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- EMDB-39188: Cryo-EM structure of human respiratory syncytial virus fusion pro... -

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Basic information

Entry
Database: EMDB / ID: EMD-39188
TitleCryo-EM structure of human respiratory syncytial virus fusion protein variant
Map data
Sample
  • Complex: Respiratory syncytial virus fusion protein
    • Protein or peptide: Fusion glycoprotein F0
KeywordsRSV / Fusion Glycoprotein / Pre-fusion / Viral protein
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus / human respiratory syncytial virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsLi QM / Su JG / Zhang J / Liang Y / Shao S / Li XY / Zhao ZX
Funding support China, 1 items
OrganizationGrant numberCountry
Other government China
CitationJournal: Science / Year: 2024
Title: Mutating a flexible region of the RSV F protein can stabilize the prefusion conformation.
Authors: Yu Liang / Shuai Shao / Xin Yu Li / Zi Xin Zhao / Ning Liu / Zhao Ming Liu / Fu Jie Shen / Hao Zhang / Jun Wei Hou / Xue Feng Zhang / Yu Qin Jin / Li Fang Du / Xin Li / Jing Zhang / Ji Guo Su / Qi Ming Li /
Abstract: The respiratory syncytial virus (RSV) fusion (F) glycoprotein is highly immunogenic in its prefusion (pre-F) conformation. However, the protein is unstable, and its conformation must be stabilized ...The respiratory syncytial virus (RSV) fusion (F) glycoprotein is highly immunogenic in its prefusion (pre-F) conformation. However, the protein is unstable, and its conformation must be stabilized for it to function effectively as an immunogen in vaccines. We present a mutagenesis strategy to arrest the RSV F protein in its pre-F state by blocking localized changes in protein structure that accompany large-scale conformational rearrangements. We generated a series of mutants and screened them in vitro to assess their potential for forming a stable pre-F. In animals, the immunogenicity of a representative mutant F protein, with a conformation confirmed by cryo-electron microscopy, elicited levels of neutralizing antibodies and protection against RSV-induced lung damage that were comparable to those of DS-Cav1, a pre-F used in a licensed vaccine.
History
DepositionFeb 21, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39188.png

Downloads & links

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Map

FileDownload / File: emd_39188.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 256 pix.
= 206.848 Å		0.81 Å/pix.
x 256 pix.
= 206.848 Å		0.81 Å/pix.
x 256 pix.
= 206.848 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.0017794542 - 1.8027993
Average (Standard dev.)0.0028025175 (±0.040031407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 206.848 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39188_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39188_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Respiratory syncytial virus fusion protein

EntireName: Respiratory syncytial virus fusion protein
Components
  • Complex: Respiratory syncytial virus fusion protein
    • Protein or peptide: Fusion glycoprotein F0

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Supramolecule #1: Respiratory syncytial virus fusion protein

SupramoleculeName: Respiratory syncytial virus fusion protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human respiratory syncytial virus

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: human respiratory syncytial virus
Molecular weightTheoretical: 54.801281 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK ENKCNGTDAK VKLIKQELDK YKNAVTELQL LMQSTPATNN QARGSGSGR SLGFLLGVGS AIASGVAVSK VLHLEGEVNK IKSALLSTNK AVVSLSNGVS VLTSKVLDLK NYIDKQLLPI V NKQSCSIS ...String:
QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK ENKCNGTDAK VKLIKQELDK YKNAVTELQL LMQSTPATNN QARGSGSGR SLGFLLGVGS AIASGVAVSK VLHLEGEVNK IKSALLSTNK AVVSLSNGVS VLTSKVLDLK NYIDKQLLPI V NKQSCSIS NIETVIEFQQ KMNRFLEITR EFSVNAGVTT PVSTYMLTNS ELLSLINDMP ITNDQKKLMS NNVQIVRQQS YS IMSIIKE EVLAYVVQLP LYGVIDTPCW KLHTSPLCTT NTKEGSNICL TRTDRGWYCD NAGSVSFFPQ AETCKVQSNR VFC DTMNSL TLPSEVNLCN VDIFNPKYDC KIMTSKTDVS SSVITSLGAI VSCYGKTKCT ASNKNRGIIK TFSNGCDYVS NKGV DTVSV GNTLYYVNKQ EGKSLYVKGE PIINFYDPLV FPSDEFDASI SQVNEKINQS LAFIRKFDEL LSAIGGYIPE APRDG QAYV RKDGEWVLLS TFL

UniProtKB: Fusion glycoprotein F0, Fusion glycoprotein F0

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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: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / 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: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4jhw

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 2706
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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