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- EMDB-20544: MERS-CoV S structure in complex with 2,3-sialyl-N-acetyl-lactosamine -

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Basic information

Entry
Database: EMDB / ID: EMD-20544
TitleMERS-CoV S structure in complex with 2,3-sialyl-N-acetyl-lactosamine
Map dataSharpened map
Sample
  • Complex: MERS-CoV S ectodomain in complex with 5-N-acetyl neuraminic acid
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: FOLIC ACID
  • Ligand: water
KeywordsCoronavirus / spike glycoprotein / MERS-CoV / membrane fusion / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN
Function / homology
Function and homology information


receptor-mediated endocytosis of virus by host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane ...receptor-mediated endocytosis of virus by host cell / membrane fusion / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. ...Spike (S) protein S1 subunit, receptor-binding domain, MERS-CoV / Spike (S) protein S1 subunit, N-terminal domain, MERS-CoV-like / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, N-terminal domain superfamily / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Spike glycoprotein, betacoronavirus / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesMiddle East respiratory syndrome-related coronavirus / Human betacoronavirus 2c EMC/2012
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsPark YJ / Walls AC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)120553 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
DepositionAug 1, 2019-
Header (metadata) releaseDec 11, 2019-
Map releaseDec 11, 2019-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing 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
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  • Surface view colored by cylindrical radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6q06
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20544.png

Downloads & links

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Map

FileDownload / File: emd_20544.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-4.173869 - 6.9629736
Average (Standard dev.)0.0034118704 (±0.10296533)
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/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-4.1746.9630.003

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Supplemental data

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Additional map: Unsharpened map

Fileemd_20544_additional.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-acetyl neuraminic acid

EntireName: MERS-CoV S ectodomain in complex with 5-N-acetyl neuraminic acid
Components
  • Complex: MERS-CoV S ectodomain in complex with 5-N-acetyl neuraminic acid
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: FOLIC ACID
  • Ligand: water

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

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

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human betacoronavirus 2c EMC/2012
Molecular weightTheoretical: 149.172062 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTVDVGPDSV KSACIEVDIQ QTFFDKTWPR PIDVSKADGI IYPQGRTYSN ITITYQGLF PYQGDHGDMY VYSAGHATGT TPQKLFVANY SQDVKQFANG FVVRIGAAAN STGTVIISPS TSATIRKIYP A FMLGSSVG ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTVDVGPDSV KSACIEVDIQ QTFFDKTWPR PIDVSKADGI IYPQGRTYSN ITITYQGLF PYQGDHGDMY VYSAGHATGT TPQKLFVANY SQDVKQFANG FVVRIGAAAN STGTVIISPS TSATIRKIYP A FMLGSSVG NFSDGKMGRF FNHTLVLLPD GCGTLLRAFY CILEPRSGNH CPAGNSYTSF ATYHTPATDC SDGNYNRNAS LN SFKEYFN LRNCTFMYTY NITEDEILEW FGITQTAQGV HLFSSRYVDL YGGNMFQFAT LPVYDTIKYY SIIPHSIRSI QSD RKAWAA FYVYKLQPLT FLLDFSVDGY IRRAIDCGFN DLSQLHCSYE SFDVESGVYS VSSFEAKPSG SVVEQAEGVE CDFS PLLSG TPPQVYNFKR LVFTNCNYNL TKLLSLFSVN DFTCSQISPA AIASNCYSSL ILDYFSYPLS MKSDLSVSSA GPISQ FNYK QSFSNPTCLI LATVPHNLTT ITKPLKYSYI NKCSRLLSDD RTEVPQLVNA NQYSPCVSIV PSTVWEDGDY YRKQLS PLE GGGWLVASGS TVAMTEQLQM GFGITVQYGT DTNSVCPKLE FANDTKIASQ LGNCVEYSLY GVSGRGVFQN CTAVGVR QQ RFVYDAYQNL VGYYSDDGNY YCLRACVSVP VSVIYDKETK THATLFGSVA CEHISSTMSQ YSRSTRSMLK RRDSTYGP L QTPVGCVLGL VNSSLFVEDC KLPLGQSLCA LPDTPSTLTP ASVGSVPGEM RLASIAFNHP IQVDQLNSSY FKLSIPTNF SFGVTQEYIQ TTIQKVTVDC KQYVCNGFQK CEQLLREYGQ FCSKINQALH GANLRQDDSV RNLFASVKSS QSSPIIPGFG GDFNLTLLE PVSISTGSRS ARSAIEDLLF DKVTIADPGY MQGYDDCMQQ GPASARDLIC AQYVAGYKVL PPLMDVNMEA A YTSSLLGS IAGVGWTAGL SSFAAIPFAQ SIFYRLNGVG ITQQVLSENQ KLIANKFNQA LGAMQTGFTT TNEAFQKVQD AV NNNAQAL SKLASELSNT FGAISASIGD IIQRLDPPEQ DAQIDRLING RLTTLNAFVA QQLVRSESAA LSAQLAKDKV NEC VKAQSK RSGFCGQGTH IVSFVVNAPN GLYFMHVGYY PSNHIEVVSA YGLCDAANPT NCIAPVNGYF IKTNNTRIVD EWSY TGSSF YAPEPITSLN TKYVAPQVTY QNISTNLPPP LLGNSTGIDF QDELDEFFKN VSTSIPNFGS LTQINTTLLD LTYEM LSLQ QVVKALNESY IDLKELGNYT YYNKGSGREN LYFQGGGGSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGHHH HHHHH

UniProtKB: Spike glycoprotein

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 21 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #9: FOLIC ACID

MacromoleculeName: FOLIC ACID / type: ligand / ID: 9 / Number of copies: 3 / Formula: FOL
Molecular weightTheoretical: 441.397 Da
Chemical component information

ChemComp-FA:
FOLIC ACID

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 216 / 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: 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

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 34458
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

Initial modelPDB ID:

6bn3


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6q06:
MERS-CoV S structure in complex with 2,3-sialyl-N-acetyl-lactosamine

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