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Yorodumi- PDB-7n8h: SARS-CoV-2 S (B.1.429 / epsilon variant) + S2M11 + S2L20 Global R... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7n8h | ||||||
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Title | SARS-CoV-2 S (B.1.429 / epsilon variant) + S2M11 + S2L20 Global Refinement | ||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / coronavirus / antibody / california / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN / 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 / suppression by virus 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 / 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 / Attachment and Entry / membrane fusion / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / 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: 2.3 Å | ||||||
Authors | McCallum, M. / Veesler, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Funding support | United States, 1items
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Citation | Journal: Science / Year: 2021 Title: SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. Authors: Matthew McCallum / Jessica Bassi / Anna De Marco / Alex Chen / Alexandra C Walls / Julia Di Iulio / M Alejandra Tortorici / Mary-Jane Navarro / Chiara Silacci-Fregni / Christian Saliba / ...Authors: Matthew McCallum / Jessica Bassi / Anna De Marco / Alex Chen / Alexandra C Walls / Julia Di Iulio / M Alejandra Tortorici / Mary-Jane Navarro / Chiara Silacci-Fregni / Christian Saliba / Kaitlin R Sprouse / Maria Agostini / Dora Pinto / Katja Culap / Siro Bianchi / Stefano Jaconi / Elisabetta Cameroni / John E Bowen / Sasha W Tilles / Matteo Samuele Pizzuto / Sonja Bernasconi Guastalla / Giovanni Bona / Alessandra Franzetti Pellanda / Christian Garzoni / Wesley C Van Voorhis / Laura E Rosen / Gyorgy Snell / Amalio Telenti / Herbert W Virgin / Luca Piccoli / Davide Corti / David Veesler / Abstract: A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429), which was originally detected in California, carries spike glycoprotein mutations S13I in the signal peptide, W152C in the N-terminal ...A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429), which was originally detected in California, carries spike glycoprotein mutations S13I in the signal peptide, W152C in the N-terminal domain (NTD), and L452R in the receptor-binding domain (RBD). Plasma from individuals vaccinated with a Wuhan-1 isolate-based messenger RNA vaccine or from convalescent individuals exhibited neutralizing titers that were reduced 2- to 3.5-fold against the B.1.427/B.1.429 variant relative to wild-type pseudoviruses. The L452R mutation reduced neutralizing activity in 14 of 34 RBD-specific monoclonal antibodies (mAbs). The S13I and W152C mutations resulted in total loss of neutralization for 10 of 10 NTD-specific mAbs because the NTD antigenic supersite was remodeled by a shift of the signal peptide cleavage site and the formation of a new disulfide bond, as revealed by mass spectrometry and structural studies. | ||||||
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 | 7n8h.cif.gz | 817.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n8h.ent.gz | 663.1 KB | Display | PDB format |
PDBx/mmJSON format | 7n8h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/7n8h ftp://data.pdbj.org/pub/pdb/validation_reports/n8/7n8h | HTTPS FTP |
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-Related structure data
Related structure data | 24236MC 7n8iC 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
-Antibody , 4 types, 12 molecules DGLEHMBINCJO
#2: Antibody | Mass: 11208.458 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: 13651.220 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #4: Antibody | Mass: 11699.961 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #5: Antibody | Mass: 13453.958 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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-Protein / Non-polymers , 2 types, 774 molecules AFK
#1: Protein | Mass: 141484.609 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 / Variant: B.1.427/B.1.429 (epsilon) / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #9: Water | ChemComp-HOH / | |
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-Sugars , 3 types, 48 molecules
#6: Polysaccharide | #7: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #8: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | Y |
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-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 | Name: SARS-CoV-2 S (B.1.429 / epsilon variant) bound to S2M11 and S2L20 Fabs Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT | ||||||||||||
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Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) | ||||||||||||
Buffer solution | pH: 8.5 | ||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||
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 FIELDBright-field microscopy |
Image recording | Electron dose: 63 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 330083 / Symmetry type: POINT |