[English] 日本語
Yorodumi- PDB-7zbu: CryoEM structure of SARS-CoV-2 spike monomer in complex with neut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7zbu | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of SARS-CoV-2 spike monomer in complex with neutralising antibody P008_60 | ||||||||||||||||||
Components |
| ||||||||||||||||||
Keywords | VIRAL PROTEIN / covid-19 / SARS-CoV-2 / spike / neutralizing antibody / immunity | ||||||||||||||||||
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 / symbiont-mediated suppression of host innate immune response / 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 Homo sapiens (human) | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.31 Å | ||||||||||||||||||
Authors | Rosa, A. / Pye, V.E. / Cronin, N. / Cherepanov, P. | ||||||||||||||||||
Funding support | United Kingdom, 5items
| ||||||||||||||||||
Citation | Journal: Cell Rep / Year: 2022 Title: A neutralizing epitope on the SD1 domain of SARS-CoV-2 spike targeted following infection and vaccination. Authors: Jeffrey Seow / Hataf Khan / Annachiara Rosa / Valeria Calvaresi / Carl Graham / Suzanne Pickering / Valerie E Pye / Nora B Cronin / Isabella Huettner / Michael H Malim / Argyris Politis / ...Authors: Jeffrey Seow / Hataf Khan / Annachiara Rosa / Valeria Calvaresi / Carl Graham / Suzanne Pickering / Valerie E Pye / Nora B Cronin / Isabella Huettner / Michael H Malim / Argyris Politis / Peter Cherepanov / Katie J Doores / Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the target for neutralizing antibodies elicited following both infection and vaccination. While extensive research has shown that the receptor binding domain (RBD) and, to a lesser extent, the N-terminal domain (NTD) are the predominant targets for neutralizing antibodies, identification of neutralizing epitopes beyond these regions is important for informing vaccine development and understanding antibody-mediated immune escape. Here, we identify a class of broadly neutralizing antibodies that bind an epitope on the spike subdomain 1 (SD1) and that have arisen from infection or vaccination. Using cryo-electron microscopy (cryo-EM) and hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS), we show that SD1-specific antibody P008_60 binds an epitope that is not accessible within the canonical prefusion states of the SARS-CoV-2 spike, suggesting a transient conformation of the viral glycoprotein that is vulnerable to neutralization. | ||||||||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7zbu.cif.gz | 215.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7zbu.ent.gz | 163.5 KB | Display | PDB format |
PDBx/mmJSON format | 7zbu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7zbu_validation.pdf.gz | 1010.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7zbu_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7zbu_validation.xml.gz | 46.8 KB | Display | |
Data in CIF | 7zbu_validation.cif.gz | 65 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/7zbu ftp://data.pdbj.org/pub/pdb/validation_reports/zb/7zbu | HTTPS FTP |
-Related structure data
Related structure data | 14591MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 142269.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 | ||||
---|---|---|---|---|---|
#2: Antibody | Mass: 25954.072 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / Strain (production host): FreeStyle293 | ||||
#3: Antibody | Mass: 23589.068 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / Strain (production host): FreeStyle293 | ||||
#4: Sugar | ChemComp-NAG / #5: Chemical | ChemComp-3Q9 / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Monomeric Spike glycoprotein ectodomain from SARS-CoV-2 in complex with a neutralising antibody P008_60 Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.125 MDa / Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 8 Details: 0.1% n-octyl glucoside in 150 mM NaCl, 20 mM Tris-HCl, pH8.0 |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: SARS-CoV-2 spike ectodomain (0.5 mg/ml), supplemented 0.2 mg/ml P008_60 Fab and 0.1% n-octyl glucoside in 150 mM NaCl, 20 mM Tris-HCl, pH8.0 |
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Details: blotted for 3 to 4 sec before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
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: 3600 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 4.1 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 16624 |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
-Processing
Software | Name: PHENIX / Version: dev_4213: / Classification: refinement | ||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||||
Image processing | Details: The micrograph stacks were aligned, binned to the physical pixel size of 1.1 A and summed, with dose weighting applied, as implemented in MotionCor2 | ||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1740430 Details: Initially, particles were picked with Gautomatch-v0.53 using 2D class averages of the trimeric spike, low-pass filtered to 20 A resolution, as templates. The resulting 1,740,430 particles, ...Details: Initially, particles were picked with Gautomatch-v0.53 using 2D class averages of the trimeric spike, low-pass filtered to 20 A resolution, as templates. The resulting 1,740,430 particles, extracted in Relion-3.1 and binned to a pixel size of 4.4 A, were subjected to two rounds of reference-free 2D classification in cryoSPARC-2. 283,956 particles belonging to well-defined 2D classes were subjected to classification into twelve 3D classes in Relion-3.1. Neither the 2D nor 3D class averages of the trimeric spike revealed features attributable to a bound Fab molecule. Next, 3,772,722 particles were picked using 2D class averages of the dissociated spikes. Following two rounds of 2D classification in cryoSPARC-2, 753,837 particles, re-extracted with pixel size of 2.2 A, were subjected to 3D classification in Relion-3.1 into 9 classes using an initial model obtained by Ab-initio reconstruction in cryoSPARC-2. The procedure revealed a single well-defined 3D class containing 208,343 particles (27.4%) of S1 protein with a bound Fab molecule. The particles, re-extracted without binning (with a pixel size 1.1 A), were subjected to two rounds of 3D classification using Ab-initio reconstruction in cryoSPARC-2 with 2 classes and class similarity set to 0. At the end of each round, the most populated class was selected, resulting in the final set of 166,619 particles. | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.31 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 166619 / Algorithm: FOURIER SPACE / Details: Non Uniform refinement in cryoSPARC / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | B value: 81 / Protocol: OTHER / Space: REAL / Target criteria: Correlation coefficient Details: The atomistic models of monomeric SARS-CoV-2 S1 protein and a Fab molecule, extracted from PDB entries 7A92 and 5WI9, were docked in the cryo-EM map using Chimera. The NTD and the RBD of the ...Details: The atomistic models of monomeric SARS-CoV-2 S1 protein and a Fab molecule, extracted from PDB entries 7A92 and 5WI9, were docked in the cryo-EM map using Chimera. The NTD and the RBD of the spike subunit were replaced with the crystal structures from PDB entries 7B62 and 7OAO, respectively. Guided by the cryo-EM map, the model was adjusted and extended interactively in Coot and refined using phenix.real_space_refine. | ||||||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||||||
Refine LS restraints |
|