Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 48.45 kDa 
• Atom Count: 3,955 
• Modelled Residue Count: 437 
• Deposited Residue Count: 443 
• Unique protein chains: 2

 6DC4

RSV-neutralizing human antibody AM22

• PDB DOI: 10.2210/pdb6DC4/pdb

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


• Deposited: 2018-05-04 Released: 2019-07-10 
• Deposition Author(s): Jones, H.G., McLellan, J.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.205 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Literature

Alternative conformations of a major antigenic site on RSV F.

Jones, H.G., Battles, M.B., Lin, C.C., Bianchi, S., Corti, D., McLellan, J.S.

(2019) PLoS Pathog 15: e1007944-e1007944

• PubMed: 31306469 
• DOI: 10.1371/journal.ppat.1007944
• Primary Citation of Related Structures:  
  6DC3, 6DC4, 6DC5


• PubMed Abstract: 
  

The respiratory syncytial virus (RSV) fusion (F) glycoprotein is a major target of neutralizing antibodies arising from natural infection, and antibodies that specifically bind to the prefusion conformation of RSV F generally demonstrate the greatest neutralization potency. Prefusion-stabilized RSV F variants have been engineered as vaccine antigens, but crystal structures of these variants have revealed conformational differences in a key antigenic site located at the apex of the trimer, referred to as antigenic site Ø. Currently, it is unclear if flexibility in this region is an inherent property of prefusion RSV F or if it is related to inadequate stabilization of site Ø in the engineered variants. Therefore, we set out to investigate the conformational flexibility of antigenic site Ø, as well as the ability of the human immune system to recognize alternative conformations of this site, by determining crystal structures of prefusion RSV F bound to neutralizing human-derived antibodies AM22 and RSD5. Both antibodies bound with high affinity and were specific for the prefusion conformation of RSV F. Crystal structures of the complexes revealed that the antibodies recognized distinct conformations of antigenic site Ø, each diverging at a conserved proline residue located in the middle of an α-helix. These data suggest that antigenic site Ø exists as an ensemble of conformations, with individual antibodies recognizing discrete states. Collectively, these results have implications for the refolding of pneumovirus and paramyxovirus fusion proteins and should inform development of prefusion-stabilized RSV F vaccine candidates.

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Organizational Affiliation: 

Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab AM22 Heavy Chain	A [auth H]	228	Homo sapiens	Mutation(s): 0  Gene Names: IGH@
UniProt
Find proteins for Q6GMX6 (Homo sapiens) Explore Q6GMX6  Go to UniProtKB:  Q6GMX6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab AM22 Light Chain	B [auth L]	215	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q8TCD0 (Homo sapiens) Explore Q8TCD0  Go to UniProtKB:  Q8TCD0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth H], D [auth H], E [auth H], F [auth H], G [auth H], H, I [auth H], J [auth H], K [auth H], L [auth H], M [auth L], N [auth L], O [auth L], P [auth L], Q [auth L], R [auth L], S [auth L]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.205 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.24	α = 90
b = 75.22	β = 90
c = 109.01	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Jones, H.G., McLellan, J.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM113132

Revision History  

• Version 1.0: 2019-07-10
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2020-01-22
  Changes: Database references