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Basic information

Entry
Database: EMDB / ID: EMD-72147
TitleStructure of the Measles virus Hemagglutinin ectodomain in complex with neutralizing antibody 1C08
Map datamap sharp
Sample
  • Complex: Structure of the Measles virus Hemagglutinin ectodomain in complex with neutralizing antibody 1C08
    • Complex: Measles virus Hemagglutinin ectodomain
      • Protein or peptide: Hemagglutinin glycoprotein
    • Complex: Antibody 1C08
      • Protein or peptide: 1C08 Fab Heavy chain
      • Protein or peptide: 1C08 Fab Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsVIRAL PROTEIN / glycoprotein / immune system / measles / high-resolution / ectodomain / attachment / antibody / complex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMeasles morbillivirus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 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: Acciani M / Zyla D / Niemeyer G / Harkins S / Parekh D / Pawlack E / Lacarbonara D / Kansara D / Ackerman ME / Niewiesk S / Porotto M / Hastie KM / Saphire EO
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_72147.png

Downloads & links

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Map

FileReleased
Annotationmap sharp
Voxel sizeX=Y=Z: 1.279 Å
Density
Contour LevelBy AUTHOR: 0.274
Minimum - Maximum-1.6452843 - 2.2565966
Average (Standard dev.)-0.00042096825 (±0.033711415)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 409.28003 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72147_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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 1C08
Components
  • Complex: Structure of the Measles virus Hemagglutinin ectodomain in complex with neutralizing antibody 1C08
    • Complex: Measles virus Hemagglutinin ectodomain
      • Protein or peptide: Hemagglutinin glycoprotein
    • Complex: Antibody 1C08
      • Protein or peptide: 1C08 Fab Heavy chain
      • Protein or peptide: 1C08 Fab Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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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 1C08
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 1C08

SupramoleculeName: Antibody 1C08 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 1C08 Fab Heavy chain

MacromoleculeName: 1C08 Fab Heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.68498 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: METDTLLLWV LLLWVPGSTG DEVQLLESGG SLVKPGGSLR LSCSASGFTF NRAWMNWVRQ APGKGLEWVG HIRNEVDGGT TEYAAPVKG RFTISRDDSK NTLYLQMNSL KAEDSATYYC TTDLFRFGFG DVWGQGTTVI VSSASTKGPS VFPLAPSSKS T SGGTAALG ...String:
METDTLLLWV LLLWVPGSTG DEVQLLESGG SLVKPGGSLR LSCSASGFTF NRAWMNWVRQ APGKGLEWVG HIRNEVDGGT TEYAAPVKG RFTISRDDSK NTLYLQMNSL KAEDSATYYC TTDLFRFGFG DVWGQGTTVI VSSASTKGPS VFPLAPSSKS T SGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RV EPKSCDK TH

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Macromolecule #2: 1C08 Fab Light chain

MacromoleculeName: 1C08 Fab Light chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.304396 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: METDTLLLWV LLLWVPGSTG DEIVMTQSPL SLSVTPGEPA SISCRSSQSL LHSNGYNYLD WYVQKPGQSP QVLIYLGSNR ASGVPDRFS GSGSGTDFTL KISRVEAEDV GVYYCMQPLQ TPRTFGQGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV C LLNNFYPR ...String:
METDTLLLWV LLLWVPGSTG DEIVMTQSPL SLSVTPGEPA SISCRSSQSL LHSNGYNYLD WYVQKPGQSP QVLIYLGSNR ASGVPDRFS GSGSGTDFTL KISRVEAEDV GVYYCMQPLQ TPRTFGQGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV C LLNNFYPR EAKVQWKVDN ALQSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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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 B-95a
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: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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: 9625 / 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: 5300000
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: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 260000
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-9q20:
Structure of the Measles virus Hemagglutinin ectodomain in complex with neutralizing antibody 1C08

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