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- PDB-9gdy: SARS-CoV-2 Spike protein Beta Variant at 37C structural flexibili... -

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Entry
Database: PDB / ID: 9gdy
TitleSARS-CoV-2 Spike protein Beta Variant at 37C structural flexibility / heterogeneity analyses
ComponentsSpike glycoprotein,Fibritin
KeywordsVIRAL PROTEIN / SARS-CoV-2 / Spike Protein / temperature dependence
Function / homology
Function and homology information


virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion ...virion component / Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / symbiont-mediated-mediated suppression of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / membrane fusion / Attachment and Entry / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / receptor ligand activity / endocytosis involved in viral entry into host cell / 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
Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. ...Fibritin C-terminal / Fibritin C-terminal region / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein, betacoronavirus / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike (S) protein S1 subunit, receptor-binding domain, betacoronavirus / Spike S1 subunit, receptor binding domain superfamily, betacoronavirus / Betacoronavirus spike glycoprotein S1, receptor binding / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Spike glycoprotein / Fibritin
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Enterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHerreros, D. / Mata, C.P. / Noddings, C. / Irene, D. / Agard, D.A. / Tsai, M.-D. / Sorzano, C.O.S. / Carazo, J.M.
Funding support Spain, European Union, Taiwan, 6items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)rant PID2022-136594NB-I00 funded by MICIU /AEI/ 10.13039/501100011033/ Spain
European Research Council (ERC)HighResCells (ERC-2018-SyG, Proposal: 810057European Union
iNEXT-DiscoveryiNEXT-Discovery (Proposal: 871037)European Union
Academia Sinica (Taiwan)(AS-KPQ-109-TPP2) Taiwan
Academia Sinica (Taiwan)NSTC 113-2740-B-006-004 Taiwan
Academia Sinica (Taiwan)AS-CFII-108-110 Taiwan
Citation
Journal: Nat Commun / Year: 2025
Title: Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN.
Authors: David Herreros / Carlos Perez Mata / Chari Noddings / Deli Irene / James Krieger / David A Agard / Ming-Daw Tsai / Carlos Oscar Sanchez Sorzano / Jose Maria Carazo /
Abstract: Single-particle analysis by Cryo-electron microscopy (CryoEM) provides direct access to the conformations of macromolecules. Traditional methods assume discrete conformations, while newer algorithms ...Single-particle analysis by Cryo-electron microscopy (CryoEM) provides direct access to the conformations of macromolecules. Traditional methods assume discrete conformations, while newer algorithms estimate conformational landscapes representing the different structural states a biomolecule explores. This work presents HetSIREN, a deep learning-based method that can fully reconstruct or refine a CryoEM volume in real space based on the structural information summarized in a conformational latent space. HetSIREN is defined as an accurate space-based method that allows spatially focused analysis and the introduction of sinusoidal hypernetworks with proven high analytics capacities. Continuing with innovations, HetSIREN can also refine the images' pose while conditioning the network with additional constraints to yield cleaner high-quality volumes, as well as addressing one of the most confusing issues in heterogeneity analysis, as it is the fact that structural heterogeneity estimations are entangled with pose estimation (and to a lesser extent with CTF estimation) thanks to its decoupling architecture.
#1: Journal: bioRxiv / Year: 2024
Title: Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN.
Authors: D Herreros / C P Mata / C Noddings / D Irene / J Krieger / D A Agard / M-D Tsai / C O S Sorzano / J M Carazo /
Abstract: Single-particle analysis by Cryo-electron microscopy (CryoEM) provides direct access to the conformation of each macromolecule. However, the image's signal-to-noise ratio is low, and some form of ...Single-particle analysis by Cryo-electron microscopy (CryoEM) provides direct access to the conformation of each macromolecule. However, the image's signal-to-noise ratio is low, and some form of classification is usually performed at the image processing level to allow structural modeling. Classical classification methods imply the existence of a discrete number of structural conformations. However, new heterogeneity algorithms introduce a novel reconstruction paradigm, where every state is represented by a lower number of particles, potentially just one, allowing the estimation of conformational landscapes representing the different structural states a biomolecule explores. In this work, we present a novel deep learning-based method called HetSIREN. HetSIREN can fully reconstruct or refine a CryoEM volume in real space based on the structural information summarized in a conformational latent space. The unique characteristics that set HetSIREN apart start with the definition of the approach as a real space-based only method, a fact that allows spatially focused analysis, but also the introduction of a novel network architecture specifically designed to make use of meta-sinusoidal activations, with proven high analytics capacities. Continuing with innovations, HetSIREN can also refine the pose parameters of the images at the same time that it conditions the network with prior information/constraints on the maps, such as Total Variation and denoising, ultimately yielding cleaner volumes with high-quality structural features. Finally, but very importantly, HetSIREN addresses one of the most confusing issues in heterogeneity analysis, as it is the fact that real structural heterogeneity estimation is entangled with pose estimation (and to a lesser extent with CTF estimation), in this way, HetSIREN introduces a novel encoding architecture able to decouple pose and CTF information from the conformational landscape, resulting in more accurate and interpretable conformational latent spaces. We present results on computer-simulated data, public data from EMPIAR, and data from experimental systems currently being studied in our laboratories. An important finding is the sensitivity of the structure and dynamics of the SARS-CoV-2 Spike protein on the storage temperature.
History
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Spike glycoprotein,Fibritin
B: Spike glycoprotein,Fibritin
C: Spike glycoprotein,Fibritin


Theoretical massNumber of molelcules
Total (without water)408,4283
Polymers408,4283
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Number of models20

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Components

#1: Protein Spike glycoprotein,Fibritin / S glycoprotein / E2 / Peplomer protein / Collar protein / Whisker antigen control protein


Mass: 136142.703 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2, (gene. exp.) Enterobacteria phage T4 (virus)
Gene: S, 2, wac / Variant: Beta / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DTC2, UniProt: P10104
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SARS-CoV-2 Spike protein Beta Variant at 37C / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.54 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Severe acute respiratory syndrome coronavirus 22697049
21Enterobacteria phage T4 (virus)10665
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster)
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 5.5
Buffer componentConc.: 100 mM / Name: Trisodium Citrate Dihydrate / Formula: C6H9Na3O9
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 37 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1500 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 7064

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4CTFFINDCTF correction
5GctfCTF correction
8UCSF Chimeramodel fitting
9Cootmodel fitting
10PHENIXmodel fitting
12cryoSPARCinitial Euler assignment
16Cootmodel refinement
17PHENIXmodel refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 309062 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeDetailsInitial refinement model-ID
17VX1

7vx1

7VX17VX11
27WEV

7wev

7WEV7WEV2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00825956
ELECTRON MICROSCOPYf_angle_d1.60335304
ELECTRON MICROSCOPYf_dihedral_angle_d4.1373468
ELECTRON MICROSCOPYf_chiral_restr0.093981
ELECTRON MICROSCOPYf_plane_restr0.0084581

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