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- EMDB-72151: Structure of the Measles virus Fusion glycoprotein ectodomain in ... -

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Entry
Database: EMDB / ID: EMD-72151
TitleStructure of the Measles virus Fusion glycoprotein ectodomain in complex with two neutralizing antibodies 4F09 and 3A12
Map datasharpened map
Sample
  • Complex: Structure of the Measles virus Fusion glycoprotein ectodomain in complex with two neutralizing antibodies 4F09 and 3A12
    • Complex: Measles virus Fusion glycoprotein ectodomain
      • Protein or peptide: Fusion glycoprotein F2
    • Complex: 3A12 neutralizing antibody
      • Protein or peptide: 3A12 Fab Heavy chain
      • Protein or peptide: 3A12 Fab Light chain
    • Complex: 4F09 neutralizing antibody
      • Protein or peptide: 4F09 Fab Heavy chain
      • Protein or peptide: 4F09 Fab Light Chain
  • Protein or peptide: Fusion glycoprotein F1
  • Ligand: alpha-D-mannopyranose
KeywordsVIRAL 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 / Fusion glycoprotein F0
Function and homology information
Biological speciesMeasles morbillivirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsZyla D / Acciani M / Niemeyer G / Saphire EO
Funding support Switzerland, United States, 7 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
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: Marissa Acciani / Dawid Zyla / Gele Niemeyer / Stephanie Harkins / Diptiben Parekh / Emily Pawlack / Davide Lacarbonara / Dhvanir Kansara / Margaret E Ackerman / Stefan Niewiesk / Matteo ...Authors: Marissa Acciani / Dawid Zyla / Gele Niemeyer / Stephanie Harkins / Diptiben Parekh / Emily Pawlack / Davide Lacarbonara / Dhvanir Kansara / Margaret E Ackerman / Stefan Niewiesk / Matteo Porotto / Kathryn M Hastie / Erica Ollmann Saphire /
Abstract: Measles virus (MeV), a highly transmissible paramyxovirus, can cause severe complications and death, particularly in infants and young children. How and where human antibodies target and neutralize ...Measles virus (MeV), a highly transmissible paramyxovirus, can cause severe complications and death, particularly in infants and young children. How and where human antibodies target and neutralize MeV remain unclear. Here, we report a panel of human monoclonal antibodies (mAbs) specific for MeV hemagglutinin (H) and fusion (F) surface proteins, derived from the memory B cells of a Measles-Mumps-Rubella (MMR) vaccinee. We mapped four and five major epitope clusters on H and F, respectively, and structurally characterized representative mAbs from each epitope cluster. MAbs against both H and F offer broad, potent, picomolar-level neutralization and substantially reduce viral loads in vivo when delivered before or after viral exposure. High-resolution cryo-electron microscopy of mAb complexes with H and F reveal highly conserved contact sites of the most protective antibodies. Characterization of these fully human mAbs provides avenues for prophylactic or therapeutic intervention against re-emerging MeV.
History
DepositionAug 14, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72151.png

Downloads & links

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Map

FileDownload / File: emd_72151.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 360 pix.
= 337.932 Å		0.94 Å/pix.
x 360 pix.
= 337.932 Å		0.94 Å/pix.
x 360 pix.
= 337.932 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9387 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.094
Minimum - Maximum-0.5832225 - 0.93421865
Average (Standard dev.)0.00022884921 (±0.021064969)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 337.932 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72151_msk_1.map
Projections & Slices
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Additional map: unsharpened map

Fileemd_72151_additional_1.map
Annotationunsharpened map
Projections & Slices
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Half map: map halfA

Fileemd_72151_half_map_1.map
Annotationmap halfA
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Half map: map halfB

Fileemd_72151_half_map_2.map
Annotationmap halfB
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Sample components

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Entire : Structure of the Measles virus Fusion glycoprotein ectodomain in ...

EntireName: Structure of the Measles virus Fusion glycoprotein ectodomain in complex with two neutralizing antibodies 4F09 and 3A12
Components
  • Complex: Structure of the Measles virus Fusion glycoprotein ectodomain in complex with two neutralizing antibodies 4F09 and 3A12
    • Complex: Measles virus Fusion glycoprotein ectodomain
      • Protein or peptide: Fusion glycoprotein F2
    • Complex: 3A12 neutralizing antibody
      • Protein or peptide: 3A12 Fab Heavy chain
      • Protein or peptide: 3A12 Fab Light chain
    • Complex: 4F09 neutralizing antibody
      • Protein or peptide: 4F09 Fab Heavy chain
      • Protein or peptide: 4F09 Fab Light Chain
  • Protein or peptide: Fusion glycoprotein F1
  • Ligand: alpha-D-mannopyranose

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Supramolecule #1: Structure of the Measles virus Fusion glycoprotein ectodomain in ...

SupramoleculeName: Structure of the Measles virus Fusion glycoprotein ectodomain in complex with two neutralizing antibodies 4F09 and 3A12
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 450 KDa

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Supramolecule #2: Measles virus Fusion glycoprotein ectodomain

SupramoleculeName: Measles virus Fusion glycoprotein ectodomain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Measles morbillivirus / Strain: Ichinose-B95a

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Supramolecule #3: 3A12 neutralizing antibody

SupramoleculeName: 3A12 neutralizing antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: 4F09 neutralizing antibody

SupramoleculeName: 4F09 neutralizing antibody / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 3A12 Fab Heavy chain

MacromoleculeName: 3A12 Fab Heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.836078 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: METDTLLLWV LLLWVPGSTG DQVQLQQSGP GLVKPSHTLS LTCTVSGGSI SSGGSYWTWI RQHPGKGLEW IGYIYYSGST FYNPSLKSR LTLSVDTSQN QFSLKVNSVT AADSAVYYCA RATSKDASGR HLLDYWGQGT LVTVSSASTK GPSVFPLAPS S KSTSGGTA ...String:
METDTLLLWV LLLWVPGSTG DQVQLQQSGP GLVKPSHTLS LTCTVSGGSI SSGGSYWTWI RQHPGKGLEW IGYIYYSGST FYNPSLKSR LTLSVDTSQN QFSLKVNSVT AADSAVYYCA RATSKDASGR HLLDYWGQGT LVTVSSASTK GPSVFPLAPS S KSTSGGTA ALGCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VD KRVEPKS CDKTH

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Macromolecule #2: 3A12 Fab Light chain

MacromoleculeName: 3A12 Fab Light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.989066 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: METDTLLLWV LLLWVPGSTG DAIRMTQSPS SLSASVGDRV TITCRASESI SRYLNWYQQK PGKAPKLLIY AASSLQSGVP SRFSGSGSQ TDFTLTISSL QPEDFATYYC QQSYSTLMWT FGQGTKVEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPREAKV ...String:
METDTLLLWV LLLWVPGSTG DAIRMTQSPS SLSASVGDRV TITCRASESI SRYLNWYQQK PGKAPKLLIY AASSLQSGVP SRFSGSGSQ TDFTLTISSL QPEDFATYYC QQSYSTLMWT FGQGTKVEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPREAKV QWKVDNALQS GNSQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #3: 4F09 Fab Heavy chain

MacromoleculeName: 4F09 Fab Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.843133 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: METDTLLLWV LLLWVPGSTG DQVQLQESGP GLVKPSQTLS LTCTVSGDSI TTGDYYWGWI RHHPGKGLAW IGYISHSGSA SYNPSLKSR SAISVDTSKN QFSLKLTSVT AADTAVYFCA RGIQGPYYYD RSGYYWPPYF DYWGQGTLVT VSSASTKGPS V FPLAPSSK ...String:
METDTLLLWV LLLWVPGSTG DQVQLQESGP GLVKPSQTLS LTCTVSGDSI TTGDYYWGWI RHHPGKGLAW IGYISHSGSA SYNPSLKSR SAISVDTSKN QFSLKLTSVT AADTAVYFCA RGIQGPYYYD RSGYYWPPYF DYWGQGTLVT VSSASTKGPS V FPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HK PSNTKVD KRVEPKSCDK TH

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Macromolecule #4: 4F09 Fab Light Chain

MacromoleculeName: 4F09 Fab Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.008094 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: METDTLLLWV LLLWVPGSTG DEIVMTQSPP TLSASVGDRV TITCRASQSI SRWLAWYQQK PGKAPKLLIY KASNLQSGVP FRFSGTGSG TEFTLTISSL QPDDFANYYC QQYNSYGANT FGQGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPREAKV ...String:
METDTLLLWV LLLWVPGSTG DEIVMTQSPP TLSASVGDRV TITCRASQSI SRWLAWYQQK PGKAPKLLIY KASNLQSGVP FRFSGTGSG TEFTLTISSL QPDDFANYYC QQYNSYGANT FGQGTKLEIK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN N FYPREAKV QWKVDNALQS GNSQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #5: Fusion glycoprotein F2

MacromoleculeName: Fusion glycoprotein F2 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Measles morbillivirus / Strain: Ichinose-B95a
Molecular weightTheoretical: 12.498768 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString:
MGLKVNVSAI FMAVLLTLQT PTGQIHWGNL SKIGVVGIGS ASYKVMTRSS HQSLVIKLMP NITLLNNCTR VEIAEYRRLL RTVLEPIRD ALNAMTQNIR PVQSVASSRR HKR

UniProtKB: Fusion glycoprotein F0

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Macromolecule #6: Fusion glycoprotein F1

MacromoleculeName: Fusion glycoprotein F1 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Measles morbillivirus / Strain: Ichinose-B95a
Molecular weightTheoretical: 44.89882 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
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 GLSSTSIGVD DDDKAGWSHP QFEK GGGSG GGSGGGSWSH PQFEK

UniProtKB: Fusion glycoprotein F0

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Macromolecule #11: alpha-D-mannopyranose

MacromoleculeName: alpha-D-mannopyranose / type: ligand / ID: 11 / Number of copies: 1 / Formula: MAN
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-MAN:
alpha-D-mannopyranose

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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 150 mM
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / 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
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 3 / Number real images: 18982 / 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 / Nominal magnification: 130000
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: 11000000
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 196000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.5)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.5)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8uut


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

PDB-9q26:
Structure of the Measles virus Fusion glycoprotein ectodomain in complex with two neutralizing antibodies 4F09 and 3A12

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