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- EMDB-0557: Structural basis for human coronavirus attachment to sialic acid ... -

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Basic information

Entry
Database: EMDB / ID: EMD-0557
TitleStructural basis for human coronavirus attachment to sialic acid receptors
Map dataSharpened map
Sample
  • Complex: HCoV-OC43 spike glycoprotein ectodomain in complex with 9-O-acetyl sialic acid
    • Protein or peptide: Spike surface glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
  • Ligand: water
KeywordsCoronavirus spike glycoprotein / sialic acid / HCoV-OC43 / fusion protein / VIRAL PROTEIN
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / 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 / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Spike (S) protein S1 subunit, receptor-binding domain, HCoV-OC43-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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, HCoV-OC43-like / Spike (S) protein S1 subunit, N-terminal domain, murine hepatitis virus-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, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / 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 / Spike S1 subunit, receptor binding domain superfamily, 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, 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesBetacoronavirus / Human coronavirus OC43
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsTortorici MA / Walls AC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM120553 United States
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Structural basis for human coronavirus attachment to sialic acid receptors.
Authors: M Alejandra Tortorici / Alexandra C Walls / Yifei Lang / Chunyan Wang / Zeshi Li / Danielle Koerhuis / Geert-Jan Boons / Berend-Jan Bosch / Félix A Rey / Raoul J de Groot / David Veesler /
Abstract: Coronaviruses cause respiratory tract infections in humans and outbreaks of deadly pneumonia worldwide. Infections are initiated by the transmembrane spike (S) glycoprotein, which binds to host ...Coronaviruses cause respiratory tract infections in humans and outbreaks of deadly pneumonia worldwide. Infections are initiated by the transmembrane spike (S) glycoprotein, which binds to host receptors and fuses the viral and cellular membranes. To understand the molecular basis of coronavirus attachment to oligosaccharide receptors, we determined cryo-EM structures of coronavirus OC43 S glycoprotein trimer in isolation and in complex with a 9-O-acetylated sialic acid. We show that the ligand binds with fast kinetics to a surface-exposed groove and that interactions at the identified site are essential for S-mediated viral entry into host cells, but free monosaccharide does not trigger fusogenic conformational changes. The receptor-interacting site is conserved in all coronavirus S glycoproteins that engage 9-O-acetyl-sialogycans, with an architecture similar to those of the ligand-binding pockets of coronavirus hemagglutinin esterases and influenza virus C/D hemagglutinin-esterase fusion glycoproteins. Our results demonstrate these viruses evolved similar strategies to engage sialoglycans at the surface of target cells.
History
DepositionFeb 13, 2019-
Header (metadata) releaseApr 17, 2019-
Map releaseJun 5, 2019-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nzk
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0557.png

Downloads & links

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Map

FileDownload / File: emd_0557.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: 1.0 / Movie #1: 1
Minimum - Maximum-4.58008 - 7.030044
Average (Standard dev.)0.0032014397 (±0.11123292)
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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-4.5807.0300.003

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Supplemental data

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Additional map: Unsharpened map

Fileemd_0557_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 : HCoV-OC43 spike glycoprotein ectodomain in complex with 9-O-acety...

EntireName: HCoV-OC43 spike glycoprotein ectodomain in complex with 9-O-acetyl sialic acid
Components
  • Complex: HCoV-OC43 spike glycoprotein ectodomain in complex with 9-O-acetyl sialic acid
    • Protein or peptide: Spike surface glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
  • Ligand: water

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Supramolecule #1: HCoV-OC43 spike glycoprotein ectodomain in complex with 9-O-acety...

SupramoleculeName: HCoV-OC43 spike glycoprotein ectodomain in complex with 9-O-acetyl sialic acid
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Betacoronavirus

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Macromolecule #1: Spike surface glycoprotein

MacromoleculeName: Spike surface glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human coronavirus OC43
Molecular weightTheoretical: 146.438312 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLAVIGDLK CTSDNINDKD TGPPPISTDT VDVTNGLGTY YVLDRVYLNT TLFLNGYYPT SGSTYRNMA LKGSVLLSRL WFKPPFLSDF INGIFAKVKN TKVIKDRVMY SEFPAITIGS TFVNTSYSVV VQPRTINSTQ D GDNKLQGL ...String:
MPMGSLQPLA TLYLLGMLVA SVLAVIGDLK CTSDNINDKD TGPPPISTDT VDVTNGLGTY YVLDRVYLNT TLFLNGYYPT SGSTYRNMA LKGSVLLSRL WFKPPFLSDF INGIFAKVKN TKVIKDRVMY SEFPAITIGS TFVNTSYSVV VQPRTINSTQ D GDNKLQGL LEVSVCQYNM CEYPQTICHP NLGNHRKELW HLDTGVVSCL YKRNFTYDVN ADYLYFHFYQ EGGTFYAYFT DT GVVTKFL FNVYLGMALS HYYVMPLTCN SKLTLEYWVT PLTSRQYLLA FNQDGIIFNA VDCMSDFMSE IKCKTQSIAP PTG VYELNG YTVQPIADVY RRKPNLPNCN IEAWLNDKSV PSPLNWERKT FSNCNFNMSS LMSFIQADSF TCNNIDAAKI YGMC FSSIT IDKFAIPNGR KVDLQLGNLG YLQSFNYRID TTATSCQLYY NLPAANVSVS RFNPSTWNKR FGFIEDSVFK PRPAG VLTN HDVVYAQHCF KAPKNFCPCK LNGSCVGSGP GKNNGIGTCP AGTNYLTCDN LCTPDPITFT GTYKCPQTKS LVGIGE HCS GLAVKSDYCG GNSCTCRPQA FLGWSADSCL QGDKCNIFAN FILHDVNSGL TCSTDLQKAN TDIILGVCVN YDLYGIL GQ GIFVEVNATY YNSWQNLLYD SNGNLYGFRD YITNRTFMIR SCYSGRVSAA FHANSSEPAL LFRNIKCNYV FNNSLTRQ L QPINYFDSYL GCVVNAYNST AISVQTCDLT VGSGYCVDYS KNGGSGGAIT TGYRFTNFEP FTVNSVNDSL EPVGGLYEI QIPSEFTIGN MVEFIQTSSP KVTIDCAAFV CGDYAACKSQ LVEYGSFCDN INAILTEVNE LLDTTQLQVA NSLMNGVTLS TKLKDGVNF NVDDINFSPV LGCLGSECSK ASSRSAIEDL LFDKVKLSDV GFVEAYNNCT GGAEIRDLIC VQSYKGIKVL P PLLSENQF SGYTLAATSA SLFPPWTAAA GVPFYLNVQY RINGLGVTMD VLSQNQKLIA NAFNNALYAI QEGFDATNSA LV KIQAVVN ANAEALNNLL QQLSNRFGAI SASLQEILSR LDALEAEAQI DRLINGRLTA LNAYVSQQLS DSTLVKFSAA QAM EKVNEC VKSQSSRINF CGNGNHIISL VQNAPYGLYF IHFSYVPTKY VTARVSPGLC IAGDRGIAPK SGYFVNVNNT WMYT GSGYY YPEPITENNV VVMSTCAVNY TKAPYVMLNT SIPNLPDFKE ELDQWFKNQT SVAPDLSLDY INVTFLDLLI KRMKQ IEDK IEEIESKQKK IENEIARIKK IKLVPRGSLE WSHPQFEK

UniProtKB: Spike glycoprotein

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #6: methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galac...

MacromoleculeName: methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid
type: ligand / ID: 6 / Number of copies: 3 / Formula: MJJ
Molecular weightTheoretical: 365.333 Da
Chemical component information

ChemComp-MJJ:
methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 396 / 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
GridModel: C-flat-1.2/1.3 4C / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / 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: EMDB MAP
EMDB ID:

6526

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 178356
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING

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