8T9Z | pdb_00008t9z

Structural of M8C10 Fab in complex human metapneumovirus fusion protein

• PDB DOI: https://doi.org/10.2210/pdb8T9Z/pdb

• Classification: VIRAL PROTEIN/Immune System
• Organism(s): human metapneumovirus, Homo sapiens
• Expression System: Homo sapiens, Cricetulus griseus
• Mutation(s): No 


• Deposited: 2023-06-26 Released: 2023-11-22 
• Deposition Author(s): Su, H.P., Eddins, M.J., Shipman, J.M., Kostas, J., Reid, J.C.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.243 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.245 (Depositor) 

Literature

Structural characterization of M8C10, a neutralizing antibody targeting a highly conserved prefusion-specific epitope on the metapneumovirus fusion trimerization interface.

Xiao, X., Wen, Z., Chen, Q., Shipman, J.M., Kostas, J., Reid, J.C., Warren, C., Tang, A., Luo, B., O'Donnell, G., Fridman, A., Chen, Z., Vora, K.A., Zhang, L., Su, H.-P., Eddins, M.J.

(2023) J Virol 97: e0105223-e0105223

• PubMed: 38032197 
• DOI: https://doi.org/10.1128/jvi.01052-23
• Primary Citation Related Structures: 
  8T9Z


• PubMed Abstract: 
  

  Human metapneumovirus (hMPV) is a common pathogen causing lower respiratory tract infections worldwide and can develop severe symptoms in high-risk populations such as infants, the elderly, and immunocompromised patients. There are no approved hMPV vaccines or neutralizing antibodies available for therapeutic or prophylactic use. The trimeric hMPV fusion F protein is the major target of neutralizing antibodies in human sera. Understanding the immune recognition of antibodies to hMPV-F antigen will provide critical insights into developing efficacious hMPV monoclonal antibodies and vaccines.

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Organizational Affiliation: 
• Infectious Diseases and Vaccines Discovery, Merck & Co., Inc., West Point, Pennsylvania, USA.
Discovery Biologics, Merck & Co., Inc., Boston, Massachusetts, USA.
MRL Postdoctoral Research Program, Merck & Co., Inc., Kenilworth, New Jersey, USA.
Protein and Structural Chemistry, Merck & Co., Inc., West Point, Pennsylvania, USA.
Quantitative Biosciences, Merck & Co., Inc., West Point, Pennsylvania, USA.
Data Science and Scientific Informatics, Merck & Co., Inc., Rahway, New Jersey, USA.

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.

Macromolecule Content 

• Total Structure Weight: 100.13 kDa 
• Atom Count: 6,136 
• Modeled Residue Count: 816 
• Deposited Residue Count: 921 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A	476	human metapneumovirus	Mutation(s): 0
UniProt
Find proteins for G3KCK8 (human metapneumovirus) Explore G3KCK8  Go to UniProtKB:  G3KCK8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
M8C10 Fab Heavy Chain	B [auth H]	231	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
M8C10 Fab Light Chain	C [auth L]	214	Homo sapiens	Mutation(s): 0

Small Molecules

Non-standard Monomers  1 Unique
ID	Chains	Type	Formula	2D Diagram
PCA	B [auth H]	L-PEPTIDE LINKING	C5 H7 N O3

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.280 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.243 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.245 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.9	α = 90
b = 117.67	β = 90
c = 181.22	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Su, H.P., Eddins, M.J., Shipman, J.M., Kostas, J., Reid, J.C.

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Funding Organization	Location	Grant Number
Other private	United States	--

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release
  
• Version 1.1: 2023-12-13
  Changes: Database references
• Version 1.2: 2023-12-27
  Changes: Database references
• Version 1.3: 2024-11-20
  Changes: Structure summary