/pix.
x 350 pix.
= 357. Å
1.02 Å/pix.
x 350 pix.
= 357. Å
1.02 Å/pix.
x 350 pix.
= 357. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.02 Å
Density
Contour LevelBy AUTHOR: 0.264 / Movie #1: 0.264
Minimum - Maximum0.0 - 1.0
Average (Standard dev.)0.054123797 (±0.21863443)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 357.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z357.000357.000357.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.8301.4600.000

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Supplemental data

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Segmentation: #1

Fileemd_20527_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire MERS S0 ectodomain trimer in complex with antibody G2

EntireName: MERS S0 ectodomain trimer in complex with antibody G2 / Number of components: 10

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Component #1: protein, MERS S0 ectodomain trimer in complex with antibody G2

ProteinName: MERS S0 ectodomain trimer in complex with antibody G2 / Recombinant expression: No

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Component #2: protein, MERS S0 ectodomain trimer

ProteinName: MERS S0 ectodomain trimer / Recombinant expression: No
SourceSpecies: Middle East respiratory syndrome-related coronavirus
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, antibody G2

ProteinName: antibody G2 / Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, S protein

ProteinName: S protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 51.301617 kDa
SourceSpecies: Middle East respiratory syndrome-related coronavirus
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, S protein

ProteinName: S protein / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 80.409109 kDa
SourceSpecies: Middle East respiratory syndrome-related coronavirus
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, G2 heavy chain

ProteinName: G2 heavy chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 24.275059 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, G2 light chain

ProteinName: G2 light chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 23.861293 kDa
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 66 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #9: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #10: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.4
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 77 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 12386
3D reconstructionSoftware: cryoSPARC / Resolution: 4.19 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Details: Model was not refined.
Input PDB model: 5W9I
Output model

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