[English] 日本語
Yorodumi- PDB-7r4q: The SARS-CoV-2 spike in complex with the 1.29 neutralizing nanobody -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r4q | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The SARS-CoV-2 spike in complex with the 1.29 neutralizing nanobody | |||||||||
Components |
| |||||||||
Keywords | VIRAL PROTEIN / coronavirus / COVID-19 / SARS-CoV-2 / spike / nanobodies / neutralization | |||||||||
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 / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / 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 Camelus dromedarius (Arabian camel) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Casasnovas, J.M. / Melero, R. / Arranz, R. / Fernandez, L.A. | |||||||||
Funding support | Spain, European Union, 2items
| |||||||||
Citation | Journal: Front Immunol / Year: 2022 Title: Nanobodies Protecting From Lethal SARS-CoV-2 Infection Target Receptor Binding Epitopes Preserved in Virus Variants Other Than Omicron. Authors: José M Casasnovas / Yago Margolles / María A Noriega / María Guzmán / Rocío Arranz / Roberto Melero / Mercedes Casanova / Juan Alberto Corbera / Nereida Jiménez-de-Oya / Pablo ...Authors: José M Casasnovas / Yago Margolles / María A Noriega / María Guzmán / Rocío Arranz / Roberto Melero / Mercedes Casanova / Juan Alberto Corbera / Nereida Jiménez-de-Oya / Pablo Gastaminza / Urtzi Garaigorta / Juan Carlos Saiz / Miguel Ángel Martín-Acebes / Luis Ángel Fernández / Abstract: The emergence of SARS-CoV-2 variants that escape from immune neutralization are challenging vaccines and antibodies developed to stop the COVID-19 pandemic. Thus, it is important to establish ...The emergence of SARS-CoV-2 variants that escape from immune neutralization are challenging vaccines and antibodies developed to stop the COVID-19 pandemic. Thus, it is important to establish therapeutics directed toward multiple or specific SARS-CoV-2 variants. The envelope spike (S) glycoprotein of SARS-CoV-2 is the key target of neutralizing antibodies (Abs). We selected a panel of nine nanobodies (Nbs) from dromedary camels immunized with the receptor-binding domain (RBD) of the S, and engineered Nb fusions as humanized heavy chain Abs (hcAbs). Nbs and derived hcAbs bound with subnanomolar or picomolar affinities to the S and its RBD, and S-binding cross-competition clustered them in two different groups. Most of the hcAbs hindered RBD binding to its human ACE2 (hACE2) receptor, blocked cell entry of viruses pseudotyped with the S protein and neutralized SARS-CoV-2 infection in cell cultures. Four potent neutralizing hcAbs prevented the progression to lethal SARS-CoV-2 infection in hACE2-transgenic mice, demonstrating their therapeutic potential. Cryo-electron microscopy identified Nb binding epitopes in and out the receptor binding motif (RBM), and showed different ways to prevent virus binding to its cell entry receptor. The Nb binding modes were consistent with its recognition of SARS-CoV-2 RBD variants; mono and bispecific hcAbs efficiently bound all variants of concern except omicron, which emphasized the immune escape capacity of this latest variant. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7r4q.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7r4q.ent.gz | 933.6 KB | Display | PDB format |
PDBx/mmJSON format | 7r4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7r4q_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7r4q_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7r4q_validation.xml.gz | 129.7 KB | Display | |
Data in CIF | 7r4q_validation.cif.gz | 173.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/7r4q ftp://data.pdbj.org/pub/pdb/validation_reports/r4/7r4q | HTTPS FTP |
-Related structure data
Related structure data | 14314MC 7r4iC 7r4rC 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: 140113.922 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 / Cell (production host): HEK293F Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others) References: UniProt: P0DTC2 #2: Antibody | Mass: 13348.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid: pcDNA Production host: Mammalian expression vector Flag-MCS-pcDNA3.1 (others) #3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-NAG / 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 |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight |
| ||||||||||||||||||||||||||||
Source (natural) |
| ||||||||||||||||||||||||||||
Source (recombinant) |
| ||||||||||||||||||||||||||||
Buffer solution | pH: 7.7 | ||||||||||||||||||||||||||||
Buffer component |
| ||||||||||||||||||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: The spike with the bound nanobody was purified by size exclusion chromatography. | ||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: DARK FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_4335: / Classification: refinement | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40000 / Symmetry type: POINT | ||||||||||||||||||||||||||||||
Atomic model building | B value: 140 / Protocol: OTHER / Space: REAL / Target criteria: correlation coefficient Details: Rigid body refinement. Real space refinement including 5 macro cycles of:Minimization_global, local_grid search and adp. Refinement at 4.0A of resolution. Refinement included NCS. | ||||||||||||||||||||||||||||||
Atomic model building |
| ||||||||||||||||||||||||||||||
Refine LS restraints |
|