4ZYP | pdb_00004zyp

Crystal Structure of Motavizumab and Quaternary-Specific RSV-Neutralizing Human Antibody AM14 in Complex with Prefusion RSV F Glycoprotein

• PDB DOI: https://doi.org/10.2210/pdb4ZYP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Human respiratory syncytial virus A2, Tequatrovirus T4, Mus musculus, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2015-05-21 Released: 2015-07-29 
• Deposition Author(s): Gilman, M.S.A., McLellan, J.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 5.50 Å
• R-Value Free: 
  0.277 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Models: experimental

Literature

Characterization of a Prefusion-Specific Antibody That Recognizes a Quaternary, Cleavage-Dependent Epitope on the RSV Fusion Glycoprotein.

Gilman, M.S., Moin, S.M., Mas, V., Chen, M., Patel, N.K., Kramer, K., Zhu, Q., Kabeche, S.C., Kumar, A., Palomo, C., Beaumont, T., Baxa, U., Ulbrandt, N.D., Melero, J.A., Graham, B.S., McLellan, J.S.

(2015) PLoS Pathog 11: e1005035-e1005035

• PubMed: 26161532 
• DOI: https://doi.org/10.1371/journal.ppat.1005035
• Primary Citation Related Structures: 
  4ZYK, 4ZYP


• PubMed Abstract: 
  

  Prevention efforts for respiratory syncytial virus (RSV) have been advanced due to the recent isolation and characterization of antibodies that specifically recognize the prefusion conformation of the RSV fusion (F) glycoprotein. These potently neutralizing antibodies are in clinical development for passive prophylaxis and have also aided the design of vaccine antigens that display prefusion-specific epitopes. To date, prefusion-specific antibodies have been shown to target two antigenic sites on RSV F, but both of these sites are also present on monomeric forms of F. Here we present a structural and functional characterization of human antibody AM14, which potently neutralized laboratory strains and clinical isolates of RSV from both A and B subtypes. The crystal structure and location of escape mutations revealed that AM14 recognizes a quaternary epitope that spans two protomers and includes a region that undergoes extensive conformational changes in the pre- to postfusion F transition. Binding assays demonstrated that AM14 is unique in its specific recognition of trimeric furin-cleaved prefusion F, which is the mature form of F on infectious virions. These results demonstrate that the prefusion F trimer contains potent neutralizing epitopes not present on monomers and that AM14 should be particularly useful for characterizing the conformational state of RSV F-based vaccine antigens.

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Organizational Affiliation: 
• Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America.
Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America.
Centro Nacional de Microbiología and CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain.
MedImmune Inc., Gaithersburg, Maryland, United States of America.
AIMM Therapeutics, Academic Medical Center, Amsterdam, Netherlands.
Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 15-mer - A6B3C3D3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 15-mer - A10B3C2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 451.61 kDa 
• Atom Count: 29,990 
• Modeled Residue Count: 3,906 
• Deposited Residue Count: 4,134 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0,Fibritin	A, B, C	498	Human respiratory syncytial virus A2, Tequatrovirus T4 This entity is chimeric	Mutation(s): 6
UniProt
Find proteins for D9IEJ2 (Enterobacteria phage T4) Explore D9IEJ2  Go to UniProtKB:  D9IEJ2
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Explore P03420  Go to UniProtKB:  P03420
UniProt Groups	P03420D9IEJ2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Motavizumab antibody Fab heavy chain	D [auth J], L [auth K], N	225	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Motavizumab antibody light chain	E [auth L], M, O	213	Mus musculus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
AM14 antibody Fab heavy chain	F, H, J [auth D]	227	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
AM14 antibody light chain	G, I, K [auth E]	215	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 5.50 Å
• R-Value Free:  0.277 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/155

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.38	α = 90
b = 210.29	β = 100.46
c = 118.2	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
Coot	model building
PHASER	phasing
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-07-29 
Deposition Author(s): Gilman, M.S.A., McLellan, J.S.

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2024-11-20
  Changes: Structure summary