[English] 日本語
![](img/lk-miru.gif)
- PDB-7n8h: SARS-CoV-2 S (B.1.429 / epsilon variant) + S2M11 + S2L20 Global R... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7n8h | ||||||
---|---|---|---|---|---|---|---|
Title | SARS-CoV-2 S (B.1.429 / epsilon variant) + S2M11 + S2L20 Global Refinement | ||||||
![]() |
| ||||||
![]() | 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 | ![]() 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 / 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 | ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å | ||||||
![]() | McCallum, M. / Veesler, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Movie |
![]() |
---|---|
Structure viewer | Molecule: ![]() ![]() |
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 817.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 663.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.9 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 3 MB | Display | |
Data in XML | ![]() | 116.3 KB | Display | |
Data in CIF | ![]() | 186 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 24236MC ![]() 7n8iC M: map data used to model this data C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
|
---|---|
1 |
|
-
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.) ![]() ![]() #3: Antibody | Mass: 13651.220 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #4: Antibody | Mass: 11699.961 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #5: Antibody | Mass: 13453.958 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
---|
-Protein / Non-polymers , 2 types, 774 molecules AFK![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#1: Protein | Mass: 141484.609 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: S, 2 / Variant: B.1.427/B.1.429 (epsilon) / Production host: ![]() #9: Water | ChemComp-HOH / | |
---|
-Sugars , 3 types, 48 molecules ![](data/chem/img/NAG.gif)
#6: Polysaccharide | #7: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose #8: Sugar | ChemComp-NAG / |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
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 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Source (natural) |
| ||||||||||||
Source (recombinant) | Organism: ![]() | ||||||||||||
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 |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
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 |
---|---|
3D reconstruction | Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 330083 / Symmetry type: POINT |