9Q5M | pdb_00009q5m

Structure of the Measles virus Fusion glycoprotein ectodomain in complex with neutralizing antibody Y10F

• PDB DOI: https://doi.org/10.2210/pdb9Q5M/pdb
• EM Map EMD-72240: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): Measles morbillivirus, Mus musculus
• Expression System: Drosophila melanogaster, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2025-08-20 Released: 2026-04-15 
• Deposition Author(s): Zyla, D., Niemeyer, G., Porotto, M., Saphire, E.O.
• Funding Organization(s): Swiss National Science Foundation, National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico

Literature

Structure of the Measles virus Fusion glycoprotein ectodomain in complex with neutralizing antibody Y10F

Zyla, D., Niemeyer, G., Porotto, M., Saphire, E.O.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A3B3C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A3B3C2 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 426.11 kDa 
• Atom Count: 12,394 
• Modeled Residue Count: 1,585 
• Deposited Residue Count: 3,902 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A, B, C, D, E, F	532	Measles morbillivirus	Mutation(s): 0
UniProt
Find proteins for Q786F3 (Measles virus (strain Ichinose-B95a)) Explore Q786F3  Go to UniProtKB:  Q786F3
Glycosylation
Glycosylation Sites: 3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Y10F light chain	G	232	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Y10F heavy chain	H [auth I]	478	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I [auth H]	3		N-Glycosylation

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, L, N, O	2		N-Glycosylation

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[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	K, M	5		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	P [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.59 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.5
MODEL REFINEMENT	PHENIX	2.0_rc1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-04-15 
Deposition Author(s): Zyla, D., Niemeyer, G., Porotto, M., Saphire, E.O.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	P2EZP3_195680
Swiss National Science Foundation	Switzerland	P500PB_210992
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS105699
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NS091263
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI176833
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R56AI183536-01A1
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	5R21AI180456-02

Revision History  

• Version 1.0: 2026-04-15
  Type: Initial release