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- EMDB-29017: Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane -

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Basic information

Entry
Database: EMDB / ID: EMD-29017
TitleCryo-EM structure of SARS-CoV-2 postfusion spike in membrane
Map data
Sample
  • Complex: local map of SRAS-CoV-2 postfusion spike protein in nanodisc from data set I
KeywordsVIRAL PROTEIN
Biological speciesSevere acute respiratory syndrome coronavirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang J / Shi W / Cai YF / Zhu HS / Peng HQ / Voyer J / Volloch SR / Cao H / Mayer ML / Song KK ...Zhang J / Shi W / Cai YF / Zhu HS / Peng HQ / Voyer J / Volloch SR / Cao H / Mayer ML / Song KK / Xu C / Lu JM / Chen B
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI147884 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI141002 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI127193 United States
CitationJournal: Nature / Year: 2023
Title: Cryo-EM structure of SARS-CoV-2 postfusion spike in membrane.
Authors: Wei Shi / Yongfei Cai / Haisun Zhu / Hanqin Peng / Jewel Voyer / Sophia Rits-Volloch / Hong Cao / Megan L Mayer / Kangkang Song / Chen Xu / Jianming Lu / Jun Zhang / Bing Chen /
Abstract: The entry of SARS-CoV-2 into host cells depends on the refolding of the virus-encoded spike protein from a prefusion conformation, which is metastable after cleavage, to a lower-energy stable ...The entry of SARS-CoV-2 into host cells depends on the refolding of the virus-encoded spike protein from a prefusion conformation, which is metastable after cleavage, to a lower-energy stable postfusion conformation. This transition overcomes kinetic barriers for fusion of viral and target cell membranes. Here we report a cryogenic electron microscopy (cryo-EM) structure of the intact postfusion spike in a lipid bilayer that represents the single-membrane product of the fusion reaction. The structure provides structural definition of the functionally critical membrane-interacting segments, including the fusion peptide and transmembrane anchor. The internal fusion peptide forms a hairpin-like wedge that spans almost the entire lipid bilayer and the transmembrane segment wraps around the fusion peptide at the last stage of membrane fusion. These results advance our understanding of the spike protein in a membrane environment and may guide development of intervention strategies.
History
DepositionDec 5, 2022-
Header (metadata) releaseMay 10, 2023-
Map releaseMay 10, 2023-
UpdateJul 26, 2023-
Current statusJul 26, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29017.png

Downloads & links

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Map

FileDownload / File: emd_29017.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 495. Å		0.83 Å/pix.
x 600 pix.
= 495. Å		0.83 Å/pix.
x 600 pix.
= 495. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.0017584928 - 1.31638
Average (Standard dev.)0.00010485117 (±0.006611977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 495.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_29017_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_29017_half_map_2.map
Projections & Slices
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Sample components

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Entire : local map of SRAS-CoV-2 postfusion spike protein in nanodisc from...

EntireName: local map of SRAS-CoV-2 postfusion spike protein in nanodisc from data set I
Components
  • Complex: local map of SRAS-CoV-2 postfusion spike protein in nanodisc from data set I

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Supramolecule #1: local map of SRAS-CoV-2 postfusion spike protein in nanodisc from...

SupramoleculeName: local map of SRAS-CoV-2 postfusion spike protein in nanodisc from data set I
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: local map of SARS-CoV-2 postfusion spike protein in nanodisc from data set I
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
Molecular weightTheoretical: 210 KDa

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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

Concentration1.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
0.15 mol/LNaClsodium chloride
0.025 mol/LTris-HClTris hydrochloride
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.01 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 18339830
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6xra

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.2) / Number images used: 123298
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationSoftware - Name: RELION

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Atomic model buiding 1

Initial modelPDB ID:

7krr


Chain - Chain ID: A / Chain - Residue range: 14-1211 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: AB INITIO MODEL

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