Biological Assembly 1  

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

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 64.28 kDa 
• Atom Count: 3466 
• Modelled Residue Count: 435 
• Deposited Residue Count: 568 
• Unique protein chains: 1

5EA7

Crystal Structure of Inhibitor BMS-433771 in Complex with Prefusion RSV F Glycoprotein

• PDB DOI: 10.2210/pdb5EA7/pdb

• Classification: CELL INVASION/INHIBITOR
• Organism(s): Human respiratory syncytial virus A2
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2015-10-15 Released: 2015-12-09 
• Deposition Author(s): Battles, M.B., McLellan, J.S., Arnoult, E., Roymans, D., Langedijk, J.P.
• Funding Organization(s): Charles H. Hood Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.241 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Literature

Molecular mechanism of respiratory syncytial virus fusion inhibitors.

Battles, M.B., Langedijk, J.P., Furmanova-Hollenstein, P., Chaiwatpongsakorn, S., Costello, H.M., Kwanten, L., Vranckx, L., Vink, P., Jaensch, S., Jonckers, T.H., Koul, A., Arnoult, E., Peeples, M.E., Roymans, D., McLellan, J.S.

(2016) Nat Chem Biol 12: 87-93

• PubMed: 26641933 
• DOI: 10.1038/nchembio.1982
• Primary Citation of Related Structures:  
  5EA3, 5EA4, 5EA5, 5EA6, 5EA7, 5EA8


• PubMed Abstract: 
  

Respiratory syncytial virus (RSV) is a leading cause of pneumonia and bronchiolitis in young children and the elderly. Therapeutic small molecules have been developed that bind the RSV F glycoprotein and inhibit membrane fusion, yet their binding sites and molecular mechanisms of action remain largely unknown. Here we show that these inhibitors bind to a three-fold-symmetric pocket within the central cavity of the metastable prefusion conformation of RSV F. Inhibitor binding stabilizes this conformation by tethering two regions that must undergo a structural rearrangement to facilitate membrane fusion. Inhibitor-escape mutations occur in residues that directly contact the inhibitors or are involved in the conformational rearrangements required to accommodate inhibitor binding. Resistant viruses do not propagate as well as wild-type RSV in vitro, indicating a fitness cost for inhibitor escape. Collectively, these findings provide new insight into class I viral fusion proteins and should facilitate development of optimal RSV fusion inhibitors.

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Organizational Affiliation: 

Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	A [auth F]	568	Human respiratory syncytial virus A2	Mutation(s): 7  Gene Names: F
UniProt
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Explore P03420  Go to UniProtKB:  P03420

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5NO	H [auth F]	1-cyclopropyl-3-[[1-(4-oxidanylbutyl)benzimidazol-2-yl]methyl]imidazo[4,5-c]pyridin-2-one C21 H23 N5 O2 KSHJXDWYTZJUEI-UHFFFAOYSA-N
NHE	G [auth F]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
SO4	B [auth F], C [auth F], D [auth F], E [auth F], F	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
5NO	BindingDB:  5EA7	EC50: min: 7.9, max: 28 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.241 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: P 4₁ 3 2
• Diffraction Data DOI: 10.15785/SBGRID/216 SBGrid

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 169.59	α = 90
b = 169.59	β = 90
c = 169.59	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: 2015-10-15 
• Released Date: 2015-12-09 
Deposition Author(s): Battles, M.B., McLellan, J.S., Arnoult, E., Roymans, D., Langedijk, J.P.

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Funding Organization	Location	Grant Number
Charles H. Hood Foundation	United States	--

Revision History  

• Version 1.0: 2015-12-09
  Type: Initial release
  
• Version 1.1: 2015-12-23
  Changes: Database references
• Version 1.2: 2016-02-03
  Changes: Database references