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- EMDB-27248: Sub-tomogram averaged map of full-length post-fusion CHIKV E1 gly... -

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Basic information

Entry
Database: EMDB / ID: EMD-27248
TitleSub-tomogram averaged map of full-length post-fusion CHIKV E1 glycoprotein trimer
Map dataSub-tomogram averaged map of membrane attached full-length post-fusion CHIKV E1 glycoprotein trimer
Sample
  • Complex: Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer from Chikungunya virus
    • Protein or peptide: Spike glycoprotein E1
  • Ligand: BROMIDE ION
  • Ligand: HOLMIUM ATOM
  • Ligand: PHOSPHATE ION
  • Ligand: water
Keywordsenvelope glycoprotein / membrane fusion / virus / VIRAL PROTEIN
Function / homology
Function and homology information


togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane ...togavirin / T=4 icosahedral viral capsid / virion assembly / small molecule binding / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / clathrin-dependent endocytosis of virus by host cell / viral translational frameshifting / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / membrane
Similarity search - Function
Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein ...Alphavirus E2 glycoprotein, domain B / Peptidase S3, togavirin / Alphavirus E2 glycoprotein / Alphavirus E3 spike glycoprotein / Alphavirus E1 glycoprotein / Alphavirus E2 glycoprotein, domain A / Alphavirus E2 glycoprotein, domain C / Alphavirus E2 glycoprotein / Alphavirus core protein / Alphavirus E3 glycoprotein / Alphavirus E1 glycoprotein / Alphavirus core protein (CP) domain profile. / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Structural polyprotein
Similarity search - Component
Biological speciesChikungunya virus strain S27-African prototype
Methodsubtomogram averaging / cryo EM / Resolution: 27.2 Å
AuthorsMangala Prasad V / Lee KK
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM099989 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
CitationJournal: Nat Commun / Year: 2022
Title: Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery.
Authors: Vidya Mangala Prasad / Jelle S Blijleven / Jolanda M Smit / Kelly K Lee /
Abstract: Chikungunya virus (CHIKV) is a human pathogen that delivers its genome to the host cell cytoplasm through endocytic low pH-activated membrane fusion mediated by class-II fusion proteins. Though ...Chikungunya virus (CHIKV) is a human pathogen that delivers its genome to the host cell cytoplasm through endocytic low pH-activated membrane fusion mediated by class-II fusion proteins. Though structures of prefusion, icosahedral CHIKV are available, structural characterization of virion interaction with membranes has been limited. Here, we have used cryo-electron tomography to visualize CHIKV's complete membrane fusion pathway, identifying key intermediary glycoprotein conformations coupled to membrane remodeling events. Using sub-tomogram averaging, we elucidate features of the low pH-exposed virion, nucleocapsid and full-length E1-glycoprotein's post-fusion structure. Contrary to class-I fusion systems, CHIKV achieves membrane apposition by protrusion of extended E1-glycoprotein homotrimers into the target membrane. The fusion process also features a large hemifusion diaphragm that transitions to a wide pore for intact nucleocapsid delivery. Our analyses provide comprehensive ultrastructural insights into the class-II virus fusion system function and direct mechanistic characterization of the fundamental process of protein-mediated membrane fusion.
History
DepositionJun 8, 2022-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27248.png

Downloads & links

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Map

FileDownload / File: emd_27248.map.gz / Format: CCP4 / Size: 251 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram averaged map of membrane attached full-length post-fusion CHIKV E1 glycoprotein trimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.61 Å/pix.
x 40 pix.
= 264.48 Å		6.61 Å/pix.
x 40 pix.
= 264.48 Å		6.61 Å/pix.
x 40 pix.
= 264.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.612 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.55
Minimum - Maximum-5.7554083 - 9.380604999999999
Average (Standard dev.)0.00000009890514 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-20-20-20
Dimensions404040
Spacing404040
CellA=B=C: 264.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Odd-half map

Fileemd_27248_half_map_1.map
AnnotationOdd-half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Even half map

Fileemd_27248_half_map_2.map
AnnotationEven half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer f...

EntireName: Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer from Chikungunya virus
Components
  • Complex: Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer from Chikungunya virus
    • Protein or peptide: Spike glycoprotein E1
  • Ligand: BROMIDE ION
  • Ligand: HOLMIUM ATOM
  • Ligand: PHOSPHATE ION
  • Ligand: water

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Supramolecule #1: Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer f...

SupramoleculeName: Sub-tomogram averaged map of post-fusion E1 glycoprotein trimer from Chikungunya virus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Chikungunya virus strain S27-African prototype
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Spike glycoprotein E1

MacromoleculeName: Spike glycoprotein E1 / type: protein_or_peptide / ID: 1
Details: The previously determined X-ray crystal structure PDB ID 1RER was rigidly docked into the sub-tomogram averaged map but no further refinement was performed
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Chikungunya virus strain S27-African prototype
Molecular weightTheoretical: 42.690125 KDa
SequenceString: YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCRHDHA SAYKAHTASL KAKVRVMYGN VNQTVDVYVN GDHAVTIGGT Q FIFGPLSS ...String:
YEHSTVMPNV VGFPYKAHIE RPGYSPLTLQ MQVVETSLEP TLNLEYITCE YKTVVPSPYV KCCGASECST KEKPDYQCKV YTGVYPFMW GGAYCFCDSE NTQLSEAYVD RSDVCRHDHA SAYKAHTASL KAKVRVMYGN VNQTVDVYVN GDHAVTIGGT Q FIFGPLSS AWTPFDNKIV VYKDEVFNQD FPPYGSGQPG RFGDIQSRTV ESNDLYANTA LKLARPSPGM VHVPYTQTPS GF KYWLKEK GTALNTKAPF GCQIKTNPVR AMNCAVGNIP VSMNLPDSAF TRIVEAPTII DLTCTVATCT HSSDFGGVLT LTY KTNKNG DCSVHSHSNV ATLQEATAKV KTAGKVTLHF STASASPSFV VSLCSARATC SASCEPPKDH IVPYA

UniProtKB: Structural polyprotein

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Macromolecule #5: BROMIDE ION

MacromoleculeName: BROMIDE ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: BR
Molecular weightTheoretical: 79.904 Da
Chemical component information

ChemComp-BR:
BROMIDE ION

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Macromolecule #6: HOLMIUM ATOM

MacromoleculeName: HOLMIUM ATOM / type: ligand / ID: 6 / Number of copies: 4 / Formula: HO
Molecular weightTheoretical: 164.93 Da
Chemical component information

ChemComp-HO:
HOLMIUM ATOM

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Macromolecule #7: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 7 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 139 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 5.1 / Details: Hepes Buffer Saline
GridModel: EMS Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 7-8 seconds.
DetailsSub-volumes picked from liposome membrane surface

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 53000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 27.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET / Number subtomograms used: 590
ExtractionNumber tomograms: 40 / Number images used: 591 / Reference model: crystal structure / Software - Name: PEET
Details: low pass filtered map of post-fusion E1--homotrimer crystal structure
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1rer


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8d87:
Fitted crystal structure of the homotrimer of fusion glycoprotein E1 from SFV into subtomogram averaged CHIKV E1 glycoprotein density

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