4ZYK | pdb_00004zyk

Crystal Structure of Quaternary-Specific RSV-Neutralizing Human Antibody AM14

• PDB DOI: https://doi.org/10.2210/pdb4ZYK/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2015-05-21 Released: 2015-07-29 
• Deposition Author(s): Gilman, M.S.A., McLellan, J.S.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.226 (Depositor), 0.226 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.188 (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: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 96.52 kDa 
• Atom Count: 7,206 
• Modeled Residue Count: 858 
• Deposited Residue Count: 884 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AM14 Fab heavy chain	A [auth H], C [auth A]	227	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AM14 light chain	B [auth L], D [auth B]	215	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth H], I [auth L]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	F [auth H], G [auth H], H, J [auth A], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	K [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.226 (Depositor), 0.226 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/156

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.68	α = 90
b = 95.88	β = 90
c = 145.95	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	1R43AI112124

Revision History  

• Version 1.0: 2015-07-29
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations, Source and taxonomy
• Version 1.2: 2019-12-11
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary