9PDX | pdb_00009pdx

Human antibody Fab MPV513 bound to hMPV DsCav-ES2

• PDB DOI: https://doi.org/10.2210/pdb9PDX/pdb
• EM Map EMD-71547: EMDB EMDataResource

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


• Deposited: 2025-07-01 Released: 2025-09-03 
• Deposition Author(s): Ghazi Esfahani, B., 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: 3.94 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: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 75.31 kDa 
• Atom Count: 5,180 
• Modeled Residue Count: 667 
• Deposited Residue Count: 678 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MPV513 Heavy Chain	A [auth C]	120	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MPV513 Light Chain	B	107	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	C [auth F]	451	human metapneumovirus	Mutation(s): 0
UniProt
Find proteins for Q6W8S4 (human metapneumovirus) Explore Q6W8S4  Go to UniProtKB:  Q6W8S4

Oligosaccharides

Help

Entity ID: 4
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	D [auth A]	5		N/A
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.94 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-03 
Deposition Author(s): Ghazi Esfahani, B., 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
  
• Version 2.0: 2026-02-11
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other, Polymer sequence, Refinement description, Source and taxonomy, Structure summary