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- EMDB-72240: Structure of the Measles virus Fusion glycoprotein ectodomain in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-72240
TitleStructure of the Measles virus Fusion glycoprotein ectodomain in complex with neutralizing antibody Y10F
Map datamap sharp
Sample
  • Complex: Structure of the Measles virus Fusion glycoprotein ectodomain in complex with neutralizing antibody Y10F
    • Complex: Measles virus Fusion glycoprotein ectodomain
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: Y10F LC
      • Protein or peptide: Y10F light chain
    • Complex: Y10F HC
      • Protein or peptide: Y10F heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
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 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsZyla D / Niemeyer G / Porotto M / 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: To Be Published
Title: Structure of the Measles virus Fusion glycoprotein ectodomain in complex with neutralizing antibody Y10F
Authors: Zyla D / Niemeyer G / Porotto M / Saphire EO
History
DepositionAug 20, 2025-
Header (metadata) releaseApr 15, 2026-
Map releaseApr 15, 2026-
UpdateApr 15, 2026-
Current statusApr 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72240.png

Downloads & links

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Map

FileDownload / File: emd_72240.map.gz / Format: CCP4 / Size: 381.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap sharp
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 464 pix.
= 408.32 Å		0.88 Å/pix.
x 464 pix.
= 408.32 Å		0.88 Å/pix.
x 464 pix.
= 408.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0969
Minimum - Maximum-0.4741799 - 0.75577736
Average (Standard dev.)-0.00011678793 (±0.015131755)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions464464464
Spacing464464464
CellA=B=C: 408.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72240_msk_1.map
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Additional map: unsharpened map

Fileemd_72240_additional_1.map
Annotationunsharpened map
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Half map: half 2

Fileemd_72240_half_map_1.map
Annotationhalf 2
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Histogram

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Half map: half 1

Fileemd_72240_half_map_2.map
Annotationhalf 1
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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 neutralizing antibody Y10F
Components
  • Complex: Structure of the Measles virus Fusion glycoprotein ectodomain in complex with neutralizing antibody Y10F
    • Complex: Measles virus Fusion glycoprotein ectodomain
      • Protein or peptide: Fusion glycoprotein F0
    • Complex: Y10F LC
      • Protein or peptide: Y10F light chain
    • Complex: Y10F HC
      • Protein or peptide: Y10F heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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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 neutralizing antibody Y10F
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Molecular weightTheoretical: 200 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: #1
Source (natural)Organism: Measles morbillivirus / Strain: Ichinose-B95a

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Supramolecule #3: Y10F LC

SupramoleculeName: Y10F LC / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Mus musculus (house mouse)

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Supramolecule #4: Y10F HC

SupramoleculeName: Y10F HC / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Measles morbillivirus
Molecular weightTheoretical: 57.379539 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: MGLKVNVSAI FMAVLLTLQT PTGQIHWGNL SKIGVVGIGS ASYKVMTRSS HQSLVIKLMP NITLLNNCTR VEIAEYRRLL RTVLEPIRD ALNAMTQNIR PVQSVASSRR HKRFAGVVLA GAALGVATAA QITAGIALHQ SMLNSQAIDN LRASLETTNQ A IEAIRQAG ...String:
MGLKVNVSAI FMAVLLTLQT PTGQIHWGNL SKIGVVGIGS ASYKVMTRSS HQSLVIKLMP NITLLNNCTR VEIAEYRRLL RTVLEPIRD ALNAMTQNIR PVQSVASSRR HKRFAGVVLA GAALGVATAA QITAGIALHQ SMLNSQAIDN LRASLETTNQ A IEAIRQAG QGMILAVQGV QDYINNELIP SMNQLSCDLI GQKLGLKLLR YYTEILSLFG PSLRDPISAE ISIQALSYAL GG DINKVLE KLGYSGGDLL GILESRGIKA RITHVDTESY FIVLSIAYPT LSEIKGVIVH RLEGVSYNIG SQEWYTTVPK YVA TQGYLI SNFDESSCTF MPEGTVCSQN ALYPMSPLLQ ECLRGSTKSC ARTLVSGSFG NRFILSQGNL IANCASILCK CYTT GTIIN QDPDKILTYI AADHCPVVEV NGVTIQVGSR RYPDAVYLHR IDLGPPISLG RLDVGTNLGN AIAKLEDAKE LLESS DQIL RSMKGLSSTS IGVDDDDKAG WSHPQFEKGG GSGGGSGGGS WSHPQFEK

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: Y10F light chain

MacromoleculeName: Y10F light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.20917 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGWSCIILFL VATATGVHSQ IVLSQSPAIL SASPGEKVTM TCRATSSVVY MHWYQQKPGS SPKPWIYATS NLASGVPTRF SGSGSGTSY SLTISRVEAE DAATYYCQQW NSNPYTFGGG TKLEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP R EAKVQWKV ...String:
MGWSCIILFL VATATGVHSQ IVLSQSPAIL SASPGEKVTM TCRATSSVVY MHWYQQKPGS SPKPWIYATS NLASGVPTRF SGSGSGTSY SLTISRVEAE DAATYYCQQW NSNPYTFGGG TKLEIKRTVA APSVFIFPPS DEQLKSGTAS VVCLLNNFYP R EAKVQWKV DNALQSGNSQ ESVTEQDSKD STYSLSSTLT LSKADYEKHK VYACEVTHQG LSSPVTKSFN RGEC

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Macromolecule #3: Y10F heavy chain

MacromoleculeName: Y10F heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 52.295902 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: MGWSCIILFL VATATGVHSQ VQLQQSGAEL MKPGASVKIS CKAAGYTFSN YWIEWVKQRP GHGLEWIGEI LPGNSYTNYN EKFRGKATI TADTSSNTAY MQLSSLTSED SAVYYCASPL SGNYVRFAYW GQGTLVTVST ASTKGPSVFP LAPSSKSTSG G TAALGCLV ...String:
MGWSCIILFL VATATGVHSQ VQLQQSGAEL MKPGASVKIS CKAAGYTFSN YWIEWVKQRP GHGLEWIGEI LPGNSYTNYN EKFRGKATI TADTSSNTAY MQLSSLTSED SAVYYCASPL SGNYVRFAYW GQGTLVTVST ASTKGPSVFP LAPSSKSTSG G TAALGCLV KDYFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKVE PK SCDKGLE VLFQGPTHTC PPCPAPELLG GPSVFLFPPK PKDTLMISRT PEVTCVVVDV SHEDPEVKFN WYVDGVEVHN AKT KPREEQ YNSTYRVVSV LTVLHQDWLN GKEYKCKVSN KALPAPIEKT ISKAKGQPRE PQVYTLPPSR DELTKNQVSL TCLV KGFYP SDIAVEWESN GQPENNYKTT PPVLDSDGSF FLYSKLTVDK SRWQQGNVFS CSVMHEALHN HYTQKSLSLS PGK

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 63 / 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: 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: 7700 / 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: 5100000
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5) / Number images used: 130000
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: 5 / Software - Name: cryoSPARC (ver. 4.5)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8uut

source_name: PDB, initial_model_type: experimental model
source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9q5m:
Structure of the Measles virus Fusion glycoprotein ectodomain in complex with neutralizing antibody Y10F

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