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- EMDB-24775: Cryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-24775
TitleCryo-EM structure of the SARS-CoV-2 HR1HR2 fusion core complex with D936Y mutation
Map data
Sample
  • Complex: SARS-CoV-2 HR1HR2 complex with D936Y mutation
    • Protein or peptide: SARS-CoV-2 HR1 D936Y linked to a scaffold,Spike protein S2'
    • Protein or peptide: Spike protein S2'
Function / homology
Function and homology information


oxidoreductase activity, acting on metal ions / ferric iron binding / 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 ...oxidoreductase activity, acting on metal ions / ferric iron binding / 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 / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / entry receptor-mediated virion attachment to host cell / 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 / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / membrane / identical protein binding / plasma membrane
Similarity search - Function
Dps protein family signature 2. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. ...Dps protein family signature 2. / DNA-binding protein Dps, conserved site / DNA-binding protein Dps / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily / Spike (S) protein S1 subunit, receptor-binding domain, SARS-CoV-2 / Spike (S) protein S1 subunit, N-terminal domain, SARS-CoV-like / Betacoronavirus spike (S) glycoprotein S1 subunit N-terminal (NTD) domain profile. / Spike glycoprotein, N-terminal domain superfamily / Betacoronavirus spike (S) glycoprotein S1 subunit C-terminal (CTD) domain profile. / Spike glycoprotein, betacoronavirus / 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 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Ferritin, Dps family protein / Spike glycoprotein
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.27 Å
AuthorsYang K / Brunger AT
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structural conservation among variants of the SARS-CoV-2 spike postfusion bundle.
Authors: Kailu Yang / Chuchu Wang / K Ian White / Richard A Pfuetzner / Luis Esquivies / Axel T Brunger /
Abstract: Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies due to structural and dynamic changes of the ...Variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenge currently available COVID-19 vaccines and monoclonal antibody therapies due to structural and dynamic changes of the viral spike glycoprotein (S). The heptad repeat 1 (HR1) and heptad repeat 2 (HR2) domains of S drive virus–host membrane fusion by assembly into a six-helix bundle, resulting in delivery of viral RNA into the host cell. We surveyed mutations of currently reported SARS-CoV-2 variants and selected eight mutations, including Q954H, N969K, and L981F from the Omicron variant, in the postfusion HR1HR2 bundle for functional and structural studies. We designed a molecular scaffold to determine cryogenic electron microscopy (cryo-EM) structures of HR1HR2 at 2.2–3.8 Å resolution by linking the trimeric N termini of four HR1 fragments to four trimeric C termini of the Dps4 dodecamer from Nostoc punctiforme. This molecular scaffold enables efficient sample preparation and structure determination of the HR1HR2 bundle and its mutants by single-particle cryo-EM. Our structure of the wild-type HR1HR2 bundle resolves uncertainties in previously determined structures. The mutant structures reveal side-chain positions of the mutations and their primarily local effects on the interactions between HR1 and HR2. These mutations do not alter the global architecture of the postfusion HR1HR2 bundle, suggesting that the interfaces between HR1 and HR2 are good targets for developing antiviral inhibitors that should be efficacious against all known variants of SARS-CoV-2 to date. We also note that this work paves the way for similar studies in more distantly related viruses.
History
DepositionAug 27, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateApr 13, 2022-
Current statusApr 13, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24775.png

Downloads & links

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Map

FileDownload / File: emd_24775.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.81625 Å
Density
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.0017727906 - 1.5706998
Average (Standard dev.)0.0006214484 (±0.01846123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 208.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : SARS-CoV-2 HR1HR2 complex with D936Y mutation

EntireName: SARS-CoV-2 HR1HR2 complex with D936Y mutation
Components
  • Complex: SARS-CoV-2 HR1HR2 complex with D936Y mutation
    • Protein or peptide: SARS-CoV-2 HR1 D936Y linked to a scaffold,Spike protein S2'
    • Protein or peptide: Spike protein S2'

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Supramolecule #1: SARS-CoV-2 HR1HR2 complex with D936Y mutation

SupramoleculeName: SARS-CoV-2 HR1HR2 complex with D936Y mutation / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightTheoretical: 40 KDa

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Macromolecule #1: SARS-CoV-2 HR1 D936Y linked to a scaffold,Spike protein S2'

MacromoleculeName: SARS-CoV-2 HR1 D936Y linked to a scaffold,Spike protein S2'
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 28.807141 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSHHHHHHGS QTLLRNFGNV YDNPVLLDRS VTAPVTEGFN VVLASFQALY LQYQKHHFVV EGSEFYSLHE FFNESYNQVQ DHIHEIGER LDGLGGVPVA TFSKLAELTC FEQESEGVYS SRQMVENDLA AEQAIIGVIR RQAAQAESLG DRGTRYLYEK I LLKTEERA ...String:
MSHHHHHHGS QTLLRNFGNV YDNPVLLDRS VTAPVTEGFN VVLASFQALY LQYQKHHFVV EGSEFYSLHE FFNESYNQVQ DHIHEIGER LDGLGGVPVA TFSKLAELTC FEQESEGVYS SRQMVENDLA AEQAIIGVIR RQAAQAESLG DRGTRYLYEK I LLKTEERA YHLSHFLAKD SLTLGFAYEN QKLIANQFNS AIGKIQYSLS STASALGKLQ DVVNQNAQAL NTLVKQLSSN FG AISSVLN DILSRLDKVE

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Macromolecule #2: Spike protein S2'

MacromoleculeName: Spike protein S2' / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 4.422881 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPDVDLGDIS GINASVVNIQ KEIDRLNEVA KNLNESLIDL Q

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.27 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 585122

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