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- EMDB-47166: Structure of the Measles virus Fusion protein ectodomain E170G E4... -

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Basic information

Entry
Database: EMDB / ID: EMD-47166
TitleStructure of the Measles virus Fusion protein ectodomain E170G E455G with mutated furin cleavage site in the pre-fusion conformation
Map data
Sample
  • Complex: Structure of the Measles virus Fusion protein ectodomain E170G E455G with mutated furin cleavage site in the pre-fusion conformation
    • Protein or peptide: Fusion glycoprotein F0
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsVIRAL PROTEIN / glycoprotein / immune system / measles / high-resolution / ectodomain / 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 morbillivirus / Measles virus strain Ichinose-B95a
Methodsingle particle reconstruction / cryo EM / Resolution: 2.05 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
DepositionOct 1, 2024-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47166.png

Downloads & links

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Map

FileDownload / File: emd_47166.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 384 pix.
= 337.92 Å		0.88 Å/pix.
x 384 pix.
= 337.92 Å		0.88 Å/pix.
x 384 pix.
= 337.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.157
Minimum - Maximum-0.76732737 - 1.4244282
Average (Standard dev.)0.00016052897 (±0.030389871)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 337.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47166_msk_1.map
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Additional map: #1

Fileemd_47166_additional_1.map
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Half map: #2

Fileemd_47166_half_map_1.map
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Half map: #1

Fileemd_47166_half_map_2.map
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Sample components

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Entire : Structure of the Measles virus Fusion protein ectodomain E170G E4...

EntireName: Structure of the Measles virus Fusion protein ectodomain E170G E455G with mutated furin cleavage site in the pre-fusion conformation
Components
  • Complex: Structure of the Measles virus Fusion protein ectodomain E170G E455G with mutated furin cleavage site in the pre-fusion conformation
    • Protein or peptide: Fusion glycoprotein F0
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Structure of the Measles virus Fusion protein ectodomain E170G E4...

SupramoleculeName: Structure of the Measles virus Fusion protein ectodomain E170G E455G with mutated furin cleavage site in the pre-fusion conformation
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Measles morbillivirus / Strain: Ichinose-B95a
Molecular weightTheoretical: 150 KDa

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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: Measles virus strain Ichinose-B95a / Strain: Ichinose-B95a
Molecular weightTheoretical: 56.819855 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGLKVNVSAI FMAVLLTLQT PTGQIHWGNL SKIGVVGIGS ASYKVMTRSS HQSLVIKLMP NITLLNNCTR VEIAEYRRLL RTVLEPIRD ALNAMTQNIR PVQSVASSRN HNRFAGVVLA GAALGVATAA QITAGIALHQ SMLNSQAIDN LRASLETTNQ A IEAIRQAG ...String:
MGLKVNVSAI FMAVLLTLQT PTGQIHWGNL SKIGVVGIGS ASYKVMTRSS HQSLVIKLMP NITLLNNCTR VEIAEYRRLL RTVLEPIRD ALNAMTQNIR PVQSVASSRN HNRFAGVVLA GAALGVATAA QITAGIALHQ SMLNSQAIDN LRASLETTNQ A IEAIRQAG QGMILAVQGV QDYINNELIP SMNQLSCDLI GQKLGLKLLR YYTEILSLFG PSLRDPISAE ISIQALSYAL GG DINKVLE KLGYSGGDLL GILESRGIKA RITHVDTESY FIVLSIAYPT LSEIKGVIVH RLEGVSYNIG SQEWYTTVPK YVA TQGYLI SNFDESSCTF MPEGTVCSQN ALYPMSPLLQ ECLRGSTKSC ARTLVSGSFG NRFILSQGNL IANCASILCK CYTT GTIIN QDPDKILTYI AADHCPVVEV NGVTIQVGSR RYPDAVYLHR IDLGPPISLG RLDVGTNLGN AIAKLEDAKE LLESS DQIL RSMKGLSSTS IGGGSGGWSH PQFEKGGGSG GGSGGGSWSH PQFEK

UniProtKB: Fusion glycoprotein F0

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / 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 #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 400 / 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

Concentration0.2 mg/mL
BufferpH: 8 / Details: HEPES 50 mM, pH 8.0, NaCl 150 mM
GridModel: Quantifoil / Material: COPPER / Mesh: 300 / 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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 3 / Number real images: 10974 / Average exposure time: 2.0 sec. / Average electron dose: 70.0 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: 1500000
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 281000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 3
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8uup


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

PDB-9dtu:
Structure of the Measles virus Fusion protein ectodomain E170G E455G with mutated furin cleavage site in the pre-fusion conformation

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