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- EMDB-51279: SARS-CoV-2 Spike protein Beta Variant at 4C structural flexibilit... -

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Basic information

Entry
Database: EMDB / ID: EMD-51279
TitleSARS-CoV-2 Spike protein Beta Variant at 4C structural flexibility / heterogeneity analyses
Map dataSARS-CoV-2 Spike protein Beta Variant at 4C unsharpened map
Sample
  • Complex: SARS-CoV-2 Spike protein Beta Variant at 4C
    • Protein or peptide: Spike glycoprotein,Fibritin
KeywordsSARS-CoV-2 / Spike Protein / temperature dependence / VIRAL PROTEIN
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 / suppression by virus 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 / 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 / host cell surface receptor binding / symbiont-mediated suppression of host innate immune response / 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 / Spike glycoprotein S1, N-terminal domain, betacoronavirus-like / Betacoronavirus-like spike glycoprotein S1, N-terminal / Betacoronavirus spike glycoprotein S1, receptor binding / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsHerreros D / Mata CP / Noddings C / Irene D / Agard DA / Tsai M-D / Sorzano COS / Carazo JM
Funding support Spain, European Union, Taiwan, 6 items
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
CitationJournal: 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
DepositionAug 6, 2024-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51279.png

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Map

FileDownload / File: emd_51279.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C unsharpened map
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AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 224 pix.
= 313.6 Å		1.4 Å/pix.
x 224 pix.
= 313.6 Å		1.4 Å/pix.
x 224 pix.
= 313.6 Å

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Voxel sizeX=Y=Z: 1.4 Å
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Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.55582166 - 1.7927017
Average (Standard dev.)0.001835482 (±0.06014959)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-112-112-112
Dimensions224224224
Spacing224224224
CellA=B=C: 313.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C sharpened map

Fileemd_51279_additional_1.map
AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C sharpened map
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 09 1UP

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 09 1UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 10 1UP

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 10 1UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 11 2UP

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 11 2UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 12 2UP

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 12 2UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 13 1UP

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 13 1UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 14 1UP

Fileemd_51279_additional_15.map
AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 14 1UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 15 1UP

Fileemd_51279_additional_16.map
AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 15 1UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 16 2UP

Fileemd_51279_additional_17.map
AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 16 2UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 17 2UP

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 17 2UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 18 2UP

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 18 2UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 01 2UP

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 01 2UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 19 1UP

Fileemd_51279_additional_20.map
AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 19 1UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 20 1UP

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 20 1UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 02 1UP

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 02 1UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 03 2UP

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 03 2UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 04 1UP

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 04 1UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 05 2UP

Fileemd_51279_additional_6.map
AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 05 2UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 06 2UP

Fileemd_51279_additional_7.map
AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 06 2UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 07 2UP

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 07 2UP
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Additional map: SARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 08 2UP

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C flexibility map 08 2UP
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Half map: SARS-CoV-2 Spike protein Beta Variant at 4C halfmap 01

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C halfmap 01
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Half map: SARS-CoV-2 Spike protein Beta Variant at 4C halfmap 02

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AnnotationSARS-CoV-2 Spike protein Beta Variant at 4C halfmap 02
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Sample components

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Entire : SARS-CoV-2 Spike protein Beta Variant at 4C

EntireName: SARS-CoV-2 Spike protein Beta Variant at 4C
Components
  • Complex: SARS-CoV-2 Spike protein Beta Variant at 4C
    • Protein or peptide: Spike glycoprotein,Fibritin

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Supramolecule #1: SARS-CoV-2 Spike protein Beta Variant at 4C

SupramoleculeName: SARS-CoV-2 Spike protein Beta Variant at 4C / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 540 KDa

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Macromolecule #1: Spike glycoprotein,Fibritin

MacromoleculeName: Spike glycoprotein,Fibritin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 136.142703 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QCVNFTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFANPV LPFNDGVYFA STEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLG VYYHKNNKSW MESEFRVYSS ANNCTFEYVS Q PFLMDLEG ...String:
QCVNFTTRTQ LPPAYTNSFT RGVYYPDKVF RSSVLHSTQD LFLPFFSNVT WFHAIHVSGT NGTKRFANPV LPFNDGVYFA STEKSNIIR GWIFGTTLDS KTQSLLIVNN ATNVVIKVCE FQFCNDPFLG VYYHKNNKSW MESEFRVYSS ANNCTFEYVS Q PFLMDLEG KQGNFKNLRE FVFKNIDGYF KIYSKHTPIN LVRGLPQGFS ALEPLVDLPI GINITRFQTL HISYLTPGDS SS GWTAGAA AYYVGYLQPR TFLLKYNENG TITDAVDCAL DPLSETKCTL KSFTVEKGIY QTSNFRVQPT ESIVRFPNIT NLC PFGEVF NATRFASVYA WNRKRISNCV ADYSVLYNSA SFSTFKCYGV SPTKLNDLCF TNVYADSFVI RGDEVRQIAP GQTG NIADY NYKLPDDFTG CVIAWNSNNL DSKVGGNYNY LYRLFRKSNL KPFERDISTE IYQAGSTPCN GVKGFNCYFP LQSYG FQPT YGVGYQPYRV VVLSFELLHA PATVCGPKKS TNLVKNKCVN FNFNGLTGTG VLTESNKKFL PFQQFGRDIA DTTDAV RDP QTLEILDITP CSFGGVSVIT PGTNTSNQVA VLYQGVNCTE VPVAIHADQL TPTWRVYSTG SNVFQTRAGC LIGAEHV NN SYECDIPIGA GICASYQTQT NSPGSASSVA SQSIIAYTMS LGVENSVAYS NNSIAIPTNF TISVTTEILP VSMTKTSV D CTMYICGDST ECSNLLLQYG SFCTQLNRAL TGIAVEQDKN TQEVFAQVKQ IYKTPPIKDF GGFNFSQILP DPSKPSKRS FIEDLLFNKV TLADAGFIKQ YGDCLGDIAA RDLICAQKFN GLTVLPPLLT DEMIAQYTSA LLAGTITSGW TFGAGAALQI PFAMQMAYR FNGIGVTQNV LYENQKLIAN QFNSAIGKIQ DSLSSTASAL GKLQDVVNQN AQALNTLVKQ LSSNFGAISS V LNDILSRL DPPEAEVQID RLITGRLQSL QTYVTQQLIR AAEIRASANL AATKMSECVL GQSKRVDFCG KGYHLMSFPQ SA PHGVVFL HVTYVPAQEK NFTTAPAICH DGKAHFPREG VFVSNGTHWF VTQRNFYEPQ IITTDNTFVS GNCDVVIGIV NNT VYDPLQ PELDSFKEEL DKYFKNHTSP DVDLGDISGI NASVVNIQKE IDRLNEVAKN LNESLIDLQE LGKYEQGSGY IPEA PRDGQ AYVRKDGEWV LLSTFLGRSL EVLFQ

UniProtKB: Spike glycoprotein, Fibritin

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.25 mg/mL
BufferpH: 5.5 / Component - Concentration: 100.0 mM / Component - Formula: C6H9Na3O9 / Component - Name: Trisodium Citrate Dihydrate
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 11137 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 479908
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Details: HetSIREN

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Atomic model buiding 1

Initial modelPDB ID:

7vx1


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: 7VX1
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9gdx:
SARS-CoV-2 Spike protein Beta Variant at 4C structural flexibility / heterogeneity analyses

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