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- PDB-8utf: Structure of the Measles virus Fusion protein in the post-fusion ... -

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Basic information

Entry
Database: PDB / ID: 8utf
TitleStructure of the Measles virus Fusion protein in the post-fusion conformation
Components(Fusion glycoprotein F0) x 2
KeywordsVIRAL PROTEIN / glycoprotein / immune system / measles / high-resolution / ectodomain / post-fusion
Function / homologyPrecursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0 / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / host cell plasma membrane / virion membrane / membrane / Fusion glycoprotein F0
Function and homology information
Biological speciesMeasles morbillivirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsZyla, D. / Saphire, E.O.
Funding support Switzerland, United States, 5items
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: Science / Year: 2024
Title: A neutralizing antibody prevents postfusion transition of measles virus fusion protein
Authors: Zyla, D.S. / Della Marca, R. / Niemeyer, G. / Zipursky, G. / Stearns, K. / Leedale, C. / Sobolik, E.B. / Callaway, H.M. / Hariharan, C. / Peng, W. / Parekh, D. / Marcink, T.C. / Diaz Avalos, ...Authors: Zyla, D.S. / Della Marca, R. / Niemeyer, G. / Zipursky, G. / Stearns, K. / Leedale, C. / Sobolik, E.B. / Callaway, H.M. / Hariharan, C. / Peng, W. / Parekh, D. / Marcink, T.C. / Diaz Avalos, R. / Horvat, B. / Mathieu, C. / Snijder, J. / Greninger, A.L. / Hastie, K.M. / Niewiesk, S. / Moscona, A. / Porotto, M. / Saphire, E.O.
History
DepositionOct 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F0
B: Fusion glycoprotein F0
C: Fusion glycoprotein F0
a: Fusion glycoprotein F0
b: Fusion glycoprotein F0
c: Fusion glycoprotein F0
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,18415
Polymers172,1936
Non-polymers1,9919
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Fusion glycoprotein F0


Mass: 12498.768 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles morbillivirus / Strain: Ichinose-B95a / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q786F3
#2: Protein Fusion glycoprotein F0


Mass: 44898.820 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles morbillivirus / Strain: Ichinose-B95a / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q786F3
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Structure of the Measles virus Fusion protein in the post-fusion conformation
Type: COMPLEX / Details: Spontaneously sprung from the pre-fusion state / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Measles morbillivirus / Strain: Ichinose-B95a
Source (recombinant)Organism: Drosophila melanogaster (fruit fly) / Strain: S2
Buffer solutionpH: 8 / Details: HEPES 50 mM, pH 8.0, NaCl 150 mM
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 6028

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2particle selection
2RELION4particle selection
3EPUimage acquisition
5cryoSPARCCTF correction
6CTFFINDCTF correction
9UCSF ChimeraXmodel fitting
11cryoSPARCinitial Euler assignment
12RELIONinitial Euler assignment
13cryoSPARCfinal Euler assignment
14RELIONclassification
15cryoSPARCv4.23D reconstruction
16PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 900000
3D reconstructionResolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 158000 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingSource name: SwissModel / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 81.61 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00279834
ELECTRON MICROSCOPYf_angle_d0.446713338
ELECTRON MICROSCOPYf_chiral_restr0.04291617
ELECTRON MICROSCOPYf_plane_restr0.00361689
ELECTRON MICROSCOPYf_dihedral_angle_d3.71861356

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