4JHW | pdb_00004jhw

Crystal Structure of Respiratory Syncytial Virus Fusion Glycoprotein Stabilized in the Prefusion Conformation by Human Antibody D25

• PDB DOI: https://doi.org/10.2210/pdb4JHW/pdb

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


• Deposited: 2013-03-05 Released: 2013-05-01 
• Deposition Author(s): Mclellan, J.S., Chen, M., Leung, S., Graepel, K.W., Du, X., Yang, Y., Zhou, T., Baxa, U., Yasuda, E., Beaumont, T., Kumar, A., Modjarrad, K., Zheng, Z., Zhao, M., Xia, N., Kwong, P.D., Graham, B.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 
  0.267 (Depositor), 0.264 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Models: experimental

Literature

Structure of RSV fusion glycoprotein trimer bound to a prefusion-specific neutralizing antibody.

McLellan, J.S., Chen, M., Leung, S., Graepel, K.W., Du, X., Yang, Y., Zhou, T., Baxa, U., Yasuda, E., Beaumont, T., Kumar, A., Modjarrad, K., Zheng, Z., Zhao, M., Xia, N., Kwong, P.D., Graham, B.S.

(2013) Science 340: 1113-1117

• PubMed: 23618766 
• DOI: https://doi.org/10.1126/science.1234914
• Primary Citation Related Structures: 
  4JHA, 4JHW


• PubMed Abstract: 
  

  The prefusion state of respiratory syncytial virus (RSV) fusion (F) glycoprotein is the target of most RSV-neutralizing activity in human sera, but its metastability has hindered characterization. To overcome this obstacle, we identified prefusion-specific antibodies that were substantially more potent than the prophylactic antibody palivizumab. The cocrystal structure for one of these antibodies, D25, in complex with the F glycoprotein revealed D25 to lock F in its prefusion state by binding to a quaternary epitope at the trimer apex. Electron microscopy showed that two other antibodies, AM22 and 5C4, also bound to the newly identified site of vulnerability, which we named antigenic site Ø. These studies should enable design of improved vaccine antigens and define new targets for passive prevention of RSV-induced disease.

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Organizational Affiliation: 
• Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 9-mer - A3B3C3 

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

Macromolecule Content 

• Total Structure Weight: 102.72 kDa 
• Atom Count: 6,778 
• Modeled Residue Count: 886 
• Deposited Residue Count: 942 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D25 antigen-binding fragment heavy chain	A [auth H]	230	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
D25 light chain	B [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion glycoprotein F0	C [auth F]	498	Human respiratory syncytial virus A2	Mutation(s): 3  Gene Names: F, fusion glycoprotein
UniProt
Find proteins for P03420 (Human respiratory syncytial virus A (strain A2)) Explore P03420  Go to UniProtKB:  P03420

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free:  0.267 (Depositor), 0.264 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.286	α = 90
b = 152.286	β = 90
c = 152.286	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-01 
Deposition Author(s): Mclellan, J.S., Chen, M., Leung, S., Graepel, K.W., Du, X., Yang, Y., Zhou, T., Baxa, U., Yasuda, E., Beaumont, T., Kumar, A., Modjarrad, K., Zheng, Z., Zhao, M., Xia, N., Kwong, P.D., Graham, B.S.

Revision History  

• Version 1.0: 2013-05-01
  Type: Initial release
  
• Version 1.1: 2013-06-12
  Changes: Database references
• Version 1.2: 2017-08-09
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-10-16
  Changes: Structure summary