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Yorodumi- PDB-7tht: CryoEM structure of SARS-CoV-2 S protein in complex with Receptor... -
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-Basic information
Entry | Database: PDB / ID: 7tht | ||||||
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Title | CryoEM structure of SARS-CoV-2 S protein in complex with Receptor Binding Domain antibody DH1042 | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / RBD antibody / DH1042 / SARS / COVID-19 / SARS-CoV-2 2P S ectodomain / VIRAL PROTEIN / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression 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 / membrane fusion / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / endocytosis involved in viral entry into host cell / receptor ligand activity / 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 Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.42 Å | ||||||
Authors | Manne, K. / May, A. / Acharya, P. | ||||||
Funding support | United States, 1items
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Citation | Journal: Mol Cell / Year: 2022 Title: Structural diversity of the SARS-CoV-2 Omicron spike. Authors: Sophie M-C Gobeil / Rory Henderson / Victoria Stalls / Katarzyna Janowska / Xiao Huang / Aaron May / Micah Speakman / Esther Beaudoin / Kartik Manne / Dapeng Li / Rob Parks / Maggie Barr / ...Authors: Sophie M-C Gobeil / Rory Henderson / Victoria Stalls / Katarzyna Janowska / Xiao Huang / Aaron May / Micah Speakman / Esther Beaudoin / Kartik Manne / Dapeng Li / Rob Parks / Maggie Barr / Margaret Deyton / Mitchell Martin / Katayoun Mansouri / Robert J Edwards / Amanda Eaton / David C Montefiori / Gregory D Sempowski / Kevin O Saunders / Kevin Wiehe / Wilton Williams / Bette Korber / Barton F Haynes / Priyamvada Acharya / Abstract: Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via ...Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor-binding domain (RBD) and neutralizing antibody epitope presentation, affecting virus transmissibility and immune evasion. Here, we determine cryo-EM structures of the Omicron and Delta spikes to understand the conformational impacts of mutations in each. The Omicron spike structure revealed an unusually tightly packed RBD organization with long range impacts that were not observed in the Delta spike. Binding and crystallography revealed increased flexibility at the functionally critical fusion peptide site in the Omicron spike. These results reveal a highly evolved Omicron spike architecture with possible impacts on its high levels of immune evasion and transmissibility. #1: Journal: bioRxiv / Year: 2022 Title: Structural diversity of the SARS-CoV-2 Omicron spike. Authors: Sophie M-C Gobeil / Rory Henderson / Victoria Stalls / Katarzyna Janowska / Xiao Huang / Aaron May / Micah Speakman / Esther Beaudoin / Kartik Manne / Dapeng Li / Rob Parks / Maggie Barr / ...Authors: Sophie M-C Gobeil / Rory Henderson / Victoria Stalls / Katarzyna Janowska / Xiao Huang / Aaron May / Micah Speakman / Esther Beaudoin / Kartik Manne / Dapeng Li / Rob Parks / Maggie Barr / Margaret Deyton / Mitchell Martin / Katayoun Mansouri / Robert J Edwards / Gregory D Sempowski / Kevin O Saunders / Kevin Wiehe / Wilton Williams / Bette Korber / Barton F Haynes / Priyamvada Acharya Abstract: Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via ...Aided by extensive spike protein mutation, the SARS-CoV-2 Omicron variant overtook the previously dominant Delta variant. Spike conformation plays an essential role in SARS-CoV-2 evolution via changes in receptor binding domain (RBD) and neutralizing antibody epitope presentation affecting virus transmissibility and immune evasion. Here, we determine cryo-EM structures of the Omicron and Delta spikes to understand the conformational impacts of mutations in each. The Omicron spike structure revealed an unusually tightly packed RBD organization with long range impacts that were not observed in the Delta spike. Binding and crystallography revealed increased flexibility at the functionally critical fusion peptide site in the Omicron spike. These results reveal a highly evolved Omicron spike architecture with possible impacts on its high levels of immune evasion and transmissibility. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7tht.cif.gz | 657.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tht.ent.gz | 530 KB | Display | PDB format |
PDBx/mmJSON format | 7tht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tht_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 7tht_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7tht_validation.xml.gz | 95.7 KB | Display | |
Data in CIF | 7tht_validation.cif.gz | 149.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/7tht ftp://data.pdbj.org/pub/pdb/validation_reports/th/7tht | HTTPS FTP |
-Related structure data
Related structure data | 25904MC 7teiC 7tf8C 7tl1C 7tl9C 7tlaC 7tlcC 7tldC 7touC 7tovC 7towC 7toxC 7toyC 7tozC 7tp0C 7tp1C 7tp2C 7tp7C 7tp8C 7tp9C 7tpaC 7tpcC 7tpeC 7tpfC 7tphC 7tplC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 1 types, 3 molecules SVC
#1: Protein | Mass: 124125.477 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 |
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-Antibody , 2 types, 6 molecules HadLcb
#2: Antibody | Mass: 13476.164 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | Mass: 11431.628 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Sugars , 3 types, 46 molecules
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #6: Sugar | ChemComp-NAG / |
-Details
Has ligand of interest | N |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 750 nm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 93.15 K / Temperature (min): 93.15 K |
Image recording | Electron dose: 54.02 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 14444 |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 175460 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||||||||||||||||||||
Atomic model building | 3D fitting-ID: 1 / Source name: PDB / Type: experimental model
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Refinement | Highest resolution: 3.42 Å | ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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