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- EMDB-20070: Structural basis for human coronavirus attachment to sialic acid ... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-20070 | |||||||||
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Title | Structural basis for human coronavirus attachment to sialic acid receptors. Apo-HCoV-OC43 S | |||||||||
![]() | Sharpened map | |||||||||
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Function / homology | ![]() 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
![]() | Tortorici MA / Walls AC / Lang Y / Wang C / Li Z / Koerhuis D / Boons GJ / Bosch BJ / Rey FA / de Groot R / Veesler D | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 15 KB 15 KB | Display Display | ![]() |
Images | ![]() | 55.7 KB | ||
Others | ![]() | 230.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ohwMC ![]() 0557C ![]() 6nzkC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Unsharpened map
File | emd_20070_additional.map | ||||||||||||
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Annotation | Unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : HCoV-OC43 spike glycoprotein ectodomain in complex with 9-O-acety...
Entire | Name: HCoV-OC43 spike glycoprotein ectodomain in complex with 9-O-acetyl sialic acid |
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Components |
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-Supramolecule #1: HCoV-OC43 spike glycoprotein ectodomain in complex with 9-O-acety...
Supramolecule | Name: HCoV-OC43 spike glycoprotein ectodomain in complex with 9-O-acetyl sialic acid type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Macromolecule #1: Spike surface glycoprotein
Macromolecule | Name: Spike surface glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 146.438312 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 15 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ![]() ChemComp-NAG: |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 186 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |