Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 15-mer - A3B3C3D3E3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 15-mer - A10B3C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 474.12 kDa 
• Atom Count: 30005 
• Modelled Residue Count: 3968 
• Deposited Residue Count: 4380 
• Unique protein chains: 5

6APD

Crystal structure of RSV F bound by AM22 and the infant antibody ADI-19425

• PDB DOI: 10.2210/pdb6APD/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Respiratory syncytial virus, Human immunodeficiency virus 1, Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2017-08-17 Released: 2018-03-21 
• Deposition Author(s): Wrapp, D., 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: 4.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Infants Infected with Respiratory Syncytial Virus Generate Potent Neutralizing Antibodies that Lack Somatic Hypermutation.

Goodwin, E., Gilman, M.S.A., Wrapp, D., Chen, M., Ngwuta, J.O., Moin, S.M., Bai, P., Sivasubramanian, A., Connor, R.I., Wright, P.F., Graham, B.S., McLellan, J.S., Walker, L.M.

(2018) Immunity 48: 339-349.e5

• PubMed: 29396163 
• DOI: 10.1016/j.immuni.2018.01.005
• Primary Citation of Related Structures:  
  6APB, 6APC, 6APD


• PubMed Abstract: 
  

Respiratory syncytial virus (RSV) is a leading cause of infant mortality, and there are currently no licensed vaccines to protect this vulnerable population. A comprehensive understanding of infant antibody responses to natural RSV infection would facilitate vaccine development. Here, we isolated more than 450 RSV fusion glycoprotein (F)-specific antibodies from 7 RSV-infected infants and found that half of the antibodies recognized only two antigenic sites. Antibodies targeting both sites showed convergent sequence features, and structural studies revealed the molecular basis for their recognition of RSV F. A subset of antibodies targeting one of these sites displayed potent neutralizing activity despite lacking somatic mutations, and similar antibodies were detected in RSV-naive B cell repertoires, suggesting that expansion of these B cells in infants may be possible with suitably designed vaccine antigens. Collectively, our results provide fundamental insights into infant antibody responses and a framework for the rational design of age-specific RSV vaccines.

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Organizational Affiliation: 

Adimab LLC, Lebanon, NH 03766, USA. Electronic address: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0,Envelope glycoprotein	A, B, C	573	Respiratory syncytial virus, Human immunodeficiency virus 1 This entity is chimeric	Mutation(s): 2
UniProt
Find proteins for P10104 (Enterobacteria phage T4) Explore P10104  Go to UniProtKB:  P10104
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Explore P03420  Go to UniProtKB:  P03420
UniProt Groups	P10104P03420

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AM22 Fab Heavy Chain,IGH@ protein	D, F, 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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
AM22 Fab Light Chain,Uncharacterized protein	E, G, I	215	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q8TCD0 (Homo sapiens) Explore Q8TCD0  Go to UniProtKB:  Q8TCD0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunoglobulin heavy variable 3-21,Immunoglobulin gamma-1 heavy chain	J, K, N	226	Homo sapiens	Mutation(s): 0  Gene Names: IGHV3-21
UniProt & NIH Common Fund Data Resources
Find proteins for P0DOX5 (Homo sapiens) Explore P0DOX5  Go to UniProtKB:  P0DOX5
Find proteins for A0A0B4J1V1 (Homo sapiens) Explore A0A0B4J1V1  Go to UniProtKB:  A0A0B4J1V1
PHAROS:  A0A0B4J1V1 GTEx:  ENSG00000211947
UniProt Groups	A0A0B4J1V1P0DOX5

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
IGL@ protein	L, M, O	218	Homo sapiens	Mutation(s): 0  Gene Names: IGL@
UniProt
Find proteins for Q6GMX4 (Homo sapiens) Explore Q6GMX4  Go to UniProtKB:  Q6GMX4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.10 Å
• R-Value Free: 0.256 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 229.47	α = 90
b = 229.47	β = 90
c = 304.05	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-08-17 
• Released Date: 2018-03-21 
Deposition Author(s): Wrapp, D., 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	T32GM008704
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41GM103393

Revision History  

• Version 1.0: 2018-03-21
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence