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- PDB-9q26: Structure of the Measles virus Fusion glycoprotein ectodomain in ... -

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Basic information

Entry
Database: PDB / ID: 9q26
TitleStructure of the Measles virus Fusion glycoprotein ectodomain in complex with two neutralizing antibodies 4F09 and 3A12
Components
  • (Fusion glycoprotein ...) x 2
  • 3A12 Fab Heavy chain
  • 3A12 Fab Light chain
  • 4F09 Fab Heavy chain
  • 4F09 Fab Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN / glycoprotein / immune system / measles / high-resolution / ectodomain / fusion / antibody / complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / alpha-D-mannopyranose / Fusion glycoprotein F0
Function and homology information
Biological speciesHomo sapiens (human)
Measles morbillivirus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsZyla, D. / Acciani, M. / Niemeyer, G. / Saphire, E.O.
Funding support Switzerland, United States, 7items
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
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R56AI183536-01A1 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R21AI180456-02 United States
CitationJournal: Cell Host Microbe / Year: 2026
Title: Human neutralizing antibodies targeting the measles virus hemagglutinin and fusion surface proteins.
Authors: Acciani, M. / Zyla, D. / Niemeyer, G. / Harkins, S. / Parekh, D. / Pawlack, E. / Lacarbonara, D. / Kansara, D. / Ackerman, M.E. / Niewiesk, S. / Porotto, M. / Hastie, K.M. / Saphire, E.O.
History
DepositionAug 14, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 3A12 Fab Heavy chain
E: 3A12 Fab Light chain
F: 4F09 Fab Heavy chain
G: 4F09 Fab Light Chain
H: 3A12 Fab Heavy chain
I: 3A12 Fab Light chain
J: 4F09 Fab Heavy chain
K: 4F09 Fab Light Chain
L: 3A12 Fab Heavy chain
M: 3A12 Fab Light chain
N: 4F09 Fab Heavy chain
O: 4F09 Fab Light Chain
a: Fusion glycoprotein F2
A: Fusion glycoprotein F1
b: Fusion glycoprotein F2
B: Fusion glycoprotein F1
c: Fusion glycoprotein F2
C: Fusion glycoprotein F1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)497,47128
Polymers492,22218
Non-polymers5,24910
Water00
1


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

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Components

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Fusion glycoprotein ... , 2 types, 6 molecules abcABC

#5: Protein Fusion glycoprotein F2


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
#6: Protein Fusion glycoprotein F1


Mass: 44898.820 Da / Num. of mol.: 3 / Mutation: E170G, E455G
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

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Antibody , 4 types, 12 molecules DHLEIMFJNGKO

#1: Antibody 3A12 Fab Heavy chain


Mass: 26836.078 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody 3A12 Fab Light chain


Mass: 25989.066 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody 4F09 Fab Heavy chain


Mass: 27843.133 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody 4F09 Fab Light Chain


Mass: 26008.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)

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Sugars , 5 types, 10 molecules

#7: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#9: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#10: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#11: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
Has protein modificationY

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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

Component
IDNameTypeEntity IDParent-IDSource
1Structure of the Measles virus Fusion glycoprotein ectodomain in complex with two neutralizing antibodies 4F09 and 3A12COMPLEX#1-#40MULTIPLE SOURCES
2Measles virus Fusion glycoprotein ectodomainCOMPLEX#51RECOMBINANT
33A12 neutralizing antibodyCOMPLEX#1-#21RECOMBINANT
44F09 neutralizing antibodyCOMPLEX#3-#41RECOMBINANT
Molecular weightValue: 0.45 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
12Measles morbillivirus645098Ichinose-B95a
23Homo sapiens (human)9606
34Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
22Drosophila melanogaster (fruit fly)7227S2
33Cricetulus griseus (Chinese hamster)10029ExpiCHO
44Cricetulus griseus (Chinese hamster)10029ExpiCHO
Buffer solutionpH: 8 / Details: HEPES 50 mM, pH 8.0, NaCl 150 mM
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
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: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / 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: 70 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 3 / Num. of real images: 18982
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.5particle selection
2EPUimage acquisition
4cryoSPARC4.5CTF correction
9cryoSPARC4.5initial Euler assignment
10cryoSPARC4.5final Euler assignment
11cryoSPARC4.5classification
12cryoSPARC4.53D reconstruction
13PHENIX2.0_rc1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 11000000
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 196000 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 8UUT

8uut


Accession code: 8UUT / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 61.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001821884
ELECTRON MICROSCOPYf_angle_d0.450529751
ELECTRON MICROSCOPYf_chiral_restr0.04193484
ELECTRON MICROSCOPYf_plane_restr0.00343734
ELECTRON MICROSCOPYf_dihedral_angle_d5.23493545

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