3IXT | pdb_00003ixt

Crystal Structure of Motavizumab Fab Bound to Peptide Epitope

• PDB DOI: https://doi.org/10.2210/pdb3IXT/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Human respiratory syncytial virus A2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2009-09-04 Released: 2010-01-19 
• Deposition Author(s): McLellan, J.S., Chen, M., Kim, A., Yang, Y., Graham, B.S., Kwong, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.274 (Depositor), 0.267 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Structural basis of respiratory syncytial virus neutralization by motavizumab.

McLellan, J.S., Chen, M., Kim, A., Yang, Y., Graham, B.S., Kwong, P.D.

(2010) Nat Struct Mol Biol 17: 248-250

• PubMed: 20098425 
• DOI: https://doi.org/10.1038/nsmb.1723
• Primary Citation Related Structures: 
  3IXT


• PubMed Abstract: 
  

  Motavizumab is approximately tenfold more potent than its predecessor, palivizumab (Synagis), the FDA-approved monoclonal antibody used to prevent respiratory syncytial virus (RSV) infection. The structure of motavizumab in complex with a 24-residue peptide corresponding to its epitope on the RSV fusion (F) glycoprotein reveals the structural basis for this greater potency. Modeling suggests that motavizumab recognizes a different quaternary configuration of the F glycoprotein than that observed in a homologous structure.

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Organizational Affiliation: 
• Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 100.57 kDa 
• Atom Count: 7,010 
• Modeled Residue Count: 898 
• Deposited Residue Count: 928 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Motavizumab Fab light chain	A [auth L], D [auth B]	213	Mus musculus	Mutation(s): 2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Motavizumab Fab heavy chain	B [auth H], E [auth A]	225	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F1	C [auth P], F [auth C]	26	Human respiratory syncytial virus A2	Mutation(s): 0
UniProt
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Explore P03420  Go to UniProtKB:  P03420

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	G [auth P], H [auth A], I [auth C]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.274 (Depositor), 0.267 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.752	α = 90
b = 90.752	β = 90
c = 232.057	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-19 
Deposition Author(s): McLellan, J.S., Chen, M., Kim, A., Yang, Y., Graham, B.S., Kwong, P.D.

Revision History  

• Version 1.0: 2010-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-11-27
  Changes: Structure summary