+Open data
-Basic information
Entry | Database: PDB / ID: 7qus | ||||||
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Title | SARS-CoV-2 Spike, C3 symmetry | ||||||
Components | Spike glycoprotein,Fibritin | ||||||
Keywords | VIRAL PROTEIN / SARS-CoV-2 Spike | ||||||
Function / homology | Function and homology information virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated endocytosis of virus by host cell / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 Enterobacteria phage T4 (virus) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.39 Å | ||||||
Authors | Naismith, J.H. / Yang, Y. / Liu, J.W. | ||||||
Funding support | 1items
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Citation | Journal: Science / Year: 2022 Title: Pathogen-sugar interactions revealed by universal saturation transfer analysis. Authors: Charles J Buchanan / Ben Gaunt / Peter J Harrison / Yun Yang / Jiwei Liu / Aziz Khan / Andrew M Giltrap / Audrey Le Bas / Philip N Ward / Kapil Gupta / Maud Dumoux / Tiong Kit Tan / Lisa ...Authors: Charles J Buchanan / Ben Gaunt / Peter J Harrison / Yun Yang / Jiwei Liu / Aziz Khan / Andrew M Giltrap / Audrey Le Bas / Philip N Ward / Kapil Gupta / Maud Dumoux / Tiong Kit Tan / Lisa Schimaski / Sergio Daga / Nicola Picchiotti / Margherita Baldassarri / Elisa Benetti / Chiara Fallerini / Francesca Fava / Annarita Giliberti / Panagiotis I Koukos / Matthew J Davy / Abirami Lakshminarayanan / Xiaochao Xue / Georgios Papadakis / Lachlan P Deimel / Virgínia Casablancas-Antràs / Timothy D W Claridge / Alexandre M J J Bonvin / Quentin J Sattentau / Simone Furini / Marco Gori / Jiandong Huo / Raymond J Owens / Christiane Schaffitzel / Imre Berger / Alessandra Renieri / / James H Naismith / Andrew J Baldwin / Benjamin G Davis / Abstract: Many pathogens exploit host cell-surface glycans. However, precise analyses of glycan ligands binding with heavily modified pathogen proteins can be confounded by overlapping sugar signals and/or ...Many pathogens exploit host cell-surface glycans. However, precise analyses of glycan ligands binding with heavily modified pathogen proteins can be confounded by overlapping sugar signals and/or compounded with known experimental constraints. Universal saturation transfer analysis (uSTA) builds on existing nuclear magnetic resonance spectroscopy to provide an automated workflow for quantitating protein-ligand interactions. uSTA reveals that early-pandemic, B-origin-lineage severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike trimer binds sialoside sugars in an "end-on" manner. uSTA-guided modeling and a high-resolution cryo-electron microscopy structure implicate the spike N-terminal domain (NTD) and confirm end-on binding. This finding rationalizes the effect of NTD mutations that abolish sugar binding in SARS-CoV-2 variants of concern. Together with genetic variance analyses in early pandemic patient cohorts, this binding implicates a sialylated polylactosamine motif found on tetraantennary N-linked glycoproteins deep in the human lung as potentially relevant to virulence and/or zoonosis. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qus.cif.gz | 813.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qus.ent.gz | 542.5 KB | Display | PDB format |
PDBx/mmJSON format | 7qus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qus_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7qus_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 7qus_validation.xml.gz | 76.9 KB | Display | |
Data in CIF | 7qus_validation.cif.gz | 108.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/7qus ftp://data.pdbj.org/pub/pdb/validation_reports/qu/7qus | HTTPS FTP |
-Related structure data
Related structure data | 14153MC 7qurC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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