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- EMDB-45779: Structure of the full-length Measles virus Fusion protein E170G E... -

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Basic information

Entry
Database: EMDB / ID: EMD-45779
TitleStructure of the full-length Measles virus Fusion protein E170G E455G in the pre-fusion conformation bound by [FIP-HRC]2-PEG11 in amphipol
Map datasharpened map
Sample
  • Complex: Structure of the full-length Measles virus Fusion protein E170G E455G in the pre-fusion conformation bound by [FIP-HRC]2-PEG11 in amphipol
    • Protein or peptide: [FIP-HRC]2-PEG11
  • Protein or peptide: Fusion glycoprotein F2
  • Protein or peptide: Fusion glycoprotein F1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsVIRAL PROTEIN / glycoprotein / immune system / measles / high-resolution / membrane protein / pre-fusion
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesMeasles virus strain Ichinose-B95a / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.65 Å
AuthorsZyla D / Saphire EO
Funding support Switzerland, United States, 5 items
OrganizationGrant numberCountry
Swiss National Science FoundationP2EZP3_195680 Switzerland
Swiss National Science FoundationP500PB_210992 Switzerland
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS105699 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)NS091263 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI176833 United States
CitationJournal: To Be Published
Title: Full-length soluble measles fusion glycoprotein as a new subunit vaccine strategy
Authors: Zyla D / Saphire EO
History
DepositionJul 16, 2024-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45779.png

Downloads & links

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Map

FileDownload / File: emd_45779.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 400 pix.
= 396. Å		0.99 Å/pix.
x 400 pix.
= 396. Å		0.99 Å/pix.
x 400 pix.
= 396. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.427
Minimum - Maximum-1.6250459 - 2.6725018
Average (Standard dev.)0.00042225159 (±0.052262787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 396.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45779_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: map unsharpened

Fileemd_45779_additional_1.map
Annotationmap unsharpened
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half 2

Fileemd_45779_half_map_1.map
Annotationhalf 2
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half 1

Fileemd_45779_half_map_2.map
Annotationhalf 1
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : Structure of the full-length Measles virus Fusion protein E170G E...

EntireName: Structure of the full-length Measles virus Fusion protein E170G E455G in the pre-fusion conformation bound by [FIP-HRC]2-PEG11 in amphipol
Components
  • Complex: Structure of the full-length Measles virus Fusion protein E170G E455G in the pre-fusion conformation bound by [FIP-HRC]2-PEG11 in amphipol
    • Protein or peptide: [FIP-HRC]2-PEG11
  • Protein or peptide: Fusion glycoprotein F2
  • Protein or peptide: Fusion glycoprotein F1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Structure of the full-length Measles virus Fusion protein E170G E...

SupramoleculeName: Structure of the full-length Measles virus Fusion protein E170G E455G in the pre-fusion conformation bound by [FIP-HRC]2-PEG11 in amphipol
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3
Source (natural)Organism: Measles virus strain Ichinose-B95a
Molecular weightTheoretical: 150 KDa

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Macromolecule #1: Fusion glycoprotein F2

MacromoleculeName: Fusion glycoprotein F2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Measles virus strain Ichinose-B95a / Strain: Ichinose-B95a
Molecular weightTheoretical: 12.498768 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MGLKVNVSAI FMAVLLTLQT PTGQIHWGNL SKIGVVGIGS ASYKVMTRSS HQSLVIKLMP NITLLNNCTR VEIAEYRRLL RTVLEPIRD ALNAMTQNIR PVQSVASSRR HKR

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: Fusion glycoprotein F1

MacromoleculeName: Fusion glycoprotein F1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Measles virus strain Ichinose-B95a / Strain: Ichinose-B95a
Molecular weightTheoretical: 50.19732 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FAGVVLAGAA LGVATAAQIT AGIALHQSML NSQAIDNLRA SLETTNQAIE AIRQAGQGMI LAVQGVQDYI NNELIPSMNQ LSCDLIGQK LGLKLLRYYT EILSLFGPSL RDPISAEISI QALSYALGGD INKVLEKLGY SGGDLLGILE SRGIKARITH V DTESYFIV ...String:
FAGVVLAGAA LGVATAAQIT AGIALHQSML NSQAIDNLRA SLETTNQAIE AIRQAGQGMI LAVQGVQDYI NNELIPSMNQ LSCDLIGQK LGLKLLRYYT EILSLFGPSL RDPISAEISI QALSYALGGD INKVLEKLGY SGGDLLGILE SRGIKARITH V DTESYFIV LSIAYPTLSE IKGVIVHRLE GVSYNIGSQE WYTTVPKYVA TQGYLISNFD ESSCTFMPEG TVCSQNALYP MS PLLQECL RGSTKSCART LVSGSFGNRF ILSQGNLIAN CASILCKCYT TGTIINQDPD KILTYIAADH CPVVEVNGVT IQV GSRRYP DAVYLHRIDL GPPISLGRLD VGTNLGNAIA KLEDAKELLE SSDQILRSMK GLSSTSIVYI LIAVCLGGLI GIPA LICCC RGRCNKKGEQ VGMSRPGLKP DLTGTSKSYV RSLGGGSGGW SHPQFEKGGG SGGGSGGGSW SHPQFEK

UniProtKB: Fusion glycoprotein F0

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Macromolecule #3: [FIP-HRC]2-PEG11

MacromoleculeName: [FIP-HRC]2-PEG11 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 503.546 Da
SequenceString:
(P6S)FFG

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 44 / 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
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.25 mg/mL
BufferpH: 8 / Details: HEPES 50 mM, pH 8.0, NaCl 500 mM
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 3 / Number real images: 8031 / Average exposure time: 2.0 sec. / 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: 2.5 µm / Nominal defocus min: 1.0 µm
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

Particle selectionNumber selected: 900000
CTF correctionSoftware: (Name: cryoSPARC, CTFFIND) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.3) / Number images used: 326000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: cryoSPARC, RELION)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5yxw


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

PDB-9cog:
Structure of the full-length Measles virus Fusion protein E170G E455G in the pre-fusion conformation bound by [FIP-HRC]2-PEG11 in amphipol

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