[English] 日本語
Yorodumi- PDB-6zp5: SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zp5 | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up closed conformation) | ||||||||||||||||||
Components | Spike glycoprotein | ||||||||||||||||||
Keywords | VIRAL PROTEIN / Spike / Prefusion / Flexibility / Closed | ||||||||||||||||||
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 | ||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
Authors | Martinez, M. / Marabini, R. / Carazo, J.M. | ||||||||||||||||||
Funding support | Spain, United States, 5items
| ||||||||||||||||||
Citation | Journal: IUCrJ / Year: 2020 Title: Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures. Authors: Roberto Melero / Carlos Oscar S Sorzano / Brent Foster / José-Luis Vilas / Marta Martínez / Roberto Marabini / Erney Ramírez-Aportela / Ruben Sanchez-Garcia / David Herreros / Laura Del ...Authors: Roberto Melero / Carlos Oscar S Sorzano / Brent Foster / José-Luis Vilas / Marta Martínez / Roberto Marabini / Erney Ramírez-Aportela / Ruben Sanchez-Garcia / David Herreros / Laura Del Caño / Patricia Losana / Yunior C Fonseca-Reyna / Pablo Conesa / Daniel Wrapp / Pablo Chacon / Jason S McLellan / Hemant D Tagare / Jose-Maria Carazo / Abstract: Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state have been ...Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state have been analysed. These studies revealed concerted motions involving the receptor-binding domain (RBD), N-terminal domain, and subdomains 1 and 2 around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. It is shown that in this data set there are not well defined, stable spike conformations, but virtually a continuum of states. An ensemble map was obtained with minimum bias, from which the extremes of the change along the direction of maximal variance were modeled by flexible fitting. The results provide a warning of the potential image-processing classification instability of these complicated data sets, which has a direct impact on the interpretability of the results. #1: Journal: bioRxiv / Year: 2020 Title: Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures. Authors: Roberto Melero / Carlos Oscar S Sorzano / Brent Foster / José-Luis Vilas / Marta Martínez / Roberto Marabini / Erney Ramírez-Aportela / Ruben Sanchez-Garcia / David Herreros / Laura Del ...Authors: Roberto Melero / Carlos Oscar S Sorzano / Brent Foster / José-Luis Vilas / Marta Martínez / Roberto Marabini / Erney Ramírez-Aportela / Ruben Sanchez-Garcia / David Herreros / Laura Del Caño / Patricia Losana / Yunior C Fonseca-Reyna / Pablo Conesa / Daniel Wrapp / Pablo Chacon / Jason S McLellan / Hemant D Tagare / Jose-Maria Carazo / Abstract: With the help of novel processing workflows and algorithms, we have obtained a better understanding of the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state. We ...With the help of novel processing workflows and algorithms, we have obtained a better understanding of the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state. We have re-analyzed previous cryo-EM data combining 3D clustering approaches with ways to explore a continuous flexibility space based on 3D Principal Component Analysis. These advanced analyses revealed a concerted motion involving the receptor-binding domain (RBD), N-terminal domain (NTD), and subdomain 1 and 2 (SD1 & SD2) around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. We show that in this dataset there are not well-defined, stable, spike conformations, but virtually a continuum of states moving in a concerted fashion. We obtained an improved resolution ensemble map with minimum bias, from which we model by flexible fitting the extremes of the change along the direction of maximal variance. Moreover, a high-resolution structure of a recently described biochemically stabilized form of the spike is shown to greatly reduce the dynamics observed for the wild-type spike. Our results provide new detailed avenues to potentially restrain the spike dynamics for structure-based drug and vaccine design and at the same time give a warning of the potential image processing classification instability of these complicated datasets, having a direct impact on the interpretability of the results. | ||||||||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6zp5.cif.gz | 542.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6zp5.ent.gz | 415.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zp5_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6zp5_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 6zp5_validation.xml.gz | 89.9 KB | Display | |
Data in CIF | 6zp5_validation.cif.gz | 139.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/6zp5 ftp://data.pdbj.org/pub/pdb/validation_reports/zp/6zp5 | HTTPS FTP |
-Related structure data
Related structure data | 11336MC 6zowC 6zp7C C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10516 (Title: Cryo electron microscopy of SARS-CoV-2 spike in prefusion state Data size: 2.1 TB / Data #1: 2.outputMovies [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Protein / Non-polymers , 2 types, 6 molecules ABC
#1: Protein | Mass: 142399.375 Da / Num. of mol.: 3 / Mutation: K986P, V987P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Gene: S, 2 / Plasmid: palphaH / Cell line (production host): FreeStyle293F / Production host: Homo sapiens (human) / References: UniProt: P0DTC2 #8: Chemical | |
---|
-Sugars , 6 types, 47 molecules
#2: 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 #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-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 #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 #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / #7: Sugar | |
---|
-Details
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: SARS-CoV-2 spike in prefusion state (flexibility analysis, 1-up closed conformation) Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Severe acute respiratory syndrome coronavirus 2 |
Source (recombinant) | Organism: Homo sapiens (human) / Cell: FreeStyle293F / Plasmid: palphaH |
Buffer solution | pH: 8 |
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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 36 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
EM software |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 45000 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT Details: Atomic structure 6ZOW was flexibly fitted to the map. | ||||||||||||||||
Atomic model building | PDB-ID: 6ZOW |