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- EMDB-72146: Structure of the Measles virus Hemagglutinin ectodomain in comple... -

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Entry
Database: EMDB / ID: EMD-72146
TitleStructure of the Measles virus Hemagglutinin ectodomain in complex with neutralizing antibody 1C02
Map datamap sharp
Sample
  • Complex: Structure of the Measles virus Hemagglutinin ectodomain in complex with neutralizing antibody 1C02
    • Complex: Measles virus Hemagglutinin ectodomain
      • Protein or peptide: Hemagglutinin glycoprotein
    • Complex: Antibody 1C02
      • Protein or peptide: 1C02 Fab Heavy chain
      • Protein or peptide: 1C02 Fab Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsVIRAL PROTEIN / glycoprotein / immune system / measles / high-resolution / ectodomain / attachment / antibody / complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell surface receptor binding / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
: / Haemagglutinin/haemagglutinin-neuraminidase, paramyxovirus / Haemagglutinin-neuraminidase / Sialidase superfamily
Similarity search - Domain/homology
Hemagglutinin glycoprotein
Similarity search - Component
Biological speciesMeasles morbillivirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 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_72146.png

Downloads & links

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Map

FileDownload / File: emd_72146.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap sharp
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.2 Å/pix.
x 340 pix.
= 409.36 Å		1.2 Å/pix.
x 340 pix.
= 409.36 Å		1.2 Å/pix.
x 340 pix.
= 409.36 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.204 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-1.2765833 - 1.9439998
Average (Standard dev.)-0.0004948784 (±0.0319408)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 409.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72146_msk_1.map
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Additional map: unsharpened map

Fileemd_72146_additional_1.map
Annotationunsharpened map
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Half map: half B

Fileemd_72146_half_map_1.map
Annotationhalf B
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Half map: halfA

Fileemd_72146_half_map_2.map
AnnotationhalfA
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Sample components

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Entire : Structure of the Measles virus Hemagglutinin ectodomain in comple...

EntireName: Structure of the Measles virus Hemagglutinin ectodomain in complex with neutralizing antibody 1C02
Components
  • Complex: Structure of the Measles virus Hemagglutinin ectodomain in complex with neutralizing antibody 1C02
    • Complex: Measles virus Hemagglutinin ectodomain
      • Protein or peptide: Hemagglutinin glycoprotein
    • Complex: Antibody 1C02
      • Protein or peptide: 1C02 Fab Heavy chain
      • Protein or peptide: 1C02 Fab Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Structure of the Measles virus Hemagglutinin ectodomain in comple...

SupramoleculeName: Structure of the Measles virus Hemagglutinin ectodomain in complex with neutralizing antibody 1C02
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 250 KDa

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Supramolecule #2: Measles virus Hemagglutinin ectodomain

SupramoleculeName: Measles virus Hemagglutinin ectodomain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Measles morbillivirus / Strain: Ichinose-B95a

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Supramolecule #3: Antibody 1C02

SupramoleculeName: Antibody 1C02 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 1C02 Fab Heavy chain

MacromoleculeName: 1C02 Fab Heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.905322 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: METDTLLLWV LLLWVPGSTG DEVQLLESGA EVKKPGSSVK VSCKASGGTF SSYGISWVRQ APGQGLEWMG GIIPIFGTAN YAQKFRGRV TITADKSTST AYMELSSLRS EDTAVYYCAR ERITVAGINY YYGMDVWGQG TTVTVSSAST KGPSVFPLAP S SKSTSGGT ...String:
METDTLLLWV LLLWVPGSTG DEVQLLESGA EVKKPGSSVK VSCKASGGTF SSYGISWVRQ APGQGLEWMG GIIPIFGTAN YAQKFRGRV TITADKSTST AYMELSSLRS EDTAVYYCAR ERITVAGINY YYGMDVWGQG TTVTVSSAST KGPSVFPLAP S SKSTSGGT AALGCLVKDY FPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KV DKRVEPK SCDKTH

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Macromolecule #2: 1C02 Fab Light chain

MacromoleculeName: 1C02 Fab Light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.095855 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: METDTLLLWV LLLWVPGSTG DRPVLTQPPS VSGAPGQRVT ISCTGSSSNI GAGYDVHWYQ QLPGTAPKLL IYGDSNRPSG VPDRFSGSK SGTSASLAIT GLQAEDEADY YCQSYDSSLS GVVFGGGTKL TVLGQPKAAP SVTLFPPSSE ELQANKATLV C LISDFYPG ...String:
METDTLLLWV LLLWVPGSTG DRPVLTQPPS VSGAPGQRVT ISCTGSSSNI GAGYDVHWYQ QLPGTAPKLL IYGDSNRPSG VPDRFSGSK SGTSASLAIT GLQAEDEADY YCQSYDSSLS GVVFGGGTKL TVLGQPKAAP SVTLFPPSSE ELQANKATLV C LISDFYPG AVTVAWKADS SPVKAGVETT TPSKQSNNKY AASSYLSLTP EQWKSHRSYS CQVTHEGSTV EKTVAPTECS

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Macromolecule #3: Hemagglutinin glycoprotein

MacromoleculeName: Hemagglutinin glycoprotein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Measles morbillivirus / Strain: Ichinose-B95a
Molecular weightTheoretical: 69.252367 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MSPQRDRINA FYKDNPHPKG SRIVINREHL MIDRPYVLLA VLFVMFLSLI GLLAIAGIRL HRAAIYTAEI HKSLSTNLDV TNSIEHQVK DVLTPLFKII GDEVGLRTPQ RFTDLVKFIS DKIKFLNPDR EYDFRDLTWC INPPERIKLD YDQYCADVAA E ELMNALVN ...String:
MSPQRDRINA FYKDNPHPKG SRIVINREHL MIDRPYVLLA VLFVMFLSLI GLLAIAGIRL HRAAIYTAEI HKSLSTNLDV TNSIEHQVK DVLTPLFKII GDEVGLRTPQ RFTDLVKFIS DKIKFLNPDR EYDFRDLTWC INPPERIKLD YDQYCADVAA E ELMNALVN STLLEARATN QFLAVSKGNC SGPTTIRGQF SNMSLSLLDL YLSRGYNVSS IVTMTSQGMY GGTYLVGKPN LS SKGSELS QLSMHRVFEV GVIRNPGLGA PVFHMTNYFE QPVSNDFSNC MVALGELKFA ALCHREDSIT IPYQGSGKGV SFQ LVKLGV WKSPTDMRSW VPLSTDDPVI DRLYLSSHRG VIADNQAKWA VPTTRTDDKL RMETCFQQAC KGKNQALCEN PEWA PLKDN RIPSYGVLSV NLSLTVELKI KIASGFGPLI THGSGMDLYK TNHNNVYWLT IPPMKNLALG VINTLEWIPR FKVSP NLFT VPIKEAGEDC HAPTYLPAEV DGDVKLSSNL VILPGQDLQY VLATYDTSRV EHAVVYYVYS PSRSFSYFYP FRLPIK GVP IELQVECFTW DKKLWCRHFC VLADSESGGH ITHSGMVGMG VSCTVTREDG TNRR

UniProtKB: Hemagglutinin glycoprotein

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 2 / 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 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 / Details: grid was washed with ethyl acetate
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: 14828 / 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: 1500000
CTF correctionSoftware - Name: cryoSPARC (ver. 4.5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 151000
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 modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9q1z:
Structure of the Measles virus Hemagglutinin ectodomain in complex with neutralizing antibody 1C02

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