9PDY | pdb_00009pdy

Human antibody Fab MPV510 bound to hMPV DsCav-ES2-IPDS F protein

• PDB DOI: https://doi.org/10.2210/pdb9PDY/pdb
• EM Map EMD-71548: EMDB EMDataResource

• Classification: VIRAL PROTEIN/IMMUNE SYSTEM
• Organism(s): human metapneumovirus, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-07-01 Released: 2025-09-03 
• Deposition Author(s): Ghazi Esfahani, N., Mousa, J., Khalil, A.M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Human metapneumovirus-specific antibodies isolated from infected children target diverse epitopes and have prophylactic efficacy in mice

Khalil, A.M., Ghazi Esfahani, B., Mousa, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 9-mer - A6B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 223.33 kDa 
• Atom Count: 15,189 
• Modeled Residue Count: 1,977 
• Deposited Residue Count: 2,028 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A, B, C	448	human metapneumovirus	Mutation(s): 0
UniProt
Find proteins for Q8B9P0 (human metapneumovirus) Explore Q8B9P0  Go to UniProtKB:  Q8B9P0
Glycosylation
Glycosylation Sites: 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MPV510 Fab heavy chain	D, F [auth E], H [auth F]	121	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
MPV510 Fab light chain	E [auth G], G [auth H], I	107	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A], K [auth A], L [auth B], M [auth B], N [auth C], O [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.85 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286

Structure Validation

Currently 9PDY does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Ghazi Esfahani, N., Mousa, J., Khalil, A.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01 AI143865

Revision History  

• Version 1.0: 2025-09-03
  Type: Initial release