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- EMDB-20829: MERS-CoV S structure in complex with 5-N-glycolyl neuraminic acid -

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Basic information

Entry
Database: EMDB / ID: EMD-20829
TitleMERS-CoV S structure in complex with 5-N-glycolyl neuraminic acid
Map dataSharpened map
Sample
  • Complex: MERS-CoV S ectodomain in complex with 5-N-glycolyl neuraminic acid
Biological speciesMiddle East respiratory syndrome-related coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsPark YJ / Walls AC / Wang Z / Sauer MM / Li W / Tortorici MA / Bosch BJ / DiMaio F / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences120553 United States
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Structures of MERS-CoV spike glycoprotein in complex with sialoside attachment receptors.
Authors: Young-Jun Park / Alexandra C Walls / Zhaoqian Wang / Maximillian M Sauer / Wentao Li / M Alejandra Tortorici / Berend-Jan Bosch / Frank DiMaio / David Veesler /
Abstract: The Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe and often lethal respiratory illness in humans, and no vaccines or specific treatments are available. Infections are ...The Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe and often lethal respiratory illness in humans, and no vaccines or specific treatments are available. Infections are initiated via binding of the MERS-CoV spike (S) glycoprotein to sialosides and dipeptidyl-peptidase 4 (the attachment and entry receptors, respectively). To understand MERS-CoV engagement of sialylated receptors, we determined the cryo-EM structures of S in complex with 5-N-acetyl neuraminic acid, 5-N-glycolyl neuraminic acid, sialyl-Lewis, α2,3-sialyl-N-acetyl-lactosamine and α2,6-sialyl-N-acetyl-lactosamine at 2.7-3.0 Å resolution. We show that recognition occurs via a conserved groove that is essential for MERS-CoV S-mediated attachment to sialosides and entry into human airway epithelial cells. Our data illuminate MERS-CoV S sialoside specificity and suggest that selectivity for α2,3-linked over α2,6-linked receptors results from enhanced interactions with the former class of oligosaccharides. This study provides a structural framework explaining MERS-CoV attachment to sialoside receptors and identifies a site of potential vulnerability to inhibitors of viral entry.
History
DepositionOct 14, 2019-
Header (metadata) releaseDec 11, 2019-
Map releaseDec 11, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20829.png

Downloads & links

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Map

FileDownload / File: emd_20829.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9 / Movie #1: 0.9
Minimum - Maximum-3.718914 - 5.936888
Average (Standard dev.)0.0032458077 (±0.098596245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z420.000420.000420.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-3.7195.9370.003

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Supplemental data

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Additional map: Unsharpened map

Fileemd_20829_additional.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_20829_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MERS-CoV S ectodomain in complex with 5-N-glycolyl neuraminic acid

EntireName: MERS-CoV S ectodomain in complex with 5-N-glycolyl neuraminic acid
Components
  • Complex: MERS-CoV S ectodomain in complex with 5-N-glycolyl neuraminic acid

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Supramolecule #1: MERS-CoV S ectodomain in complex with 5-N-glycolyl neuraminic acid

SupramoleculeName: MERS-CoV S ectodomain in complex with 5-N-glycolyl neuraminic acid
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Middle East respiratory syndrome-related coronavirus
Recombinant expressionOrganism: Homo sapiens (human)

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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: 8
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: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 23281
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

Initial modelPDB ID:

6bn3

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