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)

Experimental Data Snapshot

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

Starting Models: experimental, in silico
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

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.

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

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q786F3
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain C Focus chain E
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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

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| 3D Structure

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

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain I [auth H] Interactions & Density Focus chain I [auth H]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, L, N, O	2		N-Glycosylation	Interactions Focus chain J Focus chain L Focus chain N Focus chain O Interactions & Density Focus chain J Focus chain L Focus chain N Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain K Focus chain M Interactions & Density Focus chain K Focus chain M
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]

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

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-04-15

Deposition Author(s):

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